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

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