Why correcting inhibited bile or constipation is not always so simple.

I am asked pretty often how to correct inhibited bile flow. This is not and easy question to answer and there are many things that can cause it. I will show you how complex of a question that is. There are a huge number of things that can effect bile production. It is probably one of the most difficult things to correct because there is a lot of questions that need answered to know what is causing to occur and it is different in each individual. If bile is inhibited then gall bladder issues will pretty much be a given. A person with issues in bile flow will have trouble digesting food it will sit like a brick in their stomach and ferment. If they have motility issues the bile they do produce will enter the stomach so they would still appear to be deficient in bile. The way to break the cycle is to correct what is causing it but it is not simple figuring out why. So here is the list of things that can cause inhibited bile flow or inhibited motility (constipation). This is by no means a complete list. This is also why there are many question that need answered when constipation is chronic.

High estrogen levels.

High copper levels

Low serotonin levels.

High noadrenaline levels or high adrenal hormone levels also connected to copper.

Low substance P levels.

Inflammation

candida overgrowth or gut dysbiosis

low cholesterol or issues with cholesterol metabolism

inhibited vitamin D receptor or low vitamin D levels.

Inhibited retinoid x receptor

lactase deficiency which cause lactose intolerance and is a sigh of a deficiency in saccharmyces boulardii.

Low amylase

Poor mucous membrane health

lipase deficiency

excess pancreatic polypeptide

pancreatic elastase deficiency

hypothalamus injury or issues.

High insulin levels

Nutrient deficiency or issues with protein metabolism especially taurine

electrolyte deficiencies

Low cysteine levels

low vasoactive peptide levels

high glucagon levels

high secretin levels

high somatastatin levels

Gastin hormone from low histamines

low bombesin levels

high cholecystolinin levels

infection

leaky gut

issues with sulfation or high sulfite levels

bile duct obstruction

T cell imbalance

high oxalate levels

High Lysolecithin found in processed foods.

High COX-2 levels

Not getting enough medium chain fatty acids.

High sulfur digesting or methane producing bacteria levels , dysbiosis

Decreased COMT activity

High folic acid levels which is not the same as folate

Low betaine homocysteine S-mthyltransferase levels which leads to hypothyroidism

choline deficiency or issues with choline metabolism

Deficiency in Akkermansia Muciniphila

Issues with lipid metabolism

Issues with the Kreb’s cycle also known as the citric acid cycle.

Low HNF4a levels

High B-hydroxybutyrate levels caused by low oxaloacetate levels.

Hydrolase synthase deficiency

alkaline phosphatase deficiency which inhibits bile and decreases good gut bacteria levels in the gut increasing the bacteria that inhibit bile.

Inhibited FXR receptor

decreased motilin

Inhibited ABCB4

Inhibited CYP7a1 enzymes

pyruvate carboxylase deficiency

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Digestion probably more then you wanted to know. Enzymes and bile and stuff.

This is not medical advice I am posting this for informational and educational purposes.

This is not done I have a lot to add to it but I am kind of burned out. I will finis it later after I take a break.

Gastrointestinal motility and digestive enzymes.

This is mostly on bile but I wanted to cover the other areas of digestion before I covered bile.

Inhibited bile causes constipation. Frequent constipation increases Bilophila Wadsworthia which causes appendicitis. Trans-fats and saturated fats should be avoided when bile is inhibited or when constipated because they increase the growth of Bilophila Wadsworthia. Trans-fats should be avoided anyways they are very bad for our health.

Most know how digestion works but we need a refresher. When we chew our food it is mixed with saliva which has some digestive enzymes in it. When we swallow it is propelled down the esophogus where it is mixed with enzymes and gastric acid. The end result is called chyme. The chyme is pushed into the small intestine (duodenum). Many will ask me how to increase bile production but doing so could cause more harm then good. The problem causing the inhibited bile flow needs to be addressed. For example a dam can only hold so much water. If there is more water then the dam can hold it will flood over the top. Adding more water to the dam adds to the problems and could break the dam. When there is a blockage causing bile flow to be inhibited then increasing bile would be like adding water to a dam that is already overflowing. Most health issues mentioned in this article I have discussed elsewhere on my blog.

Peristalsis is the movement of food through the digestive system. It is the cause of the gurgling sound you hear when you are hungry or digesting food. Usually you cannot hear it. I do not know why but I and my friends experienced this. As we healed our digestive system you could feel the food moving and the sounds of digestions were very loud. As we healed they became quieter and quieter.

In the small intestine the food is combined with bile and pancreatic enzymes to break it down further and for nutrient absorption. The smooth muscle in the intestines are ring shaped and alternate between contracting and relaxing. This causes the food to move slow enough through the digestive tract for it to be broke down and for the nutrients to be absorbed. The neurons are stimulated by acetylcholine, and substance P to get them to contract. Nitric oxide, vasoactive peptide and ATP relax the muscles. This causes a motion that moves the food through the digestive tract and occurs the most in the small intestine. There are health issues that can cause a high acetylcholine and high substance P levels. High noradrenaline reduces substance P which can interfere with intestinal motility and can lead to constipation. High estrogen levels can inhibit substance P. High substance P levels can cause inflammation and lead to inflammatory bowel disease. There are health issues that can cause low acetylcholine and low serotonin levels. This also will cause a loss of motility leading to constipation. An imbalance in our immune system can cause bile flow to be inhibited. Estrogen inhibits bile flow and progesterone pormotes bile flow. This causes the liver and thyroids to become sluggish. This can also lead to interstitial cystitis. All the above mentioned things can inhibit receptors and throw hormones out of balance. If not addressed it will become chronic and start a cycle that is difficult to break and can take months to years to heal from.

https://www.selfhacked.com/blog/substance-p-roles/

If the gurgling in the gut is excessive and there is cramping, abdominal pain, and possibly nausea and vomiting it could indicate slow gut motility or a blockage. This can be caused by intestinal damage, hormone imbalance, inflammation in the intestines, dysbiosis, candida overgrowth, a deficiency in certain gut microbiota, slow or inhibited bile. This causes gas, bloating, and distention (inflammation in the gut). If we have a T cell imbalance or high B cell levels this can also cause it. If not addressed it can result in a decline of intestinal health our the health of the body. High histamines can cause inflammation that can cause blockage. We do not want to inhibit them because histamines are needed to stimulate gastric acid. It is best to work on reducing them.

If the digestive system is injured and we do not give it the things needed for it to heal then it loses the ability to sense nutrients and food that has entered it so it cannot respond to them. The longer it goes like this the worse it gets and the longer it will take to heal.

Bile acid is needed for the healthy brown fat to be produced. Bile acid is synthesized form cholesterol. Excess oxidative stress or inflammation in the liver can cause low cholesterol levels or can inhibit it’s production which would prevent the bodies ability to produce bile properly. This can also cause bile to become inhibited. When this happens bile production is reduced and it becomes thick. Phosphatydylcholine is needed to store bile in the gallbladder. I have found most who have problems with choline metabolism have benefited from sunflower seed oil. Excess oxidative stress can cause methionine and choline to become depleted. This inhibits the bodies ability to produce bile.

Enzymes.

If you are deficient in certain enzymes often times there are plants you can consume that will helps digest foods that require those enzymes.

Lactase- (B-Galactosidase)- deficiency causes lactose intolerance. It breaks down Lactose down to glucose and galactose. Damage in the gut can cause it to not be reabsorbed. If this happens the gut microbiome will break it down causing gas and bloating. Those who are lactose intolerance will usually also be intolerant of FODMAPS until they get their gut healed enough to correct the malabsorption issues. Those who have malabsorption issues may benefit from taking Lactase when consuming dairy products. Saccharmyces Boulardii has been found to increase enzyme function in those with Lactose and FODMAP intolerance. If a person is lactose intolerant if they avoid dairy products while supplementing galactooligosaccaride for about a month, it has been found to increase Lactose metabolizing bacteria which prevents the bloating and ill effects of lactose. Also slowly introducing dairy into the diet a little at a time can increase the gut microbes that produce lactase. That would prevent a reaction to lactose also.

Alpha-galactosidase- helps break down digested fats and saccharides a deficiency causes lysosomal storage diseases. If defficient in Alpha-Galactosidase when eating fiber and high sulfur foods a person will develop gas and bloating. Those who have a deficiency in Alpha-galcatosidase will be intolerant to complex carbohydrates and may be intolerant to gluten. Beans will be a problem for a person lacking this. Infection can cause A-gal to be inhibited from the LPS produced. Inducing autophagy can testore A-gal. Tick born illness can cause autoimmune disease that can cause the body to make antibodies against a-gal. Balancing the immune system is very important. If not addressed it can lead to a sensitivity to meat.

Things that help with lysosomal storage disease should help with this. https://iamajuicer.wordpress.com/2018/08/21/things-that-may-help-with-lysosomals-storage-disease/

Sucrase- secreted in the small intestine. Catalyzes sucrose , fructose, and maltose. A deficiency will cause lactose intolerance, gas , bloating and diarrhea when things containing sucrose are consumed. Inflammation can cause it’s excretion into the small intestine to be inhibited. Sucrase is also known as invertase. Thyroid hormones and corticosterone stimulate sucrase and maltase. Inflammation and intestinal damage will decrease it’s secretion. High CD8 T cell levels inhibit Sucrase. I have posted on balancing T cells.

Amylases-work with other enzymes to break down polysaccharides. It is the major form of amylase found in humans and breaks down starch to maltose and dextran. It prevents bacteria from producing biofilms by breaking them down. It is secreted in saliva and from the pancreas.

endopeptidase (enterokinase) that breaks down proteins into smaller peptides (it is a protease) It is produced in the stomach and is one of the main digestive enzymes. It transforms trypsinogn into trypsin. procarboxypeptidase into the active enzyme carboxypeptidase which is involved in the maturation of proteins produced. Carboxypeptidase is also involved in enzyme and hormone production throughtout the body. It is produced in the mucus membrane showing the importance of restoring the health of the mucous membrane. This can result in protein and enzyme deficiencies in the body.

Trypsinogen- is the precursor form of trypsin it is found in pancreatic juice that is released in the small intestine. Trypsinogen is activated by the protease enteropeptidase which is produce by the mucus of the duodenum. Trypsin breaks down proteins to ammino acids.

Chymotrypsinogen- precursor for chymotrypsin. It is activated by trypsin.

Pancreatic Lipase- It is secreted into the small intestine in it’s completed form. But it only becomes effective in the presence of colipase which is a co-enzyme.

Phospholipase-converts lipids(fats) to phospholipids.

Lipase-breaks down triglycerides to fatty acids and glycerol. Deficiency causes a lack of fats needed by the body and fats in stools. Lipase also protect the body from parasites and pathogens. If deficienct a person will suffer from malabsorption. There are microbe derived lipases that have been shown to be effective for Lipase deficiency.

Na+ Taurocholate Cotransporting Polypeptide (NTCP) is used by the liver to extract BA returning to the lever through the portal vein. Should not be stimulated in those with cholestasis it can damage the liver. A deficiency causes muscle weakness. If it is inhbited bile salts can build up in the liver resulting in liver damage. This also results in an increase in blood levels of bile acids.

Pancreatic Polypeptide self-regulates pancreatic secretion activities. It’s secretion is increased from protein consumption, fasting, exercise, and is decreased by glucose and somatostatin. It can inhibit gallblader contractions and pancreatic exocrine secretion.

Pancreatic Elastase – help finish breaking down foods. If there is excess oxidative stress , inflammation or immune imbalance that effects the pancreas it can inhibit pancreatic enzyme secretion. They usually test for this enzyme in stool to see if the pancreas is functioning properly.

Digestive hormones.

Most of these hormones are effected by our brain especially the hypothalamus. If we have endotonins, heavy metals , glyphosate or other toxins that effect the brain then our digestion will be effected which further effects our brains. The hormone imbalance causes mental issues. They can be corrected if you address what is causing the imbalance. Many will take medications, which only treat the symptoms. Most medications for those types of things effect digestive hormones adding to the problem. Then when a person starts correcting the problem their mental issues become worse because of the drugs they are taking and the body starting to function correctly will swing hormones in the other direction. When the digestive system is damaged our cells that produce hormones become less numerous. We must try and protect the so healing can begin. Also nerve cells become less numerous which makes our bodies digestive responses to be much lower. Regular and electric acupuncture have been shown to help restore normal hormone levels. Bile acid also regulates lipid and glucose homeostasis. If bile acid become inhibited Thyroxine (T4) levels increase and Tiiodothyronine (T3). Low T3 levels inhibits oxidation which is needed to use lipids and cholesterol in the body. This will cause low LDL levels and high HDL level. Low T3 levels inhibits the bodies ability to synthesize proteins. Insulin loses it’s ability to inhibit glucogenesis. This cause glycolysis to be inhibited. This also effects the heart and can cause heart palpitations. High T4 levels can cause a decrease in serotonin.

Ampulla of Vater blocakge– inflammation, oxalates, toxins, infection or damage in the body can lead to pancreatic enzymes building up causing the pancreas to digest itself.

If you have blockage inhibiting enzyme secretion I would not advice stimulating the secretion until the health problems causing the blockage have been addressed.

When we have metabolic issues, inflammation or any other of the health issues I have describe these enzymes can be effected. Especially if we have damage to our digestive system.

Serotonin – (5-HT) regulates gut motility. It is produced in the mucosa of the gut. It increases peristalsis (movement of food through digestive tract). It has been found to be low in those with inflammatory bowel diseases. A deficiency can cause gastroparisis and bile reflux. It also stimulates adenylyl cyclase which is involved in cell signaling throughout the body. Most drug agonist of the 5-HT receptors damage the liver and heart. Acupunture stimulates serotonin. There are some disorders which inhibits 5-HT from exiting the cells. This causes a build up in the cells and a person will be senstitive to 5-HT but would still have symptoms of 5-HT deficiency.

Motilin – triggered by fasting, and fatty foods. Controls peristalsis by stimulating smooth muscle contraction and relaxation to coordinate the movement of food through the digestive tract. The antibiotic erthromycin stimulates motilin. Motilin had been found to be low in those with inflammatory bowel diseases. Acupuncture increases motilin. Motilins effects are influenced by PH. Low PH motilin inhibits gastric motility at higher PH it stimulates gastrointestinal motility. Food intake slows the production of motilin. Insulin also inhibits the secretion of motilin.

Reflux can be cause by bile issues in two ways. If there is a blockage a person could experience bile acid reflux. If there is insufficient bile production the the acid from the chyme does not get neutralized by the bile and will cause acid reflux. L-taurine and betaine also known as TMG helps with bile production. Cysteine is also needed and taking NAC (N-acetylcysteine) about three times a week has been found to help. If it is taken more then that the benefits are lost.

Gastric Inhibitory Peptide – triggered by glucose and fatty foods. Decreases gastric emptying and stimulates the release of insulin. It promotes fat storage.

Vasoactive Peptide – increases blood flow to the gut, supplies eleyctrolytes to pancreatic enzymes and bile.

Guanylin – causes secretion of chloride , decreases absorption of water from the gut. It prevents the sodium levels from the body from getting too high by inhibiting salt absorption and by stimulating the secretion of bicarbonate and chloride.

Glucagon – glucagon supresses CYP7A1 which reduces bile production. This can lead to insulin resistance and glucose intolerance. Glucagon prevents blood sugar levels from getting too low. It is involved in gluconeogenesis which produces glucose form proteins.Glucagon also breaks down fat stores in the blood stream. Excess glucagon leads to diabetes and thrombosis.

Glucagon Like Protein-1 (GLP-1) Whey protein increases GLP-1, glucose also stimulates GLP-1. Slows down digestion. It increases the size and health of pancreatic B cells. Stimulates brain repair. It’s release is stimulated by TGR-5. GLP-1 is involved in appetite suppression and glucose homeostasis. Low levels causes glucose deficiency. Carbohydrates and elevated blood levels of proteins helps stimulate glucagon . If we are deficient in glucagon glycogen can build up in the livers. It brings down glycogen in the liver by breaking it down to produce glucose. Somatostatin inhibits glucagon production. Excess glucagon cause weight loss and deficiency causes weight gain. Fasting stimulates glucagon production.

Secretin- helps regulate water homeostasis in the body, helps regulate the PH of the small intestine by gastric acid. Secretin inhibits gastic acid production and stimulates the production of bicarbonate. Secretin also stimulates bile production. It is produced mainly in the mucosa of the small intestine and jejunum. It is release from the low ph caused by chyme entering the small intestine.

Secretin deficiency causes a loss of neural progenitor cells. Progenitor cells are similar to stem cells. Since secretin increases neural progenitor cells it helps with autism, motor coordination and improves memory. Secretin helps with asthma by acting as a bronchorelaxer. Secretin reduces symptoms of pancreatitits.

In order to function properly levels of cholecystokinin and insulin need to be normal. If they are dis-regulated it effects secretin levels. It also stimulates polyamines in the pancrease which is needed for cell growth. Polyamines also regulate ion channels including the NMDA recemptors, AMPA receptors and potassium channels. Excess polyamines can cause the blood brain barrier to become more porous. Showing the importance of secretin homeostasis. When H Pylori in in it’s pathogenic form it will cause a secretin deficiency. Secretin promotes the production of mucus. A decrease in secretin decreases the function of angiotensin 2. Secretin increases thirst. Secretin increases the feel good hormone oxytocin.

Now the bad if a person has bile blockage like cholestasis it can cause liver damage. I discuss things that can help with that at the end of this blog post. Secretin causes Zollinger-Ellison syndrome to worsen.

High levels of somatostatin inhibits secretin.

Cholecystokinin- stimulates the release of digestive enzymes and bile from the pancrease and bladder. Whey protein stimulates CCK. Fat intake also stimulates CCK. A deficiency in CCK causes malabsorption and can lead to Type 1 diabetes. Damage to the mucus membrane can cause a deficiency. This can also be caused by autoimmunity. This is where a dilemma occurs. High levels of bacteroidetes or high levels of methane producing bacteria can inhibit CCK. Protein stimulates CCK. I believe working on bile blockage and then once that is corrected increasing bile flow first to reduce the bacteroidetes levels and methane producing bacteria then adding protein into the diet once they are reduced would most likely correct the problem along with restoring the health of the mucus membrane.

Intrinsic Factor-important in the absorption of vitamin B12. Often times B12 deficiency is caused by a lack of the microbiota that produce B12 but is mistakenly attributed to and intrinsic factor deficiency.

Haptocorin-binds to B12 in our food protecting it from our gastric acid so it can survive the stomach. It is found in our saliva. This shows the importance of making sure we chew our food very well.

Gastrin- hormone that stimulates gastric acid secretion. It is released from the pariental cells in the stomach. It also aids in gastric motility. Elevated gastrin can cause hypergastrinaemia. Low levels can cause hypergstrinaemia. Infection can effect gastrin levels and so can histamines. Histamines are needed for Gastrin stimulation if histamine levels are too low the we will not produce enough stomach acid. If they are too high then we can get acid reflux. If someone is not producing enough acid then they most likely have low histamines and would benefit from fermented foods and aged meats which are high histamine.

Gastric inhibitory polypeptide- an inhibiting hormone of the secretin family. It stimulates insulin secretions based on how much glucose is present. It stimulates glucagon secretion and fat accumulation. It is found in intestinal mucus, small intestine, and jejunum of the gastrointestinal tract. Has many other functions throughout the body including bone growth.

Vasoactive intestinal peptide- serves functions throughout the body but relaxes smooth muscles in the trachea, gall bladder and stomach.

Bombesin- stimulates gastrin release from the pancrease. It also stimulates adrenal and pituitary hormones. It increases the thickness of the mucus membrane. It modulates the neural firing rate in the intestines so is involved with gastrointestinal motility.

Somatostatin reduces histamines which will reduce the gastric acid stimulating effects of histamine. In those with inflammatory bowel issues somatostatin in usually very high. Acupuncture has been shown to reduce somatostatin. Most lactobacillus bacteria will reduce somatostatin. Somatostatin prevents the over production of certain hormones in the body. If there is excess somatistatin it will inhibit hormones especially insulin. Somatostatin inhibits glucose and fat absorption. It inhibits insulin and glucagon in the liver. It stimulates muscle contractions in the intestines speedingup transit times. Protein stimulates somatostatin.

Cholecystokinin, glucagon-like-peptide, gastrin-releasing peptide stimulate somatostatin.

Substance P, insulin, pancreatic polypeptide, and opioids inhibit somatostatin.

Excess somatostatin inhibits bone growth, disrupts sleep, and increases dopamine, norepinephrin and epinephrine.

High levels somatostatin will cause high thyroid hormone levels because it inhibits thyroid stimulating hormone which senses hormone levels and shuts them down if they get too high. This causes weight loss no matter how much a person consumes , flushing or hot flashes, and heart palpitations.

Insulin- breaks down blood glucose. Excess insulin can lead to cancer and many other health problems. Glycoproteins increase insulin. Whey protein increases insulin and reduces blood glucose levels. This is one that confuses me and makes me believe those with inflammatory bile have blockages. Many with inflammatory bowel have high insulin levels which stimulates CYP7A1 which should increase bile production and still they have low bile flow and often times CYP7A1 levels are low. It may be that inflammation is inhibiting the receptor.

Ghrelin-triggered during hunger or calorie restriction. Stimulates appetite. Whey proteins increases Ghrelin. Ghrelin is involved with gastric emptying.

Deacyl-ghrelin – DAG decreases gastric emptying, induces postprandial fullness and improves insulin sensitivity.

Peptide YY- secreted after eating it cancels out the effects of ghrelin.

Pheonixin – expressed in the hypothalamus, it stimulates appetite.

Peptide YY- produced in the gut where short chain fatty acids are produced. Proprionate and butyrate increase expression of Peptide YY. It reduces appetite. It is stimulated from the consumption of fiber from fruits and vegetagles. It also reduces pancreatic secretion.

Leptin – regulates body fat.

http://www.jnmjournal.org/journal/view.html?uid=1395&vmd=Full&

Bile Acids

Bile stimulates the secretion of electrolytes and water into the intestines which stimulates digestion. Biles acid stimulates the release of 5-HT. Those with inflammatory bowel diseases have been found to have high levels of bile acids Taurocholic Lithocholic Acid, Taurocholic acid and Taurocholic Deoxycholate.

Bile acid promotes liver regeneration by activiating BA recperors Farnesoid X receptor and G-Protein-coupled BA receptor1 (GPBAR1 or TGR5) . This shows the importance of bile acid homeostasis. Proper bile acid production is very important for maintaining a balanced gut microbiome.

Inhibited bile can cause gall stones and lead to liver and kidney disease.

There are many things that can inhibit bile production. Inflammation, toxins, metabolic issues, especially inhibited receptors involved with bile production. Infections can cause bile to become inhibited and so can the endotoxins they produce. If we develop leaky gut the LPS (lipopolysaccharide) which is produced by pathogens and our commensals can enter the blood stream. Our microbiome uses LPS to communicate with our bodies but when it gets into the blood stream it causes the same problems a pathogen would. We also have commensal microbes that break down LPS antibiotics and farm chemicals especially glyphosate and glufonisate can kill our gut microbiome. They modulate most organs in our bodies including our brains. They even modulate some of our genes. Without them we will not have an immune system and we cannot restore the body to homeostasis. Metabolic issues can cause acidosis or alkalosis which will also interfere with the propper function of our organs and causes a lot of damage which progresses and becomes more severe if the problems causing them are not addressed. Infection can also change the PH of the body. There is a myth that alkalizing the body will make us healthier. This is not true but it promotes things that are usually commensal like Candida and H Pylori to turn pathogenic. If a person has candida and H Pylori problems they most likely have high ammonia levels. This causes BH4 to become depleted increasing the ammonia levels even more. If not addressed they will start having problems eating high protein foods and high sulfur foods. Another thing that can cause blockage that effects bile flow is oxalates. They can be produced endogenously or we can get them exogenously. If we have leaky gut oxalates that are usually excreted in our feces can easily enter our blood stream. Also many will consume a lot of raw greens. Spinach and Kale are very high oxalate and can increase oxalates in the body. We have oxalate degrading microbiota and if antibiotics or farm chemicals in our food kills them our oxalate levels can indrease. I have posted on my blog on how to deal with those issues.

Bile, an aqueous solution produced and secreted by the liver, consists mainly of bile salts, phospholipids, cholesterol, conjugated bilirubin, electrolytes, and water.The liver cells are mostly hepatocytes. Bile travels through the liver in a series of ducts, eventually exiting through the common hepatic duct. Bile flows through this duct into the gallbladder where it is concentrated and stored. When stimulated by the hormone cholecystokinin (CCK), the gallbladder contracts, pushing bile through the cystic duct and into the common bile duct. CCK is usually deficient in those with inflammatory bowel disease. Cholecystokinin is released after a meal is consumed. It is stimulated by the production of stomach acid. It is secreted along with secretin. Secretin stimulates bicarbonate in response to the acid from the chyme that enters the small intestin, and It stimulates pancreatic enzymes and forces bile into the small intestine. If we do not produce enough stomach acid then Cholecystokinin is not released and our food will sit in our stomach and ferment. This causes and increase of either methane producing bacteria or sulfur digesting bacteria. Methane and sulfur digesting bacteria cause lower motility in the intestines slowly digestion even more. Bile is needed to stimulate the Vitamin D Receptor.

Simultaneously, the sphincter of Oddi relaxes, permitting bile to enter the duodenal lumen. Lumen is the space in a tubular shape. The hormone secretin also plays an important role in the flow of bile into the small intestine. By stimulating biliary and pancreatic ductular cells to secrete bicarbonate and water in response to the presence of acid in the duodenum, secretin effectively expands the volume of bile entering the duodenum. In the small intestine, bile acids facilitates lipid digestion and absorption. Bile is needed to absorb many nutrients especially lipid (fat) soluble vitamins like Vitamin D, Vitamin E, , Vitamin A and Vitamin K. Only approximately 5% of these bile acids are eventually excreted. The majority of bile acids are efficiently reabsorbed from the ileum, secreted into the portal venous system, and returned to the liver in a process known as enterohepatic recirculation. Ileum is the final section of the small intestine.

If bile becomes inhibited it inhibits the vitamin D receptor further inhibiting bile production and adding to the problem because cholesterol production and conversion becomes inhibited. This will make bile become sludgy leading to low bile flow which will increase estrogen levels and cause high unbound copper levels in the blood. Bitter herbs increase bile flow but the vitamin D receptor has to be addressed along with balancing the microbiome in the gut and healing the intestinal tract. Inflammation needs to be reduced , and prevent thrombosis. There are many things that can block the portal vein. The above mentioned things and also thrombosis can cause it. Thrombosis is blood clotting.

This is why I often times recommend grape seed extract and bacopa to people. It prevents thrombosis. Inflammation because endotoxins can cause thrombosis. Grape seed extract and bacopa reduce inflammation and prevent thrombosis. If thrombosis occurs in the portal vein it will effect the liver, pancrease, and digestive system. This causes pain in the stomach, bloating, inflammation, pancreatic pain, pain in the gallbladder. This can lead to death. Bile flow will become inhibited speeding up the progression of portal vein thrombosis. Those with hepatitis need to use hawthorne or something else. Resveratrol activates hepatitis.

portal vein thrombosis

gastrointestinal symptoms (ex: abdominal pain, nausea, vomiting, and diarrhea), fever and constitutional symptoms (ex: fatigue, malaise, and anorexia/weight loss) [3]. We can also find hepatomegaly with elevated liver enzymes and jaundice [3], when associated with liver abscess or cholangitis [2]. Laboratory tests usually demonstrate elevated markers of inflammation [2]

https://www.journalmc.org/index.php/JMC/article/view/3050/2378

If not addressed in time it can lead to portal hypertension. This results in brain swelling, abdominal swelling . Confusion, anemia and low white blood cell count.

https://my.clevelandclinic.org/health/diseases/4912-portal-hypertension

How Bile is Formed.

Bile is produced by hepatocytes, which is then modified by the cholangiocytes lining the bile ducts. The production and secretion of bile require active transport systems within hepatocytes and cholangiocytes in addition to a structurally and functionally intact biliary tree. If this becomes blocked by stones from poor bile production, oxalates or infection a person can develop choledocholithiasis. This will cause problems with the gall bladder, liver, kidneys and digestion. This can also lead pancreatic problems. The symptoms are upper abdominal pain, nausea and vomiting.

Initially, hepatocytes produce bile by secreting conjugated bilirubin, bile salts, cholesterol, phospholipids, proteins, ions, and water into their canaliculi (thin tubules between adjacent hepatocytes that eventually join to form bile ducts). Unconjugated bile is when heme is released during red blood cell break down, the remainder is converted to unconjugated hemoglobin. This form of bilirubin travels from the blood stream to the liver. If the liver cannot convert unconjugated to conjugated it will build up in the blood and a person will develop a yellow like glow. It is normally excreted through the intestines. If there is a rapid destruction of blood cells this can also happen. Infections, toxins, excess vitmin C and excess iron can cause the red blood cells to break down. Conjugated bilirubin is water soluble and if there is a blockage it will be excreted in the urine. Testing for high bilirubin in the urine can help identify blockage.

The canalicular membrane of the hepatocyte is the main bile secretory apparatus which contains the intracellular organelles, the cytoskeleton of the hepatocyte and carrier proteins. Fluctuations in cytosolic and organelle Ca2+ following glucagon or epinephrine stimulation play a major role in hepatic control of glucose production, bile fluid movement and excretion, fatty acid, amino acid and xenobiotic metabolism, protein synthesis and secretion, cell cycle and cell proliferation, among other functions. I discussed in some of my other post about autophagy. It can help issues like this.

The carrier proteins in the canalicular membrane transport bile acid and ions. Transporter proteins found within the canalicular membrane use energy to secrete molecules into bile against concentration gradients. The citric acid cycle is involved in providing the energy for this to occur. Mitochondrial disfunction and a loss of ATP can also interfere with this process. If this occurs cholestasis can occur causing a backup of bile and it can enter the blood stream. If the problem causing the obstruction is not addressed it can lead to fibrosis and vanishing bile duct syndrome. Symptoms are frequent itchy skin, elevated triglycerides, fat growths that appear under the skin. Drugs are often times the cause especially fluorquinolones.

Through this active transport, osmotic and electrochemical gradients are formed. When conjugated bile salts enter the canaliculus, water follows by osmosis. The electrochemical gradient allows for the passive diffusion of inorganic ions such as sodium. The most significant promoter of bile formation is the passage of conjugated bile salts into the biliary canaliculus. The total bile flow in a day is approximately 600 ml, of which 75% is derived from the hepatocyte, and 25% is from the cholangiocytes. Approximately half of the hepatocyte component of bile flow (about 225 ml per day) is bile salt-dependent and the remaining half bile salt independent. Bile Salts are formed in the body by combining bile acids and alcohol sulfates. Bile acid is combined with glycine or taurine to form bile salts. This is a good article explaining how to increase bile salts and the benefits of doing so. Taurine has been found to increase sulfur digesting bacteria which would increase H2S which can inhibit bile production. The is most likely why the western diet causes health problems it is high in taurine.

https://draxe.com/bile-salts/

Osmotically active solutes such as glutathione and bicarbonate promote bile salt independent bile flow. Canaliculi empty bile into ductules or cholangioles or canals of Hering. The ductules connect with interlobular bile ducts, which are accompanied by branches of the portal vein and hepatic artery forming portal triads. Bile is subsequently modified by ductular epithelial cells as it passes through the biliary tree. These cells, known as cholangiocytes, dilute and alkalinize the bile through hormone-regulated absorptive and secretory processes. The hormones are scecretin, acetycholine, ATP, and bombesin. So you can see the importance of making sure we address any issues we have that can inhibit acetylcholine production or cause ATP to become depleted. Issues with glycolysis can cause a loss of ATP. I do not know much about increasing ATP except that creatine helps increase ATP production.

The cholangiocytes have receptors which modulate the bicarbonate-rich ductular bile flow, which is regulated by hormones. These receptors include receptors for secretin which regulates water homeostasis, somatostatin decreases stomach acid production, cystic fibrosis transmembrane conductance Regulator (CFTR) not sure how to describe this one. It is kind of an ion channel/ABC transporter and chloride-bicarbonate exchanger this is where electrolytes are important. These are listed in order of importance sodium, calcium, magnesium and postassium .

For example, when secretin stimulates receptors in the cholangiocyte, a cascade is initiated which activates the CFTR chloride channel and allows the exchange of bicarbonate for chloride. In contrast, somatostatin inhibits the cAMP synthesis within the cholangiocytes causing the opposite effect. While bombesin, vasoactive intestinal polypeptide, acetylcholine, and secretin enhances bile flow, somatostatin, gastrin, insulin, and endothelin (endothelin are involved in electrolyte homeostasis) inhibit the flow. I do not have enough experience with reducing insulin levels and had to have a friend help me with that on facebook. Some metabolic disorders can cause low glucose levels and high insulin levels. It can be corrected but takes someone who is knowledgeable.

Bile Acids Cholesterol catabolism by hepatocytes results in the synthesis of the 2 major primary bile acids, cholic acid, and chenodeoxycholic acid. This process involves multiple steps, with cholesterol 7alpha-hydroxylase (CYP7A1) acting as the rate-limiting enzyme. It is effected by steroid hormones, inflammatory cytokines, insulin and growth factors.

Primary bile acids undergo dehydroxylation by bacteria in the small intestine, forming the secondary bile acids deoxycholic acid and lithocholic acid, respectively. Deoxycholic acid breaks down fats. High protein diet increases deoxycholic acid. Excess lithocholic acid speeds up aging and is carcinogenic. Eating lost of fiber reduces lithocholic acid. Artichoke reduces lithocholic acid and stimulates bile production. If the vitamin D receptor is inhibited then lithocholic acid cannot be detoxed by the body.

Both primary and secondary bile acids are conjugated by the liver with an amino acid, either glycine or taurine. Conjugated bile acids are known as bile salts. Bile salts inhibit cholesterol 7alpha-hydroxylase (CYP7A1) , decreasing the synthesis of bile acids. Despite the increased water solubility of bile salts, they are amphipathic molecules overall (has both hydrophobic and hydropholic molecules). This critical property allows them to effectively emulsify lipids and form micelles with the products of lipid digestion. The bile acid pool is maintained via mainly the enterohepatic circulation and to a small extent (about 5%) by hepatic synthesis of bile acids, as long as the daily fecal loss of bile acids do not exceed 20% of the pool. Micelles help with fat absorption.

Venous blood from the ileum goes straight into the portal vein, and hence through the sinusoids of the liver. Hepatocytes extract bile acids very efficiently from sinusoidal blood, and little escapes the healthy liver into systemic circulation. Bile acids are then transported across the hepatocytes to be resecreted into canaliculi. The net effect of this enterohepatic recirculation is that each bile salt molecule is reused about 20 times, often two or three times during a single digestive phase. When the digestive system is healthy bile gets easily reabsorbed.

Chenodeoxy cholic Acid and Cholic Acid are the primary bile acids produced. From Chenodeoxy cholic Acid many other bile acids are produced.

Bile acid gets reabsorbed and returned to the liver to be recycled. There are secondary bile acids produced in our digestive tract by our gut bacteria. Our microbiome deconjugates bile. Deoxcycholic Acid is a secondary bile acid produced by our microbiome. It is recycled by the body and is conjugated with glycine or taurine and circulated with primary bile acids. It constitutes about 20% of biles acids.

Lithocholic Acid is a secondary bile acid. It is conjugated with glycine or taurine and sulfated producing sulfolithocholylglycine or sulfolithocholyltaurine. Lithocholic Acid is toxic and can destroy the liver. Sulfation is an important part of detoxing deconjugated bile acids. Sulfation of bile acids decreases their absorption rate which prevent them from reentering the liver so when sulfation is functioning properly then the body can easily detox the toxic bile. Sulfation can become inhibited by metabolic issues, high sulfur digesting bacteria raising hydrogen sulfide and sulfide levels in the body. If there are problems with the CBS or BH4 pathways sulfation can be effected. The SULT genes are effected by our hormones. A change in our gut bacteria, toxins, glyphosate, vaccine injury, infections, leaky gut and many other things can change our hormone levels. This can inhibit the ability for the liver to sulfate bile acids. The pregnane X receptor also know as the xenobiotic sensing nuclear receptor has been found to be inhibited in those with bile blockage disorders. Inhibited PXR can inhibit SULT genes. Those with upregulated PXR have been found to be protected from the negative effects of LCA. Constitutive Androstane Receptor (CAR) is involved in sensing and removing endobiotic, and xenobiotic substances. It detoxes foreign substances and drugs. It has be found to protect form LCA when upregulated by inducing SULT genes. CAR is also involved in energy homeostasis. Fasting can induce CAR. Vitamin D receptor, Liver X receptor, and Farnesoid X receptor are also involved in sulfation and upregulation hve been found to protect from LCA. Most of those receptors have been found to be inhibited in those with bile blockage. Showing the importance of supporting their proper function.

When there is an obstruction biles acid can spill over into the blood stream through OST a and b transporters and also can enter the blood through Multidrug Resistance-associated proteins M1M3,M4 and M6. When there is an obstruction urinary excretion of bile is the primary route of bile removal. If this continues for an extended period of time it can lead to bladder irritation from the caustic effects of the bile acid to the bladder. Constipation form inhibited bile flow is common in interstitial cystitis. This can also take place through the organic acisd transporter.

This is an interesting article on bile acid blockage. https://jamanetwork.com/journals/jamainternalmedicine/fullarticle/1105662

When Lithocholic Acid cannot be sulfated it remains toxic. Lithocholic Acid is highly carcinogenic and causes cancer. High Lithocholic Acid levels inhibits cortisone production this can cause many health issues including chronic fatigue.

Cellulose has been found to increase the mucus membrane which improves bile flow.

Not sure where to go with this information but took note of it. High nitrogen levels increases bile acid oxidation, high hydrogen levels inhibits bile acid oxidation.

https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.13064

Medium Chain Fatty Acids stimulate bile production which decreases bacteroides and actinobacteria which has been found to be high in those with dysbiosis and inflammatory bowel disease. Low bile acid production increases levels of microbes that produce potent LPS. Tempo a product made from fermented soy has been shown to reduce bacteriodes and inhibit our microbes ability to produce bile salt hydroxolase which inhibits FXR receptor. By decreasing our microbes bile salt hydrolase bile production is restore which reduces the bacteria that inhibit bile flow. If you try this route you would want to use organic because the BT-Toxin and glyphosate found in soy products destroy the gut and alter our gut microbiome causing an increase in microbiota that have a negative impact on our health. The FXR receptor is responsible for homeostasis throughout the body. If the FXR receptor is inhibited a person will develop diabetes, dislipademia, cancer, metabolic disorders, atherosclerosis and renal diseases.

If a person has cholestasis stimulating bile will damage the liver and cause excess bile to enter the blood causing many other health problems. If a person has cholestasis they should not stimulate bile production. Elevated bile production is a sign and symptom of sepsis which indicates cholestasis.

Things that can cause cholestasis is drugs, infection, metabolic issues, gene issues, gut dysbiosis,inflammatory bowel diseases,hormone imblance, T cell imbalcance, excessive inflammation, toxins and many other things. If a person has cholestasis they will have dark colored urine and light colored stools. Pain in the abdomine, excessive itching, fatigue and nausea. In more severe cases the skin and eyes my get a yellow color.

You have to address the cause of cholestasis if it is drug induced then you may have to discontinue the use of the drug, address infection and inflammation, correct metabolic issues and gene issues. Work on reducing gall stones and oxalate stones.

Some things found to help with bile blockage. Gaur Gum, milk thistle, dandelion, vitamin K, Vit D, Calcium but we must make sure we get the right type, sunflower seed lecithen, antioxidants but do not over use homeostasis is the goal. We need some oxidative stress if we completely disable ROS we will defeat the purpose. Radishes have been shown to help with bile blockage. Cod liver oil helps with bile blockage, medium chain fatty acids help with bile blockage, curcumin helps with bile blockage but after a while it should be pulsed because it chelates iron from the body and can cause anemia. Activated charcoal helps with cholestasis but should not be taken close to meals or we will lose nutrients. Soaking in epsom salt and then getting far infrared, sunlight or halogen light gives us magnesium sulfate which helps with cholestasis. If it is caused by gall stones apple juice and apple cider vinegar has been found to reduce gall stones. Lemon juice has been found to reduce gall stones. I had to put lemon juice in water because straight lemon juice was to strong for me and made my stomach hurt. Artichoke has been found to reduce gall stones. We need a variety in our diets, eating poorly can cause bile stones. The more processed foods we eat the better our chances of getting them are. Losing weight too quickly can also cause gall stones. Low HDL levels can cause gall stones that can be caused by hormone imbalances especially high estrogen levels. Citrus fruits reduce gall stones especially the white part of the fruit. Rosemary has been shown to reduce gall stones. Pear juice has also been found to dissolve gall stones. Beet root, carrots and cucumber has been found to reduce gall stones. Drinking excess amounts of soda pop and consuming excess amount of processed sugar can cause gall stones and oxalate stones.

Excess vitamin C can cause oxalates but normal levels help dissolve oxalates. High meat consumption increases oxalates, excessive salt consumption can cause high oxalates, soda pop contains phosphoric acid which increases oxalates and causes kidney stones. Excess vitamin D intake can cause oxlates most do not recommend get more then 5000 IU of vitamin D and many say 60 IU is enough. High meat consumption can decrease citrate in the body, citrate prevents oxalates. If a person take magnesium citrate it should not be taken often because the body recycles citrate and it can build up in the body causing liver and kidney damage. If a person has metabolic issues that cause acidosis it can lead to oxalates, I post on addressing acidosis. DNA damage from oxidative stress or health issues can cause high uric acid levels which can increase oxalates. Omega 3 oils help reduce oxalates. Celery, carrots, pomegranate, watermelon, pumpkin seed oil. Helps reduce oxalates. Horsetail herb helped me a lot but has an alkaloid that can build up in the body so should not be taken more then three times a week. Citric acid not to be confused with vitamin C reduces oxalates this is why lemon is very good for reducing oxalates. Bear berry and uva ursa contain berberine which reduces oxalates and uric acid. Stinging nettles reduces oxalates and toxins that can cause oxalates. Stay hydrated but avoid water that has been chlorinated or fluorinated it is toxic an increases oxalates.

High Trymethylamines produced from our microbiome breaking down choline and carnetine is converted by Flavon Mono-Oxygenase 3 to Trymethylamine-N-Oxide. TMAO inhibits bile production. Olive oil has been found to prevent our gut microbiome from producing Trymethylamines.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4215539/

Crushed flax seed and oat haul increases bile flow.

If we do not correct the health issues causing our bile receptors to be inhbited it can lead to Non Alcohol Fatty Liver Disease.

https://gut.bmj.com/content/67/10/1881.long

Balancing the immune system

https://iamajuicer.wordpress.com/2018/07/15/autoimmunity-what-causes-it-and-things-that-may-correct-it/

Reducing oxalates.

https://iamajuicer.wordpress.com/2018/07/13/high-oxalates-also-know-as-oxalosis-or-hyperoxaluria/

Healing the gut is very important.

https://iamajuicer.wordpress.com/2018/12/01/things-that-can-go-wrong-in-the-gut-and-how-you-may-be-able-to-correct-them/

information on our gut microbiome.

https://iamajuicer.wordpress.com/2018/11/19/true-cause-of-illness-and-things-that-may-help/

Things that may help with infections.

https://iamajuicer.wordpress.com/2018/08/12/herbs-that-help-with-infection/

Things that can break down scare tissue in the body is autophagy which I have posted on and HSP70 which is another thing I have posted on. Serrapeptase has been shown to break down calcium deposits and aggregates in the body. It must be used with caution. High dosage can start breaking down tissue in the body but low dose will reduce inflammation and help the body heal.

https://iamajuicer.wordpress.com/2018/07/22/heat-shock-proteins-and-their-effects-our-our-health/

Inflammation and toxins is why so many are ill now days.

https://iamajuicer.wordpress.com/2018/11/19/true-cause-of-illness-and-things-that-may-help/

Things that can go wrong in the gut and how you may be able to correct them.

This is not medical advice I am posting this for educational and informational purposes.

 

Always remember homeostasis is the goal.

This is not finished but I need to work on other things and I figure this will give people a good foundation to research and build on.

Lipopolysaccharide (LPS) is usually used when referring to pathogens. Our commensal microbes produce LPS which our body uses to identify them. Normally they are not harmful to the body and some of the other commensal consume LPS keeping levels down. But a loss of those commensal or leaky gut can cause LPS to enter our blood streams which can lead to sepsis so it is very important to protect and maintain the health of our guts.

If we develop leaky gut and do not correct it toxins like mercury that can be in our food and usually will get excreted can now easily enter the blood stream and a person may develop high levels of mercury, cadmium or other toxins in the body.

If you have leaky gut oxalates that usually get excreted can enter the body. It is very important to heal the gut because oxalates are very damaging to the body. Calcium will bond with oxalates preventing them from being absorb and is why if a person is lactose intolerant they need to work on correcting it because milk with meals would help prevent that. Some calcium supplements are not good for you so if you decide to take that route make sure you do your research. Once oxalates build up in your body it prevents the gut from healing so it is very important to reduce oxalate levels. I have posted on reducing oxalates.

There are 2 components to the intestinal barrier. Intrinsic barrier and extrinsic barrier.

Intrinsic barrier is composed of the epithelial cells lining the digestive tube and tight junctions that tie them together.

Our gut bacteria maintain the health of our gut but damage to our gut can inhibit FUT2 production. Our gut microbiome cannot get established if we are deficient in FUT2. Lactobacillus Casei increases FUT2 production by inducing ERK/JNK. Inducing ERK/JNK stimulates FUT2. Nitric Oxide induces ERK/JNK, arginine rasises NO levels. Hypoxia induces ERK/JNK. Interleukin 10 inhibits FUT2 so a person may want to be cautious when taking probiotics that stimulate IL-10. Lactobacillus species of microbiotia stimulate IL-22 especially L Johnsii. IL-22 stimulates FUT2 secretion.

Extrinsic barrier consist of secretions and other other influences like microbes that influences the epithelial layer but are not physically part of the epithelium cells and maintain their barrier function.

Intrinsic Intestinal Barrier.

The gut is lined by sheets of epithelial cells that define the structure of the mucosa they are tied together by tight junctions, which paracellular spaces and thereby establishing the basic gastrointestinal barrier. Paracellular spaces are were nutrients are transported into the blood stream and toxins can be transported to the intestines for removal. Toxins and microbes that are able to breach this barrier have unimpeded access to the circulatory system. The tight junction layer and the mucus membrane for the most part prevents this from happening when healthy. Some cells in the epithelial are not effected by acid but others do not have the protection so count on the mucus membrane to protect them.

Extrinsic Barrier

Mucus that coats the entire epithelium. Hormones and cytokines that regulate the function of our digestive system and maintain digestive health. Our gut microbiome are a part of the extrinsic barrier. They reside in the mucus membrane.

Tight junctions encircle the epithelial cells and are an important part of the intrinsic layer. Their permeability is regulated by zonulin.

Tight junction controls the equilibrium between tolerance and immunity to non-self antigens. It is involved in macromolecular transport and tolerance and immune balance. If the tight junction layer becomes too porous a person may develop autoimmunity and their bodies immune system will turn on the body and start causing autoimmune disorders. A person will develop food allergies and food intolerances. The longer this goes without being addressed the more a persons health will decline. They will develop many metabolic, genetic and immune dysfunctions. Many things can damage this vaccines have been shown to raise B cell levels which causes the tight junction layer to become more porous. BT Toxins in GMOs have been shown to cause the body to react in a way that the tight junction layer becomes more porous. Many farm chemical cause it to become more porous especially glyphosate and glufonisate cause it to become more porous. Stress and trauma can also cause the tight junction layer to become more porous.

Zonulin is the only intercellular modulator of the tight junctions. If zonulin becomes over expressed the gut becomes more porous leading to leaky gut. It is involved in the transport of macromolecules and in balance between tolerance and immune response balance. If zonulin becomes deregulated it can cause inflammatory bowel, anemia, systematic inflammation, red sore areas on the skin known as Sweet’s syndrome that can eventually develop into blisters that eventually turn ulcerative which is known as Pyoderma Gangrenosum. They can develop swelling and sores in the mouth. The eyes can become red sore and inflamed. This condition is called sceritis it can lead to uveitis which effects the iris and can lead to blindness. Bones may thin and become brittle. Oxalates will develop causing stone formation this can also effect the liver. Not only can it cause endogenous oxalates to be produced but now oxalates consumed in our foods that are normally excreted can readily enter the body. Gall stones may form because bile production and pancreatic enzymes become inhibited and a person can develop chronic diarrhea, constipation or alternate between the two.

When the bile is inhibited it is called Primary Schlerosing Cholangitis. From food particles and toxins entering the blood stream a person could start having excessive blood clotting. A person will start developing nutrient deficiencies from being unable to absorb and break down nutrients properly. A person will eventually develop high histamines if this continues they may develop asthma, they can start developing sarcoidosis throughout the body. Mast Cells can start to degranulate leading to mastocytosis or mast cell activation syndrome. This effects our immune system as you will see below. It can lead to diabetes, heart disease and many other chronic illnesses. It can also lead to obesity or anorexia depending on how the person has been effected.

In order to restore zonulin levels to normal the genetic, metabolic, oxidative stress, changes in ph for example if you have developed acidosis or alkalosis it will have to be addressed along with infections that come along with our immune system being disabled. I have posted on most of those issues and correcting them. There are three isoforms of zonulin. ZO- 1 , ZO-2 and ZO-3.

When we get an infection it is a sign we are lacking a nutrient or gut microbe that protects us. The infection produces lipopolysaccharide (LPS) which stimulates zonulin making our guts more porous. Also antibiotics can kill the butyrate producing gut bacteria which makes our gut more porous. Butyrate keeps many things at homeostasis. We cannot restore normal zonulin levels if we do not replace the butyrate producing bacteria and feed them with fiber, oligosaccharides, galactosaccharides, and fructooligosaccharides. The lower the diversity of our gut microbes the higher our zonulin levels will be showing that our digestive system needs feedback from a variety of microbes to function properly.

The fun part of all of this is they will tell you all this in in your head until you are so ill it will take months or years to heal. In the mean time they will still continue to treat the symptoms instead of the cause. It is a common theme with allopathic medicine. I have seen this with naturopathic also but for the most part naturopaths treat the cause and not the symptoms.

Things that can reduce zonulin is meditating, if you have experienced trauma work very heard to move forward. It is difficult not to look back but constantly looking back causes stress and can increase zonulin. Anger increases zonulin so try to learn to deal with frustration and bad situations in a calm way , the calmer we are the lower our zonulin levels will be.

Replace the butyric acid producing bacteria I listed many microbes that produce it if you search my blog.

Inflammation and immune dis-regulation and can increase zonulin so the microbes that increase T regulatory cells and inflammation will reduce zonulin. If your immune system has been disabled then microbiome that stimulates IL-10 will help restore immune function.

High LPS levels will increase zonulin so we need the gut microbes that reduce LPS. Studies have shown the higher our guts diversity the less ZO-1 is express which prevents leaky gut and inflammation.

Under normal conditions things with gliadin , glutin and lactose will not effect a healthy gut but increase zonulin when the mucus membrane is damaged.

There are many molecules that interact with each other to maintain the Zonulin layer and the tight junction layer.

Occludin plays a role in tight junction maintainence and assembly which is regulated by phosporylation of serine, threonine, and tyrosine risidues. It is important for maintaining TJ stability and function. Loss of occludin can lead to leaky gut, inflammatory bowel, and hyperplasia most likely from the inflammation. Occludin also regulates cell survival or death through the intrinsic system. It is important in receiving and transmitting cell survival signals. Occludin has a strong inhibitory effect on cancer. Loss of Occludin leads to cell death.

If Phosphorylation of tyrosine, threonine and serine residues is inhibited it reduces occludins interaction with zonulin. Dephosphorylation of ser/thr residues and poor phosphorylation of tyr residues causes a reduction in occludins interaction with ZO-1 leading to it’s seperation from the junctional complex and TJ disruption. It also leads to excess ROS production which increases gut permeability. Inflammation reduces occludin levels. Endotoxins also reduce occludin. Another function of occludin is in modulating the TJ response to cytokines to protect and heal the tight junction. Occludin plays an active role in cellular location of caveolin-1. Caveolin-1 is required for cytokine induced TJ barrier changes, where it is required for TJ remodeling. So addressing endotoxins, high B cell or T cell levels and reducing inflammation is very important for preserving occludin. Many of our commensals that increase T regulatory cells balance our immune system which would restore proper T and B cell levels. Many of our commensal microbes reduce inflammation and reduce LPS (endotoxins). I have posted on my blog which of those accomplish these things. TNF-a is involved in caveiolinn-1 mediated internalization of occludin which increases occludin, alleviating cytokine induced gut permeability. This can be induced by TNF-a which is an inflammatory cytokine.

Mucous Membrane

The mucus membrane is thin in most inflammatory bowel diseases but is thick in Chron’s disease which I have not researched much on. Inflammtion usually causes the globin which are the mucin secreting cells to become depleted but for some reason this does not happen in Chron’s disease.

All these genes listed below are negatively effected by leaky gut. It is very important to reduce inflammation and work on getting the gut healed to restore the mucous membrane. Damage to the digestive system and mucus membrane causes many genes to become dis-regulated. MUC2 gene is the major gene responsible for the secretion of gel-forming mucin in the intestinal tract. It coats the endothelial surface protecting it from inflammation,chemicals, damage and infection. There are 20 MUC genes. There are many mucin categories that are enriched with proline, serine, and threonine. They are modified by o-glycosylation that creates oligosaccharides that confer on mucins their individual functions. Mucin is made mostly of fat. Those with inflammatory bowel and ulcerative colitis have low B-oxidation which is needed for the break down and use of fats. Since the mucous membrane is mostly fat this causes it to become dysfunctional. This makes people sensitive to fats and is why it is best if they consume medium chain fatty acids because the body can readily use them. Eggs yolks are a good source of phosphatidylcholine which is what the mucus membrane is mostly made of. Most with inflammatory bowel or colitis are sensitive to lecithin. I used sun flower seed lecithin and I did not react to it and it helped me a lot with my healing. Most other sources of lecithin I had to avoid. There are many studies showing that using sun flower seed as a source of lecithin has been shown to heal the gut. As for Chron’s disease I have a theory I have not had a chance to research but I believe they may be deficient in commensal microbes that digest sialic acid. Many of our commensals need it to thrive. Bacteroides Fragilis, Bacteroides Thetaiotaomicron, Bifidobacterium Bifido, Bifidobacterium Longhum, Bifidobacterium Infantis, Akkermansia Muciniphila all need sialic acid to thrive. Another theory I have about Chron’s that I have not gotten to research is they may have an overgrowth of those and that inflammation or LPS is stimulating the production of excessive sialic acid causing and overgrowth of those microbes.

Phospholipase A2 activity is higher in those with inflammatory bowel and colitis.

If a person is having trouble with methyl donors they will not produce enough phosphatidylcholine because methyl groups are used in the process of producing phosphatidylcholine for the mucous membrane. So combine that with the low B-oxidation and you see why it can be so difficult to heal. Disulfide bridges are also a component of phosphatidylcholine showing the importance of addressing things that can impair sulfation.

Phospholipase A2 is high in those with inflammatory bowel and colitis. Phospholipase is stimulated by inflammation. It is a mixture between inflammation and substance P and is why those with leaky gut have high substance P levels. When substance P levels get high the skin will have a burning sensation especially in the scalp and it may go down the spine. Substance P levels increase at night so the symptoms will worsen at night.

Annexin also known as lipocortin keeps PLA2 in check. Adrenal hormones increase Annexin but in many people with inflammatory bowel the adrenals become depleted from being over activated and they develop Addison’s disease which is a deficiency of adrenal hormones. Adaptogens help alleviate this which would help restore annexin levels. Annexin also helps repair our immune system. If annexin gets low the blood brain barrier becomes porous because it helps maintain the blood brain barrier. Annexin is also involved in protecting the brain from infection. It is very important to support the adrenals with the proper nutrients and to reduce inflammation so the adrenals can recover. Oddly Okadaic Acid a toxin found in shell fish increases annexin. This is something a person would definitely need an experienced medical professional to do. IL-6 increases annexin expression. To restore normal cortisol levels stress management is very important. Increased stress depletes cortisol. Getting rest is important, even if you cannot sleep just laying and resting can help increase cortisol. Avoid, caffeine, alcohol and smoking. Our mucosal layer will take up fats and integrate them to strengthen itself. Omega 3 oils, cod liver oil, nuts, and avocados help increase cortisol. Avoid processed sugar it depletes cortisol levels. Citrus fruits especially grape fruit increases cortisol but grape fruit inhibits certain cytochrome P450 enzymes so should not be eaten too often. Eat foods high in melatonin or take melatonin supplements at night which will increase cortisol. Non processed carbohydrates help increase melatonin. Magnesium is important for maintaining proper cortisol levels. Reducing inflammation can help normalize cortisol levels. Earth grounding and getting sunlight help to normalize cortisol levels. I still laugh when I mention earth grounding because I thought how could something so simple have so many health benefits. So I was determined to find research to show those earth grounders were crazy instead it was I who was crazy and the earth grounders are correct. I could find no research to prove them wrong but plenty of research showing the many health benefits of earth grounding.

We have to keep in mind goblet cells build our mucus membrane and when inhibited by inflammation, toxins or even damage to our digestive system our ability to produce mucin is reduced or inhibited. Bismuth even though it is a metal, is for the most part none toxic it takes very high doses for a very long time to reach toxic levels. It helps the gut heal. It kills many pathogens and can cause commensals that have turned pathogenic to go back to commensal. Mucilage helps protect the gut so it can heal. I have posted on reducing inflammation if you search my blog. Oatmeal is high in mucilage but you must get organic because they use glyphosate and glufonisate on grains and beans to dry them and those destroy our gut and kill our gut microbes. Three very good sources of mucilage is okra, arrow root and oatmeal. Make sure the oatmeal is organic. Most non organic oatmeal has farm chemicals that destroy the gut.

Here is an in depth article on mucus membranes.

https://www.readkong.com/page/the-interaction-of-the-gut-microbiota-with-the-mucus-1350713?p=1

Sialylation has been found to be increased in those with inflammatory bowel dieseases. Excessive sialylation increases inflammation. IL-10 inhibits Sialylation. Their are probiotics that increase IL-10 but IL-10 inhibits FUT2. So an oligosaccharide,galactosaccharride and fructosaccharide would probably have to be supplemented with it. I suspect the body is trying to increase the commensals that rely on the nutrients produced by sialylation and they have been depleted by antibiotics. Some commensals rely on FUT2 but others rely on sialylatin. Some do not produce the enzymes to break down sialic acid and rely on other commensals to produce it. A deficiency in either of them is probably what is causing the high sialylation. The body is trying to feed them. It is not getting the feedback from those commensals.

The bacteria this would help thrive are B Fragilis, B Theaiotaomicron, B Bifidum, B Longhum, B Infantis and A Muciniphila. I believe those with inflammatory bowel especially those with Chron’s will be deficient in those because those with Chron’s have a thicker mucous membrane.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4747158/

The increased inflammation and infection caused by the above mentioned things results in an accumulation of ROS which can lead to further damage and it disturbs mitochondria function and autophagy. Once the mucus membrane has been damaged all the things mentioned below lose their protection and become dysfunctional. It may be necessary to take mucilage and bismuth to help protect them and restore their function. Once the mucus membrane breaks down it creates a cycle that has to be broken because the mucus membrane needs the things mentioned below to function properly and they need the mucus membrane to protect them and to function properly. Dysfunction in either of them from infection or toxins can start a cycle that has to be broken to heal. Our gut microbiome cannot become established without the mucus membrane because it also protects them. Our mucus membrane is a mediator between host and microbiota interactions. Decreased mucus membrane thickness causes a change in our gut microbiome and makes us more prone to infections.

This is where addressing sulfation issues, methyl group issues and issues with thiols comes in because the production of mucin requires all of those to be functioning. I have posted previously on how to deal with those issues. For the production of the oligosaccharides the endoplasmic reticulum and stem cell are required.

L-cysteine, L-arganine, L-threonine, L-serine, and L-cysteine increase mucin production in the digestive system and have been shown to promote gut microbiome homeostasis. Citrus fiber increases mucin especially the white part of the fruit. Pectin stimulates Goblet cell formation which secretes mucin. The microbiome that help restore gut health are Bifidobacterium Bifido, Bifidobacterium Breve, Bifidobacterium Lactis, Enterococcus Faecium, Lactobacillus Acidophilus, Lactococcus Lactis

For those who do not have glutamate issues bone broth heals the gut very quickly. Those who have high levels of sulfur digesting bacteria will have problems with the consumption of bone broth also.

The small intestine is the portal for the absorption of most nutrients in the body. The chyme which is the digested food that has exited the stomach enters the small intestine pancreatic enzymes and bile is secreted. This breaks the food down and if functioning properly it will be almost liquid when it enters the lower intestinal tract. Bicarbonate is also added by the body to reduce the acidity before it enters the large intestine. The enteric nervous system and gastrointestinal hormones regulate this process and the intestinal motility. Intestinal dysbiosis can cause incorrect communication or inhibited communication which leads to inflammation, intestinal damage and it could lead to a loss of the ability to produce bile and digestive enzymes. To restore proper function we must reduce the microbe causing the problem. Those who have high sulfur digesting bacteria will develop high hydrogen sulfide levels which interferes with sulfation and can interfere with the proper function of the CBS and BH4 pathways. This can lead to high sulfide levels in the body. BH4 levels will become low causing ammonia to build up when protein is consumed. The high ammonia levels will cause some commensals to go into protection mode and they will become pathogenic. Candida and H Pylori are two examples. To make matters worse they also start producing ammonia to protect themselves from the acidic environment. The digestive tract is supposed to be acidic. Ammonia alkalizes it this also makes us more prone to infections because the commensal microbes that protect us cannot survive in an alkaline environment. When we lose our commensal bacteria we lose proper immune function and our zonulin levels increase and our gut becomes more porous leaving things enter the blood stream that could not normally enter. Inflammation and oxalates can inhibit bile flow causing it to back up, when this happens the gallbladder is effected. Instead of addressing the problem modern medicine gets rid of the symptom by removing the gallbladder thus the illness continues to worsen and taking the gallbadder out can contribute to it’s progression.

If bile becomes inhibited it inhibits the vitamin D receptor further inhibiting bile production and adding to the problem because cholesterol production and conversion becomes inhibited. This will make bile become sludgy leading to low bile flow which will increase estrogen levels and cause high unbound copper levels in the blood. Bitter herbs increase bile flow but the vitamin D receptor has to be addressed along with balancing the microbiome in the gut and healing the intestinal tract.

This is why I often times recommend grape seed extract and bacopa to people. It prevents thrombosis. Inflammation because endotoxins can cause thrombosis. Grape seed extract and bacopa reduce inflammation and prevent thrombosis. If thrombosis occurs in the portal vein it will effect the liver, pancrease, and digestive system. This causes pain in the stomach, bloating, inflammation, pancreatic pain, pain in the gallbladder. This can lead to death. Bile flow will become inhibited speeding up the progression of portal vein thrombosis. Those with hepatitis need to use hawthorne or something else. Resveratrol activates hepatitis.

portal vein thrombosis

gastrointestinal symptoms (ex: abdominal pain, nausea, vomiting, and diarrhea), fever and constitutional symptoms (ex: fatigue, malaise, and anorexia/weight loss) [3]. We can also find hepatomegaly with elevated liver enzymes and jaundice [3], when associated with liver abscess or cholangitis [2]. Laboratory tests usually demonstrate elevated markers of inflammation [2]

https://www.journalmc.org/index.php/JMC/article/view/3050/2378

If not addressed in time it can lead to portal hypertension. This results in brain swelling, abdominal swelling . Confusion, anemia and low white blood cell count.

https://my.clevelandclinic.org/health/diseases/4912-portal-hypertension

Autophagy is very important in maintaining health and we need a proper balance. It can be disrupted if we have intestinal damage. If autophagy is inhibited we become prone to infection and mitochondrial dysfunction. Autophagy is the housekeeper of our cells. One common theme you will see is inflammation and shows the importance of reducing inflammation. Which could involve diet changes, addressing metabolic issues, reducing toxins and infections. Addressing detox issues and detoxing in an appropriate manor for the individual. Addressing gene issues which could be caused by any number of things including a lack of the microbe in the gut that may modulate that genes function.

The mucus membrane in our digestive system protects us from infection, physical and chemical harm. Our commensal bacteria cannot exist without it. It is very important to restore our mucus membrane when damaged in order to restore intestinal homeostasis. Many genes mentioned below are effected when it is damaged because it causes a dysfunction in them. Autophagy is very important for the maintenance or proper gene function.

Paneth cells are located within our mucus membranes and provide immunity, prevent damage to the digestive system and is involved with nutrient absorption. Loss of our mucus membrane from loss of microbiotia, drugs or farm chemicals found in our food can destroy our mucus membrane. This causes damage to the digestive system which can further inhibit the bodies ability to produce mucin. This makes us more susceptible to infection. Paneth cells stimulate the production of AMPs which fight infection and modulate commensal microbiome and innate immunity. A list of AMPs are defensin-like human lyzosome, defensin (HD)-5 and 6, lyzosome, regenerating islet derived gamma(Reg3y), and phospholipase A2 group 2A(sPLA2) as well as inflammatory cytokines such as Transforming Tumor Necrosis Factor A (TNF-a), Growth Factor B1 (TGF-B1), and Postaglandin E2. AMPs are sensitive to ER stress which I discuss below.

Autophagy protects against infection by producing Antimicrobial Peptides and degrading organelles that break down misfolded proteins and AMPs break down pathogens. This can ease the over activated inflammatory response and over active immune response. Some AMPs are defensin and cathelicidens which protect against microbes.

Intestinal Epithelial Cells. (IECs) – form a physical and chemical barrier involved in inflammatory response and immune reaction. IECs work as an interface between the quantitive microbial ecosystem in the intestinal lumen. Lumen is inside space or opening in a tubular structure.

There are 6 types of IECs

Goblet Cells which secrete mucin to build up the mucin barrier.

Enteroendocrine cells which produce gastrointestinal hormones that communicate with the nervous system, the brain and organs throughout the body. They respond to nutrients within the intestines. Helps restore intestinal tissue.

Absorptive Enterocytes – epithelial cells in small intestine. They are involved in nutrient absorption, absorption of conjugated bile acid, lipid uptake, Issues with Absorptive Enerocytes can inhibit glucose absorption and can result in lactose intolerance and many other food intolerances. It can also result in an electrolyte imbalance. Enterocytes secrete a series of chemokines and cytokines which regulate immune responses of subjugant mucosal. (Mucosal control)

Tuft Cells – brush cells which are chemosensory cells in the intestinal epithelial lining. Tuft refers to microvilli projecting from the cells. They increase during parasite infection. They are the sole source of Interleuken 25 which induces NF-kB activation which helps protect from infection. High levels of IL-25 raises eosinophils which causes inflammation and is suspected of causing inflammatory bowel diseases. Eosinophils have been shown to kill many types of cancer cells. Infection also stimulates Tuft Cell to produce IL-25. They are increased through a T cell response through a type of lymphatic tissue. Tuft cell also secret endogenous opioids. Eosinophils cause asthma, cardiovascular disease and can even cause headaches, mood swings and brain fog.

Microfold Villous Cells – are found in the Gut-associated Lymphoid Tissue (GALT) of the Peyers Patches in the small intestine and the Mucus-associated Lymphoid Tissue (MALT). M Cells initiates mucosal immunity. They allow the transport of microbes and across the epithelial cell layer. From the gut lumen to the lamina propria. M cells contain Epidermal growth factor which acts as a sensor to stimulate repair through the intestines including the mucus membrane , tight junction protein layer and it stimulates goblet cell differentiation and many other things in the colon.

Endoplasmic Reticulum are organelles within our cells and plays a major role in the production of proteins and lipids. So this is where our enzymes , hormones and even our detox enzymes are produced.

Endoplasmic Reticulum Stress Unfolded Protein Response (UPR) is activated in response to unfolded or misfolded proteins in the endoplasmic reticulum. It stops the production of unfolded or misfolded proteins it is the quality control mechanism. It will stop production and start cleaning the bad proteins out. If it continues for too long then it will induce apoptosis which is cell death. If overactivated which vaccines and many farm chemicals can cause to happen it can lead to prion disease. It plays a valuable role in intestinal endoplasmic reticulum survival and function. Dysfunction of endoplasmic reticulum can result from genes that have been effected from infection, toxins, or even stress can result in abnormal UPR function. This is referred to as Endoplasmic reticulum stress.

ER stress activates three kinds of proteins which reside in the ER membrane to detect UPR in ER Lumen and resolve them. Autophagy reduces ER stress.

inositol-rquiring membrane kinase endonuclease1 (IRE1) via a really long pathway that I am certain you do not want me to type out. Issues with the genes involved in these mediators in intestinal endothelial cells will change the histological structure of the intestinal epithelium.

XBP1- inhibition will exhibit impaired Paneth Cells, which leads to dysbiosis and spontaneous intestinal inflammation which may induce activation of NF-kB pathway which can lead to inflammation, anxiety, chronic depression, insulin and leptin resistance, it increases risk of cardiovascular disease and high TH17 levels which can lead to psoriasis or lupus, Many who have intersitial cystitis have high TH17 levels. It can cause bone lose and Alzheimers. On the other end of the scale not enough NF-kB can produce many health problems. Like lower cognitive function, inhibited ability to heal, inhibited nerve growth and brain plasticity. This is a good article covering it in more detail. https://www.selfhacked.com/blog/nuclear-factor-kappa-b/

The second gene that can increase risk of inflammatory bowel disease is oromucoid-like3 (ORMDL3). Over expression can lead to immune/inflammatory diseases. It has been linked to childhood asthma. Over expression causes inhibited calcium buffering capacity of the mitochondria. This can disrupt endocytosis, enzyme control , cell growth and proliferation and cell apoptosis. ORMDL3 takes part in protein folding and in regulating UPR. It is believed ERs induced inflammation in paneth cells may disturb ORMDL3 levels leading to inflammation.

TREM1 (Triggering Receptor Expressed On Myeloid Cells-1) inhibits autophagy and increases ERs stress levels. This has been shown to increase the severity of inflammatory bowel diseases. Defective autophagy in the endoplasmic reticulum can predispose someone to inflammatory bowel diseases form a decreased clearance of IRE1 during ERs. High IRE1 levels impairs insulin signaling this can lead to many metabolic diseases. TREM1 can either increase inflammation or decrease it. During infection TREM1 increases inflammation. TREM1 also interacts with other inflammatory pathways which can also result in TREM1 increasing inflammation. TREM1 is high during septic shock. Sustained increased levels of TREM1 can lead to inflammatory bowel disease, cardiovascular disease and atherosclerosis. TREM1 is needed to help clear infection. Unfortunately when an infection that contains OspA protein that are difficult for the body to clear like HIV and Borellia (Lyme Disease) it can cause TREM1 levels to remain high. This is why it is very important to work on reducing inflammation and address infection. Most infectious diseases there are no test for and the test they do have has a high failure rate at detecting the microbe responsible for the illness. But the body and what genes are effected and cytokines present can indicate when there is an infectious agent present. The more difficult infections can be killed but it takes a multilevel approach because most that carry the OspA take multiple forms and have to be addressed differently for each form it has taken.

Inflammatory bowel disease have been shown to have a dis-regulation of T Cell which can be induced by toxins, drugs, vaccine injury, farm chemical or processed foods.

Autophagy is a conserved lysosome-dependent catabolic process involved in degrading and recycling aggregates as well as damaged organelles. Enhancement of autophagy promotes the survival of various cells including intestinal endothelial cells, and nuetrophils by protecting them from microbial toxins. A disturbance in autophagy could disturb the function of intestinal endothelial cells and influence inflammatory response, immune response, ROS levels and endoplasmic reticulum stress. This can lead to inflammatory bowel diseases. Autophagy plays a vital role in alleviating of intestinal inflammtion, degredation of damage associated molecular patterns (DAMPS), which can help prevent inflammatory bowel diseases. PAMPs refer to various kinds of endogenous materials produced by stress, impaired or dying cells covering DNA, RNA, ATP, histones, hyaluronan, uric acid, heparin sulfate, the S100A calgranulins, IL-1, HSP, and chromatin-associated high motility box1(HMGB1).

Basal autopaghy occurs in nearly every cell to maintain homeostasis of the ammino acid pools. There are three types of autophagy.

Macropahy – targets material such as cytoplasmic components or invasive bactria which are surrounded by a double-membrane bound autophagosome.

Autophagosome when combined with lysosomechanges into a single-layer membrane autolysome with a strong degradative and digestive ability.

Microautophagy – during the process of microautophagy lysosomal/vacuolar membranes invaginate (fold in on itself) to engulf intracellular components via a non-selective degradative mechanism.

Chaperone-mediated autophagy transports organelles and proteins into lysosomes only with the assistance of chaperones which are located in lysosomal lumen. Chaperons are proteins that assist in convalent folding or unfolding and the assembly or disassembly of other macromolecular structures. They assist in the assembly of nucleosomes which are basic units of DNA.

Two steps of Autophagy.

The first step of autophagy cup-shaped double membrane phagophores are shaped in the cytoplasma of the cell, and then misfolded proteins, damaged organelles or bacteria are engulfed to become sperical double membraned autophagosomes. Autophagosomes are usually considered to be produced from the nucleation and membrane expansion of phagophores.

During the second step autophgosomes fuse with lysosomes and endosomes to form a single-lipid layer autolysome, which is regard as basal units for degradation and digestion. Autophagy process is induced by the detection of various specific cues such as starvation or invasion by pathogens.

Two proteins are known to participate in autophagy which include Mammaian Target of Rapamycin (mTOR) as an inhibitor and adenosine monophosphate activated protein kinase as an indicator. mTOR is often activated by lower levels of Adenosine Triphosphate (ATP) caused by nutrient sufficiency or several growth factor stimulations. mTORC1 inhibits autophagy in the presence of nutrients. mTORC1 regulates glycolysis, lipid biosynthesis, and the pentose phosphate pathway has been found to be under the control of mTORC1. mTORC1 mediates upregulation of SREBP-1 activity which is necessary for lipid biogenesis. mTORC1 increases mitochondrial DNA copy number and as well as encoding many genes involved in oxidative metablolism. It has been found that mTORC1 promotes transcriptional activity of PPARy coactivator (PCG-1a) which is usually low in those who have inflammatory bowel diseases. This leads to the inability to break down fats and cholesterol causing many health problems because lipids are needed by almost all cells of the body especially the digestive system to maintain proper function and health. Ironically mTORC1 inhibition leads to longer lifespan. mTORC1 inhibits autophagy. mTORC1 increases NRF2 activity the master regulator of the antioxidant system.

Excess mTORC1 activation can cause endoplasmic reticulum stress and excess ROS production.

Low ATP levels inhibits mTORC1. Inhibiting mTORC1 increases glucose uptake. Hypoxia (oxygen deprivation) inhibit mTORC1. Amino Acid deprivation can inhibit the citric acid cycle (TCA cycle) this also inhibits mTORC1. The body inhibits mTORC1 when it senses DNA damage. Autophagy reactivates mTORC1 whose activity then promotes the replacement of lysosomes consumed during autophagy.

Symptoms of excess mTORC1 . Since there is no information on what excess mTORC1 does I will have list the symptoms of inhibited autophagy and high ROS levels since those are issues caused by high mTORC1 levels.

Symptoms of inhibited autophagy. Nuerological problem , inhibited autophagy can lead to inflammation in the brain, mental illness. Mitochondrial dysfunction, decreased antioxidant function which can lead to high levels of ROS. Pancreatic inflammation. Fat accumulation throughout the body and can lead to fatty liver disease. Issues with lysosomal storage, diabetes and sickle cell anemia. Frequent illness from infectious agents.

Symptoms of high ROS. ROS is needed for redox signaling but becomes damaging if levels get too high. High levels of ROS cause inflammation. Leaky gut and can cause a leaky blood brain barrier. This also can lead to nuerological damage and brain inflammation causing mental illness. Can cause liver damage resulting in a hepatic liver. Fatigue from reduced energy levels. Mitochondrial dysfunction which can lead to MS. Here is a link to a good article on oxidative stress.

https://www.selfhacked.com/blog/oxidative-stress-101/

Things that stimulate mTORC1. Resistance training, amino acid L-Luecine, Beta Hydroxy Beta-methylbutyric acid which is a precursor of butyric acid. High intake of Iron stimulates mTORC1.

Inhibitors of mTORC1 are green tea, resveratrol, curcumin, caffeine and alcohol. Iron deficiency inhibits mTORC1. Green tea can damage the liver if taken for too long and curcumin chelates iron so can make a person anemic if consumed too long.

VDR

Vitamin D receptor (VDR) mediates the activities of vitamin D3 which is the activated form of vitamin D. A deficiency can effect our digestive system in many ways. The VDR is involved in regulating 33% of the genes in the body so problems with it can effect many things. VDR and Retinoid X receptor interact to with each other and can activate each other so issues with either one can effect vitamin D homeostasis. Inhibited VDR effects calcium homeostasis, electrolyte balance, and blood pressure.

Vitamin D3 acts as a hormone a hormone and helps regulate innate and adaptive immune responses. Those with low vitamin D levels or inhibited VDR receptor are prone to infection with Mycoplasma Tuberculosis. VDR is involved in producing the antimicrobial peptide/IL-37, defensin beta B, CLDN2 encoding claudin 2 and ATG16L1 related autophagy which protects us from inefection.

The VDR receptor is involved in gut microbiome balance and autophagy. Autophagy is the house keeper of our cells it helps clean them out, protect them from infection and helps to prevent misfolded proteins. Inhibited vitamin D receptor can cause inhibited bile flow and a decrease in LDL and increase in HDL. The reduced LDL causes bile to become sludgy which leads to biliary issues and gallbladder problems and can result in gall stones and biliary blockage.

When the VDR receptor is inhibited or there is a vitamin D deficiency we can develop inflammatory bowel diseases. IKBa is an inhibitor of pro-inflammatory NF-kB.

VDR inhibition or vitamin D deficiency alters the composition of intestinal microbiome. Butyrate producing bacteria become less numerous. Butyrate increases expression of VDR so a deficiency in Butyrate would further add to the inhibition of the VDR receptor. Butyrate also suppresses intestinal inflammation and enhances AMPs. AMPs help protect us from infection.

Toxins, mold toxins, infection and a lack of nutrients can inhibit the vitamin D receptor. High levels of vitamin D3 indicates the body has recognized an infection and is trying to fight it.

Farm chemicals especially glyphosate and glufonisate inhibit the vitamin D receptor. Many toxins found in processed food can also inhibit the vitamin D receptor.

Symptoms of inhibited VDR.

If the VDR is inhibited a person may experience problems with methyl donors and low dopamine levels. They may experience frequent infections and be low in GcMAF. Inhibited VDR can cause bone loss, hair loss, brain fog, increased TH17 levels resulting in lupus, psoriasis and/or skin rashes, tooth decay and poor oral health, inflammation throughout the body, can lead to high blood pressure. Low LDL which inhibits bile production resulting in biliary and gall bladder problems and can lead to stone formation. Electrolyte imbalance and iron deficiency. Low dopamine and GABA levels is a result of VDR inhibition. Prolactin level become low when VDR is inhibited. Gut dysbiosis and inflammation in the digestive system. Increased creatine and albumin levels and decreased alkaline phosphatase are symptoms of low vitamin D or inhibited vitamin D receptor. VDR inhibition or vitamin D deficiency can result in mast sell activation syndrome. CYP3a4 an enzyme needed for detoxing xenobiotics and drugs becomes inhibited. Hormonal imbalance is also a result of VDR inhibition. Hashimoto’s syndrome can result from VDR inhibition. Heart disease can be a result of VDR receptor inhibition or vitamin D deficiency. In more severe cases VDR inhibition can lead to liver and kidney disease.

Symptoms of Vitamin D deficiency.

Joint stiffness or pain, back aches, tooth decay, bleeding gums or gum disease, muscle cramps, hair loss, bone loss, weakening of bones, increases risk for cancer, sleep apnea, brain fog, fatigue, depression, leaky gut, excess sweating especially in the head area.

Excess vitamin D can lead to many health problems and can result in loss of bone from a disruption in the mechanisms that control calcium homeostasis. Though it is needed for calcium absorption high doses can have the opposite effects. High levels of vitamin D can lead to oxalate formation. Many studies show anything over 5000 IU a day can lead to oxalate formation and many health problems.The recommended daily allowance of vitamin D is 600 IU. It is best to get vitamin D from food sources. Exposure to sunlight, far infrared, halogen lights can increase the bodies production of vitamin D. Short term raised levels have been found to be beneficial but long term raised vitamin D levels have been found to be harmful to our health. High levels of vitamin D can contribute to the inhibition of the VDR. Excess vitamin D can result in high levels of calcium in the blood resulting in calcium deposits forming in the organs including the lungs.

Sources of vitamin D. Sunlight, halogen lights, far infrared light increases the bodies production of vitamin D. Excess sunlight has been shown to cause high levels of vitamin D and is why life guards have some of the highest rates of kidney stones. Fish oil contains vitamin D. Sardine , salmon and cod liver oil are good sources. I try to make sure the fish is not from contaminated areas. Most sea food is high in vitamin D. Mushrooms and eggs are a good source of vitamin D. Animal liver is another good source of vitamin D. Cestrum Diurnum, Waxy leaf nightshade (solanum glaucophyllum), yellow oat grass (trisetum flavescens) are plant sources of vitamin D. Those plants are so high in vitamin C that they cause calcinosis in grazing animals. Brown and read seaweed are also sources of vitamin D and cholesterol. Mercury found in fish is for the most part only a problem if we have leaky gut. When the gut is intact only about 5% of the toxins like mercury get absorbed that have been consumed and when healthy the body can easily detox that amount unless it is shot directly into the blood stream. I mention this because even though they claim vaccines do not contain mercury some still do.

Things needed for the body to be able to use vitamin D. Vitamin K2, Vitamin A, zinc, sulfur is needed to sulfate vitamin D so sulfation issues need to be addressed. Magnesium increases the bodies response to vitamin D. Boron increases vitamin D in the blood stream. Water is needed, dehydration inhibits many receptors in the body. Silica helps improve the function of many receptors in the body. Sunlight helps to sulfate nutrients. DAO and lysine are also needed to sulfate vitamin D. Boron is touchy, low levels reduce estrogen high levels increases estrogen.

Things that enhance vitamin D receptor activity. Parathyroid hormone, Sirt 1, Dopamine, Omega 3 , Omega 6, Phytoestrogens, Testosterone, Postaglandulins and bile activates VDR. Bitter herbs stimulate bile production. Even if you do not swallow bitter herbs just tasting them stimulates bile production. Resveratrol activates the vitamin D receptor. Querciten enhances vitamin D receptor activity. Curcumin stimulates the vitamin D receptor but if taken for too long it can lead to anemia because it chelates iron from the body. So one may use it at first to help stimulate the VDR receptor but probably should just take maintenance doses to make sure it continues to function. Human Growth Hormone stimulates the vitamin D receptor. Sleep, fasting, and strength training increase HGH.

Things that can inhibit VDR are cortisol/glucocorticoids, high prolactin levels, imbalance in thyroid hormones, TGF-Beta, phosphatonins which regulate phosphate homeostasis, and ubiquitin can inhibit VDR. Many of these things are inhbited by autophagy which would prevent them from inhibiting the VDR receptor. Caffeine can also inhibit the VDR. High TGF-B levels can be an indication of T cell imbalance and/or B cell imblance. Probiotics that reduce inflammatin and increase T regulatory cells should reduce TGF-B. High phosphatonins is a sign of low klotho levels. Exercise increases klotho, Most Acidophilus bacteria and Lactobacillus Lactis increases klotho. Cordyceps mushrooms increase kltoho. PPAR Gamma activators stimulate klothos, Some PPAR gamma activators are berberine, magnolia, and Omega 3s. Those who are obese should not stimulate PPAR gamma because they are usually PPAR gamma dominant. Adaptogenic herbs like suma root and maca root can help normalize adrenal levels. Ubiquitin levels are reduced by autophagy. High prolactin levels can result from toxins in plastic containers used to store food and some farm chemicals found in our food supply. There are also chemicals in processed foods that can cause high prolactin levels. Those who are taking drugs should not use berberine or things that contain it because it inhibits the cytochrome P450 enzymes needed to detox medications.

Fulvic acid and nobiline induce autophagy. We do not want to overstimulate autophagy. Fasting also stimulates autophagy but those who are Type1 diabetics have to be careful fasting can induce ketoacidosis in them. Branch Chain fatty acids can inhibit autophagy. Tumeric, ginger, berberine, gensing, mushrooms and elderberries can stimulate autophagy.

NOD2 – Nucleotidebinding Oligomerization Domaincontaining Protein 2 whew that was a lot. A member of the NLP family which is a group of immune regulating proteins. It is a sensor of muramyl dipeptide which is a constituent of both gram negative and gram positive bacteria. It is found in macropages and paneth cells. When inhibited a-defensin numbers are decreased, lower sensitivity to bacteria infection, and altered immune function from Toll Like Receptors becoming suppressed. This results in the inability to clear bacteria infections from the intestines. Inate and adaptive immunity is impaired. Nod2 induces autophagy through the NOD2 pathway. NOD2 is induced by NLP or bacteria infection, this promotes the delivery of NOD2 which enhances inflammation. Showing that if You have high NOD2 levels you would not want to induce autophagy. NOD2 prevents infection in cells which is mediated by ROS and MAPK pathways. NOD2 altered expression can lead to inflammatory bowel disease. Many cellular proteins interact with NOD2 directly and regulate it’s function positively or negatively. Among these proteins is Erbin. Erbin regulates Erbb2 if Erbin is inhibited Erbb2 levels can go up resulting in cancer growth. Centaurin B1 which I have no idea what it’s function is. Angio-associated migratory protein which is involved in endothelial tube formation and endothelial cell migration. It is involved in angiogenesis. Carbamoyl-phosphate synthase 2 is involved in the production of nucelotides in cells. Mitogen-activated protein 1 which helps down regulate NOD2. Heat shock protein 90 interacts with NOD2. HSP90 is involved in folding , intracellular transport and the degradation and maintenance of proteins. I have post on heat shock proteins like HSP90 and HSP70.

NOD deficiency. NOD2 is involved in maintaining balance between the microbiome and immune response. NOD2 deficiency results in loss of epithelium integrity, and increased susceptibility to intestinal inflammation. NOD2 deficiency can cause dysfunction in intestinal paneth and goblet cells. Deficiency increases IFN-y, and decrease ROS production which protects from infection so we need a balance because excess ROS can damage tissues in the body.

NOD2 upregulation. Vitamin D supplementation has been shown to increase NOD2 which helps to fight infection. Excess NOD2 can lead to rheumatoid arthritis, and systematic inflammation. Excess NOD2 has been linked to cardiovascular disease and pulmonary disease. NOD2 prevents inflammation in the eyes.

NOD2 deficiency causes low TH17 levels, inhibited immunity, and will be more prone to cancer. NOD2 is also involved in the detection and eradication of viruses.

Excess NOD2 causes systematic inflammation and sarcoidosis. Often times it is mistaken for cancer or copd. High NOD2 levels is a sign of infection.

Damage to the mucus membrane and intestinal tissue can cause it’s dis-regulation. This shows the importance of restoring mucus membrane and work on healing the gut.

Atg16L1

Autophagy-Related Protein 16-like Protein 1 – Deficiency in Atg16L1 impairs recruitment of Atg12-Atg-5 complex which impairs the engulfment of pathogens and cellular organelles during the process of autophagic catabolism. Atg16L1 defeciency cause Paneth cell dysfunction and increases inflammation. Atg16L1 causes high leptin and adiponectin levels. A deficiency in Atg16L1 leads to intestinal lesions. Leptin tells the brain we do not need to eat. Leptin increases inflammation in the body. High leptin levels lead to chronic fatigue. Leptin can cause Th1 dominance. Those with high IL-10 levels would want to avoid probiotics that increase IL-10 because leptin increases IL-10. Leptin causes mast cells to become more inflammatory. Leptin causes lower T regulatory cells which keep our immune system at homeostasis. Leptin can cause excess blood clotting (throbosis). Leptin can cause high blood pressure. Leptin increases estrogen levels. Adiponectin is a protein hormone involved in glucose levels and fatty acid breakdown. High adiponectin levels causes a loss of appetite it causes weight loss and works synergistically with leptin. Adiponecton decreases gluconeogenesis. It increases B-oxidation of fats. It protects against endothelial dysfunction. It increases insulin sensitivity. So you can see the importance of Atg16L1 homeostasis.

Mir223 restores autophagy and Atg16L1 homeostasis. Mir233 downregulates inflammation. Mir233 is reduced in sepsis. Mir233 increase HDL cholesterol levels. But Mir233 is upregulated in inflammatory bowel diseases. Increasing Claudin-8 inhibits Mir233 inflammatory effects.

ROS (Reactive Oxygen Species)

ROS or Reactive Oxygen Species modulates cellular function under normal conditions. ROS is produced during the process of oxidative phosphorylation and can be handled by instracellular antioxidants. Injury, toxins , vaccine injury, infection, and stress can cause an over production of ROS which can exceed the generation of antioxidants leading to oxidative stress which can cause a lot of damage throughout the body. It causes inflammation, cell damage and even cell death. When the mitochondria become dysfunctional this can cause a rearrangement of the cytoskeleton which is framework of the plasma membrane and effects the balance between kinases, and phosphatases which promotes the ability of microorganisms to enter the cell and contributes to many inflammatory diseases. Excess ROS increases the permeability of intestinal epithelial. When levels of ROS are normal it will induce autophagy and microphagy which reduces inflammation. Reducing ROS levels too low can have the opposite effect because it would prevent it from inducing autophagy and we would lose the protection it gives us from infection.

Antioxidants can reduce oxidative stress but when homeostasis is achieved a person should only take maintenance doses. Over use of antioxidants can promote cancer by protecting it from apoptosis it also increases our risk of infection by reducing ROS levels too low.

Xenophagy

Xenophagy is the clearance of pathogens regulated by autophagy. Reduces Xenophagy leads to alterations of intestinal microbiota. This leads to a higher rate of infection. The microbiotia induce xenophagy in basal paneth cells which is induced by INF-y to maintain intestinal integrity. This impairs sensing of intracellular micro organisms in the intestinal endothelial cells and contributes to the progression of inflammatory bowel disease. Showing the importance on healing the intestinal tract so that the mucus membrane can be restored. Prebiotic fiber and the tryptophan metabolizing gut microbiota increases IFN-y. The commensal strains of E Coli increases IFN-y. Lactobacillus Gasseri increases IFN-y. Bacteroides Fragilis increases IFN-y and has been found to protect from many types of infections. Butyric Acid must be present to maintain IFN-y homeostasis. So it would also be a good idea to make sure the butyrate producing microbes are established.

IRGM (Immunity Related GTPase Family M protein) – is involved in killing of bacteria, vacuolar trafficking and acidification, it is also involved in autophagy. It is involved in fighting mycoplasmas. Damage to the digestive tract can impair it’s function which wold make you susceptible to mycoplasma infection. Inflammation inhibits IRGM. Our digestive tract needs to be acidic. If it becomes to alkaline then it creates an environment that promotes infection and dysbiosis and we lose our commensal microbiota.

Choline deficiency is very common.

 

This is not medical advice I am posting this for educational and informational purposes.

Many are deficient in choline , it has a dramatic impact on our health.  A deficiency effects everything from digestion to our brain.

Signs of choline deficiencies and sources. Once you read this you will see how choline and betaine deficiency can effect every part of the body even the citric acid cycle.

https://draxe.com/what-is-choline/

When we lose our butyrate producing bacteria it can cause glycogen storage issues. This can effect our ATP levels. We know we can experience dysfunction with choline if ATP levels get low.

https://bmcphysiol.biomedcentral.com/articles/10.1186/1472-6793-8-19

Choline helps with insulin resistance.

http://www.nrcresearchpress.com/doi/abs/10.1139/bcb-2016-0105?journalCode=bcb#.W5MIIR6YXMo

Choline serves so many functions a deficiency in choline has a dramatic whole body especially the liver and the brain.

https://lpi.oregonstate.edu/mic/other-nutrients/choline

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2782876/

https://veganhealth.org/choline/

A deficiency in choline also causes high hydrogen peroxide levels. Also oxidative stress can deplete choline.

https://www.ncbi.nlm.nih.gov/pubmed/10783322

https://www.ncbi.nlm.nih.gov/pubmed/19897276

https://mybiohack.com/blog/postural-orthostatic-tachycardia-syndrome-pots-intolerance

The body raises creatine levels to try and protect itself during choline deficiencies.

https://academic.oup.com/ajcn/article/80/1/163/4690274

Bile is important for the digestion of food and nutrient absorption. Choline is needed to produce bile. Our body uses bile to remove many toxins.

https://www.ncbi.nlm.nih.gov/pubmed/9748591

Choline is important for lipid metabolism,the production of VLDL and mitochondrial function.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4113756/

https://www.drweil.com/vitamins-supplements-herbs/supplements-remedies/choline/

https://www.physiology.org/doi/full/10.1152/ajpendo.00331.2010

Choline is involved in homocystiene metabolism and issues with methyl-groups can cause homocystenuria.

https://www.sciencedirect.com/science/article/pii/S0014579309001860

https://mostlymeatiswhatieat.blogspot.com/2012/12/homocysteine-and-glutathione-nutrients.html

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3798916/

Bradykinin causes a rise in acetylcholine receptor which is a sign of inflammation.

https://www.ncbi.nlm.nih.gov/pubmed/2842493

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2658795/

Transmethylation inhibition raises homocysteine levels and leads to brain damage from inhibiting the bodies ability to metablolize choline. Farm chemicals can inhibit transmethylation especially glyphosate and glufosinate. This can also effect sulfation and the CBS pathways.

https://www.ncbi.nlm.nih.gov/pubmed/18591504

https://chrismasterjohnphd.com/2017/08/12/living-with-mthfr/

https://www.mthfrsupport.com.au/wp-content/uploads/2017/04/PPT-CBS-Pathway-6-slides-per-page.pdf

When this happens bioavialable forms of vitamins will help return things to normal levels.

https://health-boundaries.com/what-is-a-healthy-b12-level/methylcobalamin/

It is important to get the supporting nutrients to properly metabolize and use choline.

https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1471-4159.2011.07616.x?

Choline metabolism is just as important as magnesium for our health.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3601486/

http://geneticgenie.org/blog/2013/10/21/acetylcholine-deficiency-in-chronic-illness-the-hunt-for-the-missing-egg/

https://lpi.oregonstate.edu/mic/other-nutrients/choline

The vagus nerve effects PEMT expression.

https://www.ncbi.nlm.nih.gov/pubmed/25433161

TMAO has been linked to heart disease and is produced mostly by our gut microbiome. It also effects the availability of choline.

https://www.ncbi.nlm.nih.gov/pubmed/21475195

https://mbio.asm.org/content/6/2/e02481-14.full

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5127123/

DMB found in balsamic vinegar and Wine inhibit TMAO production in our gut microbiome.

https://www.cell.com/cell/fulltext/S0092-8674(15)01574-3?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867415015743%3Fshowall%3Dtrue

Excessive meat consumption leads to high bacteroides levels. This causes IBD and can lead to cardiovascular disease.

https://www.ncbi.nlm.nih.gov/pubmed/26160437

This can also lead to impaired renal function.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5431124/

This can lead to fatty liver disease.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4813164/

Food sources that raise TMAO.

https://www.ncbi.nlm.nih.gov/pubmed/27377678

https://www.selfhacked.com/blog/tmao/

TMAO levels can be reduced with a combination of B vitamins and vitamin D.

https://onlinelibrary.wiley.com/doi/abs/10.1002/mnfr.201600358?

Methyl-group metablolism issues and methy-group donor deficiencies can effect DNA methylation, and gene expression. Remember Choline is a methyl donor and needs the other methyl donors.

https://academic.oup.com/jn/article/132/8/2333S/4687556

Estrogen regulates PEMT expression aberrant estrogen levels can cause liver dysfunction in a situation like this. There are many toxins that can cause this and even vaccine injury can cause this to happen.

https://www.ncbi.nlm.nih.gov/pubmed/21059658

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3020773/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2430895/

Inflammation, oxidative stress, metabolic issues can cause phospholipase A activity which can cause problems with the gall bladder.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2365627/

Aluminum negatively impacts the effects of choline on the brain.

https://www.ncbi.nlm.nih.gov/pubmed/10437134

Folic Acid which is man made has been shown to be linked to cancer, mental illness and even metabolic issues. Folate is natural , but they fortify much of our food with folic acid which is man made. Folic Acid should be avoided it can cause psuedo MTHFR issues.

https://www.ncbi.nlm.nih.gov/pubmed/25733650

Japanese Honeysuckle protects from fatty liver.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4632443/

Reduce Basal Ganglia function has been found to be common in those with chronic fatigue syndrome. This can be caused by inflammation, stress, toxins, and autoimmune issues. It is not mentioned in the first study but this is a result of a change in choline levels in the brain. Choline levels become elevated in the brain. This is why it is important to reduce inflammation , learn to deal with stress better and to treat infection. Farm chemicals found in high amounts in our food can also cause this and when possible try to eat organic. Glufosinate a chemical with very similar properties as glyphosate has many of the same ill health effects. Heavy metals can also cause this to happen which are often times found in vaccines.

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0098156#s5

https://www.nature.com/articles/npp201739

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0098156

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4392553/

https://www.e-jnc.org/journal/view.php?number=135

http://amalgam.org/381-2/

https://vaccinepapers.org/wp-content/uploads/ganrot-aluminum-health-effects1986.pdf

All the above mentioned things can effect BCHE and ACHE levels which are known to be high in multiple sclerosis. Farm chemicals have been shown to reduce BCHE which is important for ACHE homeostasis. High BCHE levels can cause myocardial infarction. BCHE levels is found to be high in obestiy, uremia, hyperthyroidism, and hypertension. Those are all inflammatory dieses. BCHE is elevated during inflammation. This shows the importance of addressing things that cause inflammation.

BCHE levels is low in liver disease and cancer. Low BCHE levels are a sign of malnutrition. Low BCHE levels can cause higher ACHE levels. High ACHE levels can cause mental illness.

https://www.nature.com/articles/s41598-018-19701-7

https://www.ncbi.nlm.nih.gov/pubmed/10794391

BCHE levels decline in malnutrition.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3581611/

Ghrelin is involved in glucose and insulin homeostasis. BCHE regulates Ghrelin levels I have posted on Ghrelin and it’s involvement in glucose and insulin homeostasis. BCHE reduces Ghrelin.

https://www.nature.com/articles/ijo2017123

Information how various things effect ACHE and BCHE.

http://turkjbiochem.com/2003/054_061.pdf

Autoimmunity can effect choline status and lead to chronic illness. I have posted about autoimmunity and how to correct it. Myasthemia Gravis is caused by autoantibodies detroying, altering or inhibiting the acetylcholine receptors. Most of the things I have mentioned in my post on autoimmunity that can cause these issues.

https://www.drweil.com/health-wellness/body-mind-spirit/autoimmune-disorders/myasthenia-gravis/

http://www.lifeextension.com/Protocols/Neurological/Myasthenia-Gravis/Page-01

Choline is important in the production of VLDL which has been found to be low in those with inflammatory bowel disorders. Inflammation and autoimmune issues can cause low VLDL levels.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5241147/

https://www.hindawi.com/journals/mi/2016/1363818/

https://www.selfhacked.com/blog/ibd-ulcerative-colitis-crohn-genetics-lifestyle-stress-infections/

This is why phosphatidylcholine (Lecithin). Helps with inflammatory bowel disorders. Most of my friends said that sun flower seed oil is the most effective.

https://www.ncbi.nlm.nih.gov/pubmed/20926877

Antiphospholipid syndrome which leads to excessive blood clotting can is tied to choline metabolism.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4112255/

Metabolic issues can effect choline status which can lead to POTS.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4415014/

https://mcb.asm.org/content/30/7/1746

Activation of a7 nicotinic acetycholine receptors in the presence of choline helps with Alzheimers and mental illness by enhancing glutamate release.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4112255/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4600449/

Our gut bacteria effect the status of our choline levels.

https://genomemedicine.biomedcentral.com/track/pdf/10.1186/gm228

High Leptin levels can cause cardiovascular disease and low leptin levels can lead to obesity. I have covered leptin in previous post.

http://www.yourhormones.info/hormones/leptin/

https://www.selfhacked.com/blog/the-root-causes-of-leptin-resistance-and-12-ways-to-reverse-it/

An increase in Dgat1 causes fatty liver disease. Betaine and choline prevents fatty liver by inhibiting Dagat1.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3097135/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5647077/

https://www.frontiersin.org/articles/10.3389/fnut.2018.00061/full

https://atrium.lib.uoguelph.ca/xmlui/bitstream/handle/10214/4975/Sivanesan_Sugashan_201212_Msc.pdf;sequence=3

Betaine and choline help restore many of the metabolic pathways involved in the metabolism of choline.

https://www.frontiersin.org/articles/10.3389/fnut.2018.00061/full

http://www.nrcresearchpress.com/doi/full/10.1139/bcb-2016-0105

Betaine helps maintain the citric acid enzymes.

http://jhs.pharm.or.jp/data/53(6)/53_671.pdf

Phosphatidylcholine which is responsible for cell membrane integrity is regulated by cytidylyltranssfrerase.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5936825/

The microbes that help heal the gut.

 

This is not medical advice I am posting this for informational and educational purposes.

Most with inflammatory bowel disease have too many bacteriodes which is caused by excess meat consumption, antibiotics, glyphosate, glufosinate and other farm chemicals. This results in nutrient deficiencies which lead to metabolic and gene problems. Before you can get your gut bacteria reestablished you have to address those health issues because our gut microbes communicate with and modulate our genes. These are the bacteria that was found to help restore intestinal health in those with inflammatory bowel disease or leaky gut. They also help those with autoimmune issues and chronic illness.

Studies have shown that by alternating probiotics and taking lower doses of them and taking a break from them to leave them balance out is more effective at establishing a balance of our gut bacteria.

Each of our triggers are different so it is important to keep a food diary on how various food effects you.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4021001/

Our gut bacteria modulate our genes. So an imbalance in them or a deficiency has effects on our genes,

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5915727/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5892391/

We need a diversity in our gut bacteria for them to stay established.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6107516/

A loss of short chain fatty acid and butyrate producing bacteria cause inflammatory bowel disease and constipation.

https://jcm.asm.org/content/52/2/398

Our diets influence out gut bacteria for example meat alkalizes the gut producing an environment that will permit the rise of certain bacteria that can lead to health problems. If we consume too much meat it can lead to inflammatory bowel diseases because it raises bacteroides levels and kills the bacteria that produce the good fats we need and the short chain fatty acids the body needs. High bacteroides levels can also lead to heart disease, diabetes, and even autoimmunity. Also a diet high in meat can increase the bacteria in our guts that cause inflammation.

Transfats and oils like vegetable oil and canola oil were found to raise bacteroides levels and decrease our good short chain fatty acid producing bacteria. Oils like olive oil, coconut oil and fish oil have been found to promote good gut bacteria.

Whey protein and the glycoproteins found in mushrooms have been found to reduce bacteroides and increase the good gut bacteria.

Lactose has been found to increase the good bacteria that helps produce butyrate and short chain fatty acids. This is why it is important to address lactose intolerance, it can be corrected.

Sugar increases Bifidobacterium, this could be bad for those who are over weight but good for those who are under weight and need to gain weight.

Prebiotics like resistant starch, oligosaccharides, fructosaccharides increase our short chain fatty acid producing bacteria. Short chain fatty acids are very important keeping us healthy. They have also been found to increase the microbes that protect and strengthen the health of our digestive system.

Polyphenols found in fruit especially berries, promote good bacteria while reducing the bad.

Artificial sweeteners especially aspartame has been shown to increase bacteroides to the point it could lead to irritable bowel syndrome.

https://www.hyperbiotics.com/blogs/recent-articles/89735302-your-diet-changes-your-microbiome-fast

https://translational-medicine.biomedcentral.com/articles/10.1186/s12967-017-1175-y

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4417592/

A list of foods that increase our good gut bacteria.

https://cfsremission.com/2017/08/24/food-to-increase-bifidobacteria-and-lactobacillus/

In order to establish our good bacteria we need FOMAPs I found introducing them very slowly worked best for me as my gut bacteria received the food they needed and increased I could increase my FODMAP intake. If we stay on a FODMAP diet too long it will make it difficult to reestablish our good bacteria. Adjust the diet to your body do not stick strictly to diet but base it on how your body responds. I used a paleo diet after the FODMAP but did not stick to either diet strictly but based them on how my body responded.

https://gut.bmj.com/content/gutjnl/64/1/93.full.pdf

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5830546/

paleo diet.

http://paleozonenutrition.com/2018/02/21/autoimmune-paleo-protocol-in-inflammatory-bowel-disease-clinical-study-shows-remission-in-73/

Akkermana Muciniphila It is found in the upper part of the intestines and helps regulate bile acid production. Bile acids help regulate our pancreatic enzymes so indirectly it also regulates our digestive enzymes. It is believe to restore the mucous membrane in the digestive system. Polyphenols from berries helps to feed it and increase it’s numbers. Oligosaccharides also increase A Muciniphila. It has been found to be low in those with obesity. A deficiency in A Muciniphila will cause a deficiency in short chain fatty acids and inhibited lipogenesis. A person deficient in A Muciniphila will develop insulin resistance and low glucose levels.

https://ubiome.com/blog/post/akkermansiamuciniphila/

http://www.mdpi.com/2076-2607/6/3/75

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5614963/

Oligosaccharides and inulan have been shown to increase A. Muciniphila. This is why green algae and seaweed have so many health benefits they are high in oligosaccharides.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5983298/

https://www.sciencedirect.com/science/article/pii/S1756464617301627

https://gut.bmj.com/content/67/2/271.long

Roseburia species help produce butyric acid, short chain fatty acid and protects us from diabetes and obesity. They help prevent inflammatory bowel disease. Beta Glucan in mushrooms and oats , chitan and inulin help raise Roseburia levels. Butyric acid protects the gut and our brains. It also protects our nerves and is important in the absorption of nutrient. If we are deficient in butyrate we will not absorb nutrients. Butter and ghee are good sources of butyrate until the gut bacteria are restored.

https://www.futuremedicine.com/doi/abs/10.2217/fmb-2016-0130?src=recsys&journalCode=fmb

https://gut.bmj.com/content/63/8/1275.long

https://academic.oup.com/femsec/article/87/1/30/508741

Faecalibacterium Prautsnitzii increases IL-10, this is important because Lyme and other illnesses that carry the OspA protein inhibit IL-10 to stealth themselves from the bodies immune defense. There isn’t much known about it except that it is low in many types of digestive disorders. We get it from being around others who have it.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5705805/

https://www.nature.com/articles/ismej2016176

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5492426/

Clostridium Butyricum is a butyrate producing bacteria . Clostridum butyricum kills it’s cousin that cause negative health effects. It also increases IL-10 . It also decreases inflammatory cytokines. There are studies that have shown if the other healthy gut bacteria are not present this one like many of the bacteria species used in probiotics could start causing health problems.

https://www.ncbi.nlm.nih.gov/pubmed/30159141

https://www.ncbi.nlm.nih.gov/pubmed/30141701

https://www.ncbi.nlm.nih.gov/pubmed/29851202

It promotes better bowel movements.

https://www.ncbi.nlm.nih.gov/pubmed/30058712

https://academic.oup.com/cid/article/61/7/1107/289593

E Coli Nissle 1977 doesn’t only protect us from it’s cousins that cause ill health effects it also protects against other types of infections. It has been shown to put inflammatory bowel disorders into remission. It has too many benefits to mention. The only way I know of getting this one is through a probiotic called Multaflor.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5987069/

https://www.tandfonline.com/doi/full/10.3109/08910600903444267

E Coli Nissle 1977’s cousin can cause many health problems if not kept in check.

https://www.physiology.org/doi/10.1152/ajpgi.00091.2016

Lactobacillus Casei and L. Longum have been find to be deficient in many types of digestive disorders. They do not establish well of one or the other is missing it is best if they are taken together if you use a probiotic. The improve the bodies antioxidant capacity. We need SOD to produce H2O2 which the body uses to detox cells and transport nutrients and enzyme into and out of the cells. When deficient in these cellular macrophagy is inhibited. This help protect against cancer and other illnesses.

If we are deficient in them we can develop liver disease, lysosomal storage disorders and glycogen storage issues, insulin resistance and lose the ability to absorb nutrients. Our blood sugar levels will become low because insulin levels will increase. Bifidobacterium Bifidum has many of the same benefits and probably would benefit from taking it along with these. Also we cannot absorb proteins without the Lactobacillus strains.

https://www.hindawi.com/journals/omcl/2016/1340903/

https://www.ncbi.nlm.nih.gov/pubmed/30158369

They also help protect us from mold toxins.

https://www.frontiersin.org/articles/10.3389/fmicb.2018.01503/full

http://pubs.rsc.org/en/Content/ArticleLanding/2018/FO/C8FO00252E#!divAbstract

Lactobacillus Longum also produces folate for us.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4654071/

protects our lungs.

https://www.ncbi.nlm.nih.gov/pubmed/30020533

https://www.ncbi.nlm.nih.gov/pubmed/24830455

Insulin and glycogen issues.

http://www.ijpvmjournal.net/article.asp?issn=2008-7802;year=2016;volume=7;issue=1;spage=102;epage=102;aulast=Sharma;type=3

Protein absorption.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4741550/

A species of bacteria called lactobacillus casei shiroto is important in regulating our tryptophan levels. A deficiency in this strain will cause reduce tryptophan levels resulting in anxiety and the inability to sleep. A deficiency in this one can result in phenylketonuria which causes high ammonia levels in the body. A person who has this issues will get ill when they eat meat , potatoes or other things high in phenylalanine. Low levels of tryptophan can cause a loss of the beneficial bacteria in the Roseburia family which can lead to leaky gut and inflammatory bowel disease and sever constipation.

https://aem.asm.org/content/82/12/3649

https://www.researchgate.net/publication/287309677_Lactobacillus_casei_Shirota_modulation_of_ammonia_metabolism_in_physical_exercise

Fermented milk like butter milk and kefir help them get established.

https://www.jstage.jst.go.jp/article/fstr/10/2/10_2_143/_article

Many have been found to be deficient in Streptococcus Salivarius protects us from lung, oral and nasal infections. It also protects us from inflammation. Those who are deficient in S Salivarius will be prone to infection especially from it’s cousins in the streptococcus family that cause negative health effects. The only way I know to safely increase this is with lozenges that contain it because too much can cause health problems so you would want to avoid taking capsules of this.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3911234/

https://www.futuremedicine.com/doi/abs/10.2217/fmb.12.113?rfr_dat=cr_pub%3Dpubmed&url_ver=Z39.88-2003&rfr_id=ori%3Arid%3Acrossref.org&journalCode=fmb

https://www.nature.com/articles/s41598-017-11446-z

Lactobacillus Rhamnosus helps prevent diarrhea , has been shown to reduce symptoms of inflammatory bowel disease. It helps protect us from infection. Helps protect us from allergies,obesity and diabetes. It also helps protect us from staph infection.

H Pylori is commensal but without Lactobacillus Rhamnosus to keep it in check it can cause gastric ulcers.

https://www.selfhacked.com/blog/l-rhamnosus/

https://aem.asm.org/content/80/18/5773

https://www.frontiersin.org/articles/10.3389/fmicb.2018.01873/full

We also need fungus for example Saccharomyces Cerevisiae know as brewers yeast helps prevent diabetes. They used to think S Boulardii was a separate species but it has been found to be the same. I couldn’t afford the supplement so I bout a package of brewers yeast and consumed it. Wasn’t sure it would make it through my stomach acid but I felt improvement so I believe it does. Now this is one you do not want to increase too much, also you do not want to take this if you have autoimmune issues or leaky gut. It can act as a pathogen if it gets into the blood stream, many of our microbiome can if they get too high in numbers or get into our blood stream.

https://www.ncbi.nlm.nih.gov/pubmed/23967428

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4705302/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5605952/

S Cerevisaiae helps reduce vaginalis and candida.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6037478/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5354225/

https://onlinelibrary.wiley.com/doi/full/10.1111/j.1574-6968.2010.02037.x

Lactobacillus Rueteri produces folate those who have folate deficiency have been found to be low in folate and have high inflammation levels. L Rueteri also regulates our oxytocin which can give us a feeling of self worth and well being. A deficiency in L Rueteri can lead to extreme depression.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5061717/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5431580/

Our gut bacteria produce B vitamins for each other and maintain each other. If the ones who produce the B vitamins are missing then the microbiome will get them from our foods which will prevent us from receiving them. This is why it is important to eat foods high in B vitamins and to protect our gut bacteria from antibiotic, farm chemicals and toxins in our foods like artificial sweeteners.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4403557/

Lactobacillus Acidophilus prevents diarrhea, helps protect against clostridium infections. Those with interstitial cystitis are usually deficient in this one. It helps reduce symptoms of inflammatory bowel disorder. Acidophilus regulates our ph of our digestive system and bladder and keeps it at the correct ph. Our bladders and digestive system need to be acidic. An akaline environment can cause a loss of our good gut bacteria and promote the growth of the bad. It can also cause candida to go from commensal to a pathogenic form. Many with interstitial cystitis have found relief using L Acidophilus suppositories. Those who are having difficulty gaining weight usually have excess L acidophilus levels because it speeds up metabolism and those who have problems with weight gain are often deficient in acidophilus. Fermented foods are high in this but those with high histamine must reduce their histamine before eating fermented food I addressed that in my autoimmune post.

https://www.healthline.com/nutrition/lactobacillus-acidophilus#section3

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705118/

Bifidobacterium increased the acid levels of our digestive tract which inhibits bad bacteria from growing and help keep our digestive tract acidic. It has been shown to reduce symptoms of irritable bowel disease.

https://www.nature.com/articles/ajg200925

Bifidobacterium Infantis protects us from autoimmune disorders by regulating our T cells. B infantis also helps protect our digestive tract.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4277968/

https://www.ncbi.nlm.nih.gov/pubmed/28230606

This is an in depth discussion of probiotics.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3424311/

more information on microbiome and folate production.

http://www.mdpi.com/2072-6643/3/1/118

Bifidobacterium Breve reduces symptoms of celiac disease.

https://www.ncbi.nlm.nih.gov/pubmed/26134988

Frequent constipation is a sign of a deficiency in the bifidobacterium species.

https://www.ncbi.nlm.nih.gov/pubmed/28884754

If we are deficient in the lactobacillus species we are more prone to salmonella infection.

https://www.ncbi.nlm.nih.gov/pubmed/29120368

https://www.ncbi.nlm.nih.gov/pubmed/28975642

Lactobacillus Bulgaris increases T Regulatory cells which prevents on over active immune response.

https://www.thieme-connect.com/DOI/DOI?10.1055/s-0043-117612

Too many Lactobacillus Delbrueckii can cause urinary tract infection.

https://jcm.asm.org/content/47/1/275

Our gut microbiome produce many of our nutrients so a deficiency in a specific strain can cause nutrient deficiencies especially in the B vitamins.

https://microbialcellfactories.biomedcentral.com/articles/10.1186/s12934-017-0691-z

Quinones like PQQ is needed by our gut bacteria to thrive and balance out. They convert it to vitamin K2.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5738691/

Phylloquinone (vitamin K) is also used by our gut bacteria and converted to vitamin K2. Animal products and leafy green vegetables are good sources of vitamin K . Many should be cooked especially spinach and kale because they are very high in oxalates.

http://www.jbc.org/content/283/17/11270.full

https://www.medicalnewstoday.com/articles/219867.php

https://www.cambridge.org/core/journals/british-journal-of-nutrition/article/phylloquinone-vitamin-k1-intakes-and-food-sources-in-1864-year-old-irish-adults/00B5ECF7B563D1A3ADAA94986FC83223

Some food sources of quinones are. Natto, Green Tea, Parsley, Paypaya and green peppers. Some may benefit from supplementing PQQ because many of the foods that contain it are very high oxalate like kiwi.

https://biofoundations.org/dietary-sources-of-pyrroloquinolone-quinone-pqq/

https://optinghealth.com/foods-high-in-pqq/

Soil based probiotics have been shown to improve digestive health.

Bacillus Subtilis produces and antibiotic that protects us but is none toxic to the good bacteria. B Subtilis has antioxidant properties. B Subtilis has been shown to restore normal gut flora. B Subtilis has been shown to relieve constipation and diarrhea. It has reduce symptoms of inflammatory bowel disease. It boost immunity and fights H Pylori. It improves the health of the liver. It promotes the production of digestive enzymes which improves gut health.

https://www.ncbi.nlm.nih.gov/pubmed/21204933

https://www.selfhacked.com/blog/b-subtilis/

https://www.globalhealingcenter.com/natural-health/bacillus-subtilis-probiotic-strain/

Bacillus Coagulans improves insulan sensitivity. High insulin levels are common in inflammatory bowel disease, this would help reduce insulin levels. It helps reduce diabetes symptoms. B Coagulans improves muscle recovery and prevent arthritis. It helps increase the beneficial microbes in the gut. It relieves intestinal pain inflammation and constipation. B coagulans reduces the risk of urinary tract infections.

https://www.selfhacked.com/blog/b-coagulans/

https://www.verywellhealth.com/bacillus-coagulans-for-better-bowel-health-89601

Bacillus Clausii protects us from respiratory infection. It fights the infections that cause diarrhea. It reduces symptoms of inflammatory bowel disease.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1936284/

https://www.omicsonline.org/open-access/bacillus-clausii–the-probiotic-of-choice-in-the-treatment-of-diarrhoea-2157-7595-1000211.php?aid=63792

Two soil based probiotics to watch out for because they can cause major health problems are bacillus Licheniforms and Enteroccocus Faecium.

Those with inflammatory bowel disorders have high bacteroides. They produce high levels of Beta Glucuronidase. This inhibits glucuronidation which is needed to detox mold toxins.

What is Beta-glucuronidase?

http://www.pjm.microbiology.pl/archive/vol6232013319.pdf

Things that may help those who have the more difficult digestive problems.

Mundinus,_Anatomia_Mundini..._Wellcome_L0027530

This is not medical advice I am posting this for informational and educational purposes.

If you truly want to heal it takes time and persistence. You have to develop your own protocol there is no one size fits all your protocol must be unique to you and your health problems. There is no magic bullet, pharmaceuticals treat the symptoms not the cause. So you may feel better but will slowly get worse until you will start needing other medications to hide the new symptoms that arise from the declining health which pharmaceuticals contribute to.

It takes a lot of research and patients. Take notes of what works and what does not and keep readjusting your protocol. As you heal your protocols will need to change.  Homeostasis is the goal once you start feeling better try cutting supplements out. If it goes well then take a maintenance dose of the supplement once in a while.

Mucilage every few hours helps a lot with leaky gut. When you have leaky gut it causes high oxalate levels. This causes a cycle that is hard to break because oxalates prevent the gut from healing. Mucilage can help heal the gut breaking the cycle. Mucilage helped me the most with healing my gut.

Things that are high in mucilage are Okra, organic Oatmeal, Aloe Vera I found the liquid gel worked the best dried aloe vera seemed ineffective. Besella Alba known as Malabar Spinach, Irish moss but you have to watch consuming it, it has a cannabinoid that reduces pain but has side effects if you consume too much. Most plants in the mallow family are very high in mucilage and have very good healing properties. Most plants in the dioscera family are high in mucilage especially the chinese wild yam. Fenugreek is high in mucilage. Flax seeds are high mucilage but if you have leaky gut they should be ground up to prevent other heath issues. Most seaweeds are high in mucilage. Licorice root is high mucilage but you have to make sure it is deglycyrrhizinated if not it can cause many health problems. Mullein is high mucilage and helps with lung infections. Most edible plants in the daisy and sunflower family are high in mucilage. Wild Daisy helped me a lot. Pysillium seed husk are high in mucilage they are seeds from the plantain herb. Plantain herb itself is very high in mucilage. Wild violet is very high in mucilage. Chia seed is high in mucilage most seed is. Slippery Elm is high in mucilage but some claim it is high oxalate , I have never tried it. Most roots herbs are high in mucilage. Arrow root is very high in mucilage.

https://mavcure.com/mucilaginous-herbs/

https://www.invitehealth.com/article-demulcents-and-mucilages-true-healers.html

Various gut microbiome and what they do.

https://www.vitamodularis.org/articles/how_to_interpret_your_microbiome_data.shtml

https://biofoundations.org/increasing-and-maintaining-akkermansia-muciniphila-for-a-healthy-gut-microbiome/

Oregano oil kills just about all pathongens in the gut.

https://www.bmj.com/content/352/bmj.i939/rr-1

Sage also is effective against bad gut bacteria.

http://www.scielo.br/scielo.php?pid=S0034-89102004000200025&script=sci_arttext&tlng=en

Verbana fights Citrobacter. I don’t know much about it but it has sedative effects and helps with seizures.

https://www.cogentoa.com/article/10.1080/23312009.2017.1363342.pdf

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5174135/

Beta Glucuronidase is low it can effect hormones. If it is high it can cause toxins reabsorption.

https://biofoundations.org/maintaining-a-proper-balance-of-beta-glucuronidase-for-disease-and-cancer-prevention/

High beta glucuronidase causes high estrogen.

https://www.planetnaturopath.com/hormones/high-beta-glucuronidase-and-how-it-affects-estrogen-and-detoxification/

Herbs that strengthen the immune system.

http://www.chiro.org/nutrition/FULL/Bacteria_That_Strengthen.shtml

We also need to reduce oxidative stress and nitrositive stress.

https://iamajuicer.wordpress.com/2018/08/02/oxidative-stress-the-antioxidant-systems-and-how-they-effect-our-health/

https://iamajuicer.wordpress.com/2018/07/11/nitrosative-stress/

Streptoccocus bacteria produce an exotoxins streptolysin and NAG -glycohydrolase which help it evade the immune system.

Inhibiting NLRP3 helps resolve the issues Streptolysin causes. It uses a tactic similar to Lyme disease it stimulates inflammation to evade the immune system.

https://www.frontiersin.org/articles/10.3389/fcimb.2018.00211/full

Rabdosia contains oridonin which inhibits NLRP3.

https://www.nature.com/articles/s41467-018-04947-6

There are a number of ways being used to inhibit NLRP3 inflammasome.

https://www.frontiersin.org/articles/10.3389/fphar.2015.00262/full

Resveratrol, quercetin and curcumin are NLRP3 inhibitors.

https://www.hindawi.com/journals/mi/2016/5460302/

Paeonia is a CBR2 activator which inhibits NLRP3.

https://www.ncbi.nlm.nih.gov/pubmed/25854559

CB2R receptor activation protects and heals the nerves.

https://www.nature.com/articles/cddis2014364

Hypoxia reduces NLRP3 and induces autophagy.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5524634/

https://www.tandfonline.com/doi/full/10.4161/auto.22783

bacillus subtillus kills most bad gut bacteria.

https://aac.asm.org/content/59/11/6844.full

https://www.tandfonline.com/doi/full/10.4161/viru.29514

https://www.sciencedirect.com/science/article/pii/S0168160511007136?via%3Dihub

We need butyrate producing bacteria to protect from inflammation. Also it protect the brain.

https://gut.bmj.com/content/63/8/1275.long

Fodmap diet helps with IBS.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5555627/

Increasing Treg through FOXP3 cells helps.

https://www.hindawi.com/journals/jdr/2013/621693/

https://www.ndcn.ox.ac.uk/publications/692350

Our gut bacteria regualate T Reg cells.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3276397/

https://ctajournal.biomedcentral.com/articles/10.1186/s13601-016-0108-9

Mycobacteria can inhibit NOD2 which can cause gut issues.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4316803/

Infection can lead to NOD2 deficiency this causes a reduction in V-ATPase which is needed to produce stomach acid.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4316803/

https://www.ncbi.nlm.nih.gov/pubmed/25335775

https://www.frontiersin.org/articles/10.3389/fimmu.2016.00367/full

Over stimulation of NOD2 can also make us prone to infections and chronic illness. Homeostasis should be the goal.

https://www.nature.com/articles/srep08383

https://www.spandidos-publications.com/10.3892/etm.2017.4288

https://www.kidney-international.org/article/S0085-2538(15)55943-7/pdf

HSP70 Restores NOD2 function. I have posted on HSP70

https://pubs.acs.org/doi/abs/10.1021/acs.biochem.7b00470?src=recsys&journalCode=bichaw

http://www.jbc.org/content/289/27/18987.long

Our diet and many probiotic strains can induce HSP70 which will restore NOD2 function which would restore dendric cell funtion.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4892289/

Trypterygium Wilfordii may help restore NOD2 function though this is a single case report.

https://journals.lww.com/md-journal/fulltext/2017/11270/Case_report___remarkable_remission_of_SAPHO.114.aspx

Our diet and our gut interactions.

https://www.frontiersin.org/articles/10.3389/fimmu.2016.00290/full

Sulfation is involved in hormone production and use. Gut dysbiosis, glyphosate, mercury and other toxins can inhibit sulfation. This can result in hormone dysregulations. This can also result in high DHEA levels.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6016456/

https://www.ncbi.nlm.nih.gov/pubmed/28153960

https://www.ncbi.nlm.nih.gov/pubmed/30087535

To much hydrogen sulfide producing bacteria lead to chronic illness.

https://www.physiology.org/doi/pdf/10.1152/physrev.00017.2011

https://pdfs.semanticscholar.org/1fda/f6c18c0b184ae8e41c8a777b2979bedd2494.pdf

Too many methane producing bacteria can lead to constipation there are some probiotics that will help with that.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5609747/

http://www.talkingaboutthescience.com/studies/Donohue-Sulfoxidation.pdf

The craziest part of all of this is I seen supposed pathogens that could correct many of these issues but did not include them in this but they turn certain genes of which could restore the function of non-functioning genes.

Diets effect on gut bacteria.

https://www.aivpa.it/files/upload/rivista_articolo/00152_microbioma-dieta-disturbi-gastroenterici-e-disbiosi.pdf

https://watermark.silverchair.com/fux022.pdf?

http://www.drwallyschmitt.com/Newsletters/issue-43-molybdenum/

http://www.drmyhill.co.uk/wiki/Fermentation_in_the_gut_and_CFS

Tributyrin found in butter helps with dysbiosis

https://www.fasebj.org/doi/abs/10.1096/fasebj.31.1_supplement.994.9

https://biofoundations.org/multiple-health-benefits-tributyrin-triglyceride-form-butyrate/

Sulfur regulation in the body is very improtant.

https://www.mthfrsupport.com.au/wp-content/uploads/2017/04/PPT-CBS-Pathway-Final-full-page-slides.pdf

Dysbiosis often leads to impaired renal function.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5431124/

Those who have gut issues will be deficient in short chain fatty acids and they are very important in maintaining our health.

https://biofoundations.org/multiple-health-benefits-tributyrin-triglyceride-form-butyrate/

Many will have high oxalate levels which are produced endogenously. I have posted on oxalates. This can prevent the gut from healing.

https://mthfrsupport.com/2018/03/understanding-sulfation-and-oxalate/

http://www.lowoxalate.info/research.html

https://people.csail.mit.edu/seneff/DC2016/CynthiaSmith_DC2016.pptx

Autophagy corrects lipid metablolism which is needed to produce bile and digestive enzymes. Bile homeostasis is very important for the health of the whole body.

http://jem.rupress.org/content/early/2018/01/12/jem.20171965.long

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5930069/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4247383/

Hydrogen peroxide is needed for lipogenesis.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5369955/

https://www.sciencedirect.com/science/article/pii/S0014579300021979

SOD increases H2O2. The only bioavialable source in food is the chaga mushroom.

https://jonbarron.org/herbal-library/nutraceuticals/superoxide-dismutase

http://www.worthington-biochem.com/sodbe/default.html

Curcumin increase SOD but should not be taken too long it chelates iron and can cause anemia.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3705117/

http://www.raysahelian.com/superoxidedismutase.html

http://www.foodtrients.com/inside/sod-do-you-know-about-this-powerful-antioxidant/

Sidt2 deficiency can inhibit autophagy. Unfortunately I have not research this Gene much.

https://www.ncbi.nlm.nih.gov/pubmed/29363559

Though I do not believe in taking enzymes the body can produce if all else fails what else are we to do. Often times taking enzymes the body can produce can disable the bodies ability to produce them.

https://empoweredsustenance.com/fat-malabsorption/

Increasing brush oder enzymes helps with malabsorption.

https://www.ncbi.nlm.nih.gov/pubmed/11346204

You must heal the endothelium to correct malabsorption. Saccharomeyces Boulardii is needed for that. This also improve lipid abosorption.

https://www.ncbi.nlm.nih.gov/pubmed/29762474

https://metabolichealing.com/villous-atrophy-leaky-gut-intestinal-dysbiosis/

Dietary nucleotide supplementation helps heal the digestive tract.

https://www.sciencedaily.com/releases/2014/04/140416143313.htm

https://www.selfhacked.com/blog/dietary-nucleotides-health-benefits-of-nucleotides/

https://www.researchgate.net/publication/275771517_Nucleotides_supplementation_improves_various_function_of_the_body

https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1440-1754.2002.00056.x

Mucins and tight junctions regulate what passes in and out of the intestines.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5548832/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6095905/

High zonulin levels causes the gut to become more permeable.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3458511/

High zonulin levels has been linked to many diseases.

https://www.mygenefood.com/zonulin-leaky-gut/

https://www.jillcarnahan.com/2013/07/14/zonulin-leaky-gut/

Probiotics to reduce zonulin.

https://www.realnatural.org/probiotics-help-reduce-intestinal-permeability-also-called-leaky-gut-syndrome/

colostrum reduces zonulin.

https://www.researchgate.net/publication/316676047_Oral_Supplementation_with_Bovine_Colostrum_Decreases_Intestinal_Permeability_and_Stool_Concentrations_of_Zonulin_in_Athletes

https://www.naturalnewsblogs.com/healing-leaky-gut/

Brush border enzymes are needed to break down and absorb food.

http://www.vivo.colostate.edu/hbooks/pathphys/digestion/smallgut/bbenzymes.html

https://www.core3training.com/can-improve-gut-overall-health/

Black Seed Oil improves carbohydrate digestion.

https://www.ncbi.nlm.nih.gov/pubmed/28959553

Thyme improves brush border enzymes.

https://www.ncbi.nlm.nih.gov/pubmed/29223554

How bile is secreted.

https://www.ncbi.nlm.nih.gov/pubmed/29262229

http://www.sophiahi.com/how-to-increase-your-digestive-fire-by-jeannie-oliver-chc-cpt/

Foods that contain natural digestive enzymes.

https://www.healthline.com/nutrition/natural-digestive-enzymes#section2

They mention Kiwi in this one. It is high oxalate so would not be good for someone who has leaky gut.

https://starmystuff.com/top-7-foods-contain-natural-digestive-enzymes

 

I am sorry these are things I forgot to post with this post. It is concerning restoring the ability to produce short chain fatty acids.

Diasccharidase in involved in our digestion and absorption of carbohydrates and sugars. If we are not producing enough then our food will sit and ferment in our upper intestine possibly feeling like a brick is sitting in our stomaches. This will cause excess gas and can lead to the production of hydroxl sulfide which inhibits sulfation and can cause issues with the CBS and BH4 pathways. This can lead to high ammonia levels, proteinuria, phenyketonuria and even porphria. Infection can cause this, an imbalance in our gut bacteria brought on by farm chemicals especially glyphosate, antibiotics, and even chemicals found in processed food. If you have diarrhea and you are not absorbing then you may be producing too much disaccaride which is an indication of high insulin levels. High oxalates will prevent the gut from healing. I have posted on oxalates and the gut. If we produce too much diasaccaride then we will experience similar symptoms only instead of being constipated we would have diarrhea.

https://drhoustonanderson.com/disaccharidase-deficiency-causes-and-treatment/

Vinegar seemed to help me but this studies shows it actually reduces Disaccharidase. Not sure what to think about this one.

https://academic.oup.com/jn/article/130/3/507/4686196

We know those with IBD usually have high insulin levels showing they have lost their sensitivity to insulin. This leads to high leptin levels.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4159716/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3959465/

I know those with IBD connot do some of these things. You have to learn to figure out what in the information that is out there you can apply and what you cannot.

https://www.healthline.com/nutrition/improve-insulin-sensitivity#section8

Though being insulin resistant is usually found in obesity it is common in many inflammatory bowel disorders.

Increasing insulin sensitivity will help with leptin levels.

https://www.marksdailyapple.com/25-ways-to-improve-your-insulin-sensitivity/

https://www.selfhacked.com/blog/top-tips-for-fixing-insulin-resistance/

Increased insulin levels inhibits disaccharidase levels.

https://www.ncbi.nlm.nih.gov/pubmed/21946084

Decreased insulin levels increases disaccharide levels.

http://www2.ufpel.edu.br/biotecnologia/gbiotec/site/content/paginadoprofessor/uploadsprofessor/8aff603648377229ebdb3b655ecdf854.pdf

Now if you look at MAPK it is involved in IBD. So now we can see the connections. We need to increase insulin sensitivity . I read many research articles and decreasing insulin levels seem to make IBD worse but improving insulin sensitivity improved IBD. Inhibiting TNF-a improves insulin sensitivity.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2792822/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5859792/

There are naturals that inhibit TNF-a but nothing that inhibits it directly. Also inhibiting it for too long makes us more prone to infection.

https://www.researchgate.net/profile/Solomon_Habtemariam/publication/12454244_Natural_Inhibitors_of_Tumour_Necrosis_Factor-a_Production_Secretion_and_Function/links/09e4150bb180eefd74000000/Natural-Inhibitors-of-Tumour-Necrosis-Factor-a-Production-Secretion-and-Function.pdf?origin=publication_detail

Resvertrol inhibits TNF-a it is found in grape seed extract.

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0091406

Reducing insulin levels reduces P38 MAPK which reduces symptoms of IBD.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4218950/

Those who have IBD have been found to be deficient in bacteria in the up digestive track especially Oscillospira and Akkermansia.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5573342/

https://helda.helsinki.fi/bitstream/handle/10138/236401/Akkermansia_muciniphila.pdf?sequence=1

Lactobacillus Fermentan increases Akkermansia.

https://www.ncbi.nlm.nih.gov/pubmed/28935567

Host microbe prebiotic and fiber interactions. Interesting lets you know how each type of saccharide effects the gut bacteria.

https://www.tandfonline.com/doi/full/10.1080/19490976.2017.1290756?src=recsys

Studies confuse me, some says stay away from carbohydrates will others show that those carbs increase the very bacteria those who have IBD are deficient in.

https://academic.oup.com/jcem/article/101/1/233/2806797

Beta Glucan found in Oats and mushrooms increases Oscillospira.

https://www.frontiersin.org/articles/10.3389/fmicb.2017.00966/full

Meditarrian diet can increase Oscillospira.

https://www.ncbi.nlm.nih.gov/pubmed/26505825

L-arginine has been found in many studies to help normalize the gut bacteria even in chickens.

https://www.ncbi.nlm.nih.gov/pubmed/28901890

Nanosilver can kill specific gut bacteria depending on the size and shape. In theory this could be used to reduce specific gut bacteria that may be too numerous.

https://www.researchgate.net/publication/241100111_Comparison_of_the_anti-bacterial_activity_on_the_nanosilver_shapes_Nanoparticles_nanorods_and_nanoplates

The shape of the silver determines which bacteria it is effective against.

https://www.ncbi.nlm.nih.gov/pubmed/28588204

Glutamine reduces Oscillospira which would be detrimental to IBS.

https://cfsremission.com/2017/10/15/decreasing-oscillospira-genus/

Black Raspberries increase Oscillospira.

https://www.ncbi.nlm.nih.gov/pubmed/29502392

Most with IBD are difficient in Oscillopira. This is found in the upper digestive tract. I believe it is the cause of the low disaccharidase production but I cannot find studies to prove it.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4437018/

A deficiency in Oscillopira causes food allergies.

Food additives have a negative impact on the gut.

https://www.ncbi.nlm.nih.gov/pubmed/29914144

This is a good list of bacteria and what they do. Bifidobacteria Bifidum and Breve increase short chain fatty acid production.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5964481/

Our gut bacteria regulate cell that produce antibiotics.

https://www.frontiersin.org/articles/10.3389/fmicb.2018.00736/full

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5801817/

More on Oscillopora.

https://www.datapunk.net/substrata/display.pl?119852+S

Bile acid also increases Oscillopora.

https://onlinelibrary.wiley.com/doi/abs/10.1111/1758-2229.12319

https://drjockers.com/25-ways-improve-gallbladder-health/

Gut homeostasis is controlled by the endocannbinoid system. Those with inflammatory bowel issues have been found to have low endocannbinoids. This raises diaglycerols which can prevent the proper production of digestive enzymes leading to the inability to digest and absorb saccharides and produce short chain fatty acids (carbohydrates and sugar). This is caused by the upregulation of the protein kinase pathway.

https://www.ncbi.nlm.nih.gov/pubmed/22917662

Black pepper increases endocannbinoids which would help with IBD.

https://www.ncbi.nlm.nih.gov/pubmed/24412246

HSP70 is a transport for anamide and other endocannabinoids. I have posted on HSP70.

FAAH inibitors increase endocannabinoids.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2882713/

Biochanin A found in read clover, the red covering on peanuts, and in chick peas is an FAAH inhibitor.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2931556/

Here is information on other cannabinoids and their effects on the body.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5429335/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2538700/

Kaempferol found in pine tree bark extract and magnolia is an FAAH inhibitor.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2538700/

Bilirubin is inhibited with IBD and other inflammatory bile diseases. This is cause by the inflammation which can lead to scarring and obstruction of biliary ducts. Serrapeptase helps remove scar tissue and so doe HSP70. Also using anti-inflammatory herbs helps.

http://www.crohnscolitisfoundation.org/resources/liver-disease-and-ibd.html

https://inflammatoryboweldisease.net/symptoms/complications/gallstones/

https://kresserinstitute.com/little-known-connection-leaky-gut-gluten-intolerance-gallbladder-problems/

This is the oddest part about IBD and other inflammatory diseases. TMAO is low in those who have an intestinal inflammatory disease. Most have too much of the bacteria that produces TMAO but those with IBD have too few.

https://www.ncbi.nlm.nih.gov/pubmed/26160437

This is a list of gut bacteria that increase TMAO consuming choline will increase these bacteria.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4453578/

https://lpi.oregonstate.edu/mic/other-nutrients/choline

https://draxe.com/what-is-choline/

Faecalibacterium Prausnitzii has been found to be low in those with inflammatory bowel disease. This causes a dificiency in nicotinic acid which leads to an increase in phenylalamine. This lead to a conditions called phenyketonuria which causes high ammonia levels in the body and can effect many metabolic pathways and cause us to become ill when we eat meat, potatoes or anything else that has phenylalanine in it. A deficiency in Faicalibacterium Prausnitzii also results in high cadaverine and putrescine levels which causes inflammation.

https://emedicine.medscape.com/article/945180-overview?pa=70SvUf61EZjJeh01GcM07cjK0CdaeXT%2FVguJkgES6Vuf4MsXKJuI2VMwKp69ZMinm%2BKlpX80V6KaHMrB8SW%2FFlaycSibeA0Q%2FJsWK%2BpGHzs%3D

https://www.healthline.com/health/phenylketonuria

Our gut bacteria need iron tho thrive but the iron they fortify food with is the wrong type. Iron found in curly dock and burdock root will supply you with iron without causing toxicity unless you have certain liver diseases. If you have iron toxicity lactoferrin will restore iron homeostasis. Curcumine will reduce iron levels in the blood also but do not take it too long or you can become anemic.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5491036/

Ghrelin stimulates our appetite and increase stomach acid.

https://www.theunion.com/news/twi/glyphosate-roundup-and-its-link-to-celiac-disease-gluten-intolerance/

Fatty acid and vagus nerve stimulate ghrelin.

https://academic.oup.com/abbs/article/41/3/188/655

https://www.ncbi.nlm.nih.gov/pubmed/29632576

https://www.selfhacked.com/blog/32-ways-to-stimulate-your-vagus-nerve-and-all-you-need-to-know-about-it/

https://thelivingproofinstitute.com/19-ways-to-stimulate-your-vagus-nerve/

https://www.psychologytoday.com/us/blog/the-athletes-way/201607/vagus-nerve-stimulation-dramatically-reduces-inflammation

I had to alternate types of diets until I got things straightened out. I had to do a FODMAP diet first then as I healed I had to switch to a Paleo diet. Then when I had healed enough I was able to fast it took me a while to build up to being able to fast for a day. Some can go longer and it is dangerous for others like those with lysosomal storage issues.

https://paleoleap.com/butyrate-anti-inflammatory-fat/

Hydrogen Sulfide produced by gut bacteria can cause sulfation issues.

https://sibosurvivor.com/hydrogen-sulfide-sibo/

When we have too much hydrogen sulfide being produce by our gut microbiome it will cause us to become constipated.

 https://www.ncbi.nlm.nih.gov/pubmed/28971603

https://www.sciencedirect.com/science/article/pii/S2213007117300485

now you have reached a state that has caused a cycle that is hard to break and results in ulcerative coalititis and even IBS.

 https://link.springer.com/article/10.1023/A:1018867516575

Excess H2S causes low blood pressure and a reduced body temperature. It will slow our metabolism causing us to feel drowsy.

http://www.ei-resource.org/…/gut-bacteria-the-hydrogen…/

The inhibited phosphorylation causes a deficiency in the redox ions needed by many metabloic pathways. Mainly Mg2+, Mn2+, Zn2+ and indirectly Ca2+. So it pretty much shuts cellular function down.


https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4010430/

Not all will get drowsy with the inhibited phosphorylation it may cause NMDA issues which is what happened to me. When this happens and your glutamate levels sky rocket it will fell like your head is going to spit open, you will not be able to sleep and you will experience anxiety.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3966912/

This thread is long enough but the can effect the CBS and BH4 pathways which can lead to sulfur intolerance and meat intolerance. Even after correcting this problem you have to heal the gut and get the oxalates down to restore the function of the metabolic pathways.

http://www.talkingaboutthescience.com/studies/Donohue-Sulfoxidation.pdf

Having to many H2S producing bacteria has been shown to raise blood levels of H2S. I could not find studies on the prolonged effects but I have found information on prolonged exposure. It causes sulfhemoglobin which cannot be broken down by the body.

http://www.theijoem.com/ijoem/index.php/ijoem/article/view/482

https://www.ncbi.nlm.nih.gov/pubmed/25237136

https://www.frontiersin.org/articles/10.3389/fped.2018.00098/full

Thiamine and B6 deficiency can cause high oxalates.

https://www.ncbi.nlm.nih.gov/pubmed/3947375

https://draxe.com/thiamine-foods/

the gut and cholestokinin

http://www.yourhormones.info/hormones/cholecystokinin/

https://www.selfhacked.com/blog/good-bad-effects-cck/

Trypsin inhibitors increase cholecystokinin.

https://naldc.nal.usda.gov/download/26115/PDF

Things that raise GABA like , mugwort, wormwood and rooibos reduces cholecystokinin levels. High estrogen levels cause high cholecystokinin levels. High dopamine levels increases cholecystokinin. High levels of cholecystokinin causes glutamate toxicity and NMDA toxicity.

https://www.acnp.org/g4/GN401000056/CH056.html

Potatoes increase cholecystokinin

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3033477/

If not addressed it leads to autism.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4628252/

Proprionate is high in Ibs. This strikes me as odd because acetate and butyrate are low in IBS. How can one short chain fatty acid be high and the test dificient?

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4847229/

https://www.healthline.com/nutrition/short-chain-fatty-acids-101#section1

High proprionate can cause loss of appetite and weight loss.

https://gut.bmj.com/content/64/11/1744

it is from having to high of bacteroides.

https://jb.asm.org/content/jb/134/1/84.full.pdf

This article partially explains the high bacteroides levels.

http://humanfoodproject.com/going-feral-one-year-journey-acquire-healthiest-gut-microbiome-world-heard/

Meat increases bacteriodes.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4820228/

meat alkalizes the gut so it makes sense that those with IBD may consume more meat which will make them have raised bacteroides levels. This can lead to many health problems.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3949257/

Betaine reduces bacteriodes by increasing stomach acid.

https://www.selfhacked.com/blog/tmg-health-benefits/

http://drlwilson.com/articles/TRIMTHYLGLYCINE.htm

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2176045/

Snail1 involvement in inflammatory bowel diseases indicates macrophagy issues.

https://www.ncbi.nlm.nih.gov/pubmed/21830269

https://translational-medicine.biomedcentral.com/articles/10.1186/s12967-015-0450-z

Macrophagy issue also cause lipogenesis issues.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6108423/

https://translational-medicine.biomedcentral.com/articles/10.1186/s12967-015-0450-z

Glycolysis issues are also an indication of inhibited macrophagy and sure enough those with inflammatory bowel disorders have glycolysis issues.

https://onlinelibrary.wiley.com/doi/abs/10.1002/ibd.21388

Macrophagy genes have been impicated in inflammatory bowel disease.

http://www.els.net/WileyCDA/ElsArticle/refId-a0025006.html

Good information from my friend David Anderson.

For people with digestive issues

Hydrophilic colloidal diet

1. Hydrophilic colloids bring about conditions in the stomach during digestion which approach those resulting from the consumption of foods in their natural state.

2.Hydrophilic colloids lessen gastric irritation by absorbing the digestive secretions of the stomach so that digestion takes place within a mass of food.

3. Gelatin, because of its availability, relatively low cost, non-toxicity, adaptability as an item of dietary and its thorough digestibility becomes an admirable hydrophilic colloid for dietary usage.

4. The amount of gelatin to be used in a given case depends on the patient’s needs, but it must be of good quality and sufficient in amount.

5. It has a wide range of usefulness in gastrointestinal ailments ranging from the atonic conditions met in the chronic invalid to the irritating condition presented in gastric ulcer.

In some instances, gelatinized arrowroot powder has been used to achieve similar results.. Arrowroot/pectin, etc… Could possibly be used if oxalates are an issue.

 

https://link.springer.com/article/10.1007%2FBF03010602

 

Medium chain triglycerides improve bile flow and decrease bile reabsorption.

https://med.virginia.edu/ginutrition/wp-content/uploads/sites/199/2014/06/Parrish-February-17.pdf

https://nutritionandmetabolism.biomedcentral.com/articles/10.1186/s12986-018-0267-x

MCTs help heal leaky gut and inflammatory bowel disorders.

https://www.ncbi.nlm.nih.gov/pubmed/27187452

https://www.frontiersin.org/articles/10.3389/fimmu.2016.00290/full

Organic acids help heal the gut mucosa.

https://www.researchgate.net/profile/Ulker_Eren2/publication/282700134_Effects_of_dietary_organic_acid_supplementation_on_the_intestinal_mucosa_in_broilers/links/5649b1d908ae451880af661a/Effects-of-dietary-organic-acid-supplementation-on-the-intestinal-mucosa-in-broilers.pdf?origin=publication_detail

http://www.mdpi.com/2072-6643/9/9/920/pdf

file:///home/homuser/Downloads/nutrients-09-00920.pdf

They recommend glutamate in this. That is not correct because those with inflammatory bowel issues have high bacteriodes and glutamate feeds them which can make things worse. But there is useful information in this.

There is an error in this. Those with inflammatory bowel have high bacteroides which causes a lot of problems. They claim glutamate helps but it feeds bacteroides so would make things worse but I found useful information in this.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5622680/

Interesting information on inflammatory bowel disease.

https://www.hindawi.com/journals/mi/2017/6869259/

Those with inflammatory bowel issues are low in biotin which is probably caused by the inflammation inhibiting absorption.

https://europepmc.org/abstract/med/19056639

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5129763/

A biotin deficiency causes the inability to break down proteins, fats and other nutrients.

https://www.physiology.org/doi/abs/10.1152/ajpcell.00141.2016

Those with inflammatory bowel usually have low biotin which can cause many metabolic issues. Biotin needs Adenosylcobalamin which is a form of B12 in the body. Some may have to supplement if the body is not converting it.

Adenosylcobalamin helps with biotin absorption and use.

https://www.globalhealingcenter.com/natural-health/adenosylcobalamin-4-facts-know/

Biotin and pantothenic acid compete for absorption and pantothenic acid can inhibit biotin absorption.

https://www.ncbi.nlm.nih.gov/pubmed/9814986

Alkaline Phosphotase is low in those with inflammatory bowel disorders. Lactobacillus Casei increases it and will help with nutrient absorption.

https://www.ncbi.nlm.nih.gov/pubmed/22783049

Before increasing it make sure you know the dangers of too much.

https://www.selfhacked.com/blog/alkaline-phosphatase/

How to increase ALP.

https://health.onehowto.com/article/how-to-increase-alkaline-phosphatase-11707.html

http://www.newhealthguide.org/Low-Alkaline-Phosphatase.html

If you take curcumin once the gut bacteria start getting established stop taking it. It can cause anemia because it chelates iron.

https://www.ncbi.nlm.nih.gov/pubmed/25474287

Cissus stimulates ALP.

https://www.ncbi.nlm.nih.gov/pubmed/25449449

https://examine.com/supplements/cissus-quadrangularis/

High estrogen levels effect bile production. Bile protects the intestines from inflamation.

https://hormonesbalance.com/articles/gallbladder-hormone-balance-connection-mean-dont-gallbladder/

Hormones involved with bile flow.

https://hormonesbalance.com/articles/gallbladder-hormone-balance-connection-mean-dont-gallbladder/

Inhibited bile flow can cause estrogen dominance.

http://www.jbc.org/content/early/2018/06/21/jbc.RA118.001789.full.pdf

This causes a cycle that is hard to break and results in high cck levels.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2756670/

Activation of the CCK1 receptor by estrogen can lead to gall stones.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6037422/

Dim3 (diinoylmethane) inhibits the estrogen receptor which should lower cholestokinin levels.

https://www.ncbi.nlm.nih.gov/pubmed/25486199

http://joe.endocrinology-journals.org/content/195/3/393.full.pdf

Things that inhibit Era.

https://www.hindawi.com/journals/omcl/2018/6040149/

They mentioned soy isoflavons in the previous study but it could make things worse.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5633874/

ursolid acid that was mentioned is found in the wax on skins of apples , in rosemary and thyme.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3379974/

 

These are enzymes and hormones that are usually dis-regulated in inflammatory bowel.

Cholesterols function in bile secretion. Issues with the liver X receptor can cause issues with cholesterol metabolism.

http://www.jbc.org/content/278/18/15565.long

https://www.ncbi.nlm.nih.gov/pubmed/29523554

Olive Oil help resolve liver X receptor issues. But inhibits glucuronidation.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5521785/

Butyrate found in butter and ghee also help.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6111843/

High estrogen inhibits sulfation. Increasing UDP-glucuronosyltransferases will reduce estrogen levels.

http://www.jbc.org/content/275/46/36164.full.pdf

http://dmd.aspetjournals.org/content/30/5/564

DHA, oleic acid, and linoleic acid inhibit those enzymes.

https://www.nature.com/articles/srep02903

Foods that increase UDP-glucuronosyltransferase.

http://dmd.aspetjournals.org/content/30/5/564

https://www.heart-health-guide.com/apigenin.html

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2874462/

https://www.selfhacked.com/blog/apigenin-top-11-science-based-health-benefits-apigenin/

Luteiolin is good at increasing UDP-glucuronosyltransferase.

http://secretsofnaturalhealing.blogspot.com/2010/12/luteolin-rich-foods-shown-to-reduce.html

https://www.selfhacked.com/blog/top-11-science-based-health-benefits-luteolin/

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0166239

Diosmetin is found in the white parts of citris fruit and dates.

https://pubs.acs.org/doi/abs/10.1021/jf502359x?src=recsys&journalCode=jafcau

https://www.researchgate.net/publication/228115816_Bioactivity_of_Diosmetin_Glycosides_Isolated_from_the_Epicarp_of_Date_Fruits_Phoenix_dactylifera_on_the_Biochemical_Profile_of_Alloxan_Diabetic_Male_Rats