Fungi / Bacteria, Not Autoimmunity, Cause IBD (Chron's, UC) And IBS

haidut

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I posted a study recently that chronic alcohol consumption increases Candida overgrowth in the gut while simultaneously decreasing the number of benign bacteria.
Candida Overgrowth Is A Major Factor In (alcoholic) Liver Damage / Cirrhosis

Actually, the term "benign bacteria" is wrong as there is no benign bacteria in our gut. There are just less or more pathogenic types. The same applies to the fungi, with Candida being an example of a highly nefarious one.
This new study finds that high-fat diet (and by extension from the above study - alcohol) causes not only an imbalance in our microbiome (with a shift towards more pathogenic bacteria and fungi) but also allows the bacteria and fungi to enter into a highly effective symbiosis. This symbiosis likely leads to developing of a number of inflammatory bowel disease (IBD) conditions like Chron's and ulcerative colitis (UC), as well as more benign (but more common) ones like IBS. The link between bacteria and Chron's is already considered highly causative and in some countries patients get treated with a high course of antibiotics.
Mycobacterium avium subspecies paratuberculosis - Wikipedia

If the findings of the study below are true then the current immunosuppressive "treatments" for IBD such as Humira or Remicade are not just ineffective - they are the exact opposite of what should be administered and possibly criminally negligent. The study below proposes instead treating such patients with an anti-fungal, which I think can be made eve more effective by combining with a non-absorbable antibiotic like Rifaximin (already approved for treating SIBO and IBS).

http://www.dldjournalonline.com/article/S1590-8658(17)31015-0/fulltext
High-Fat Diet Changes Fungal Microbiomes and Interkingdom Relationships in the Murine Gut | mSphere
Gut fungi might be linked to obesity and inflammatory bowel disorders
"...High-fat diets may alter relationships between bacteria and fungi in mice’s intestines, contributing to obesity, researchers report October 11 in mSphere. In independent work, researchers report that a fungus teams up with two types of bacteria to fuel gut inflammation in people with Crohn’s disease. That work was summarized October 4 in Digestive and Liver Disease. Together, the studies are part of a growing body of research indicating that relationships between the bacterial and fungal kingdoms can affect health, says David Andes, a fungal biologist at the University of Wisconsin School of Medicine and Public Health in Madison. Andes wasn’t involved in either study."

"...Meanwhile, other researchers are investigating how a microbial triad might contribute to an irritable bowel syndrome. People with Crohn’s disease have an overabundance of Candida tropicalis fungus along with Escherichia coli and Serratia marcescens bacteria, say Christopher Hager and Mahmoud Ghannoum of Case Western Reserve University School of Medicine in Cleveland. When grown separately in lab dishes, the organisms “grew fine,” says Hager. “They formed nice little colonies. But when you mixed all three of them together, they just grew out of control. They form these intense, large robust biofilms.” Biofilms are structured microbial communities that can shield bacteria from antibiotics, making them hard to kill."

"...By itself C. tropicalis grows as a harmless budding yeast, Hager says. But in the presence of bacteria, the fungus stretches out into long filaments. Electron microscopy showed that E. coli fuse to the fungal growths. Meanwhile S. marcescens make protein strings that somehow stabilize the biofilm. That’s good news for the microbes: Their partnership allows them to outcompete loner bacteria and fungi. But biofilms are bad news for the gut. Mice harboring the three organisms developed intestinal inflammation, a symptom of Crohn’s disease and other bowel disorders."

"...Hager and Ghannoum propose that giving Crohn’s disease patients antifungal drugs and then adding beneficial fungi, such as S. cerevisiae, could create a healthier microbe balance in the gut."
 

Regina

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I posted a study recently that chronic alcohol consumption increases Candida overgrowth in the gut while simultaneously decreasing the number of benign bacteria.
Candida Overgrowth Is A Major Factor In (alcoholic) Liver Damage / Cirrhosis

Actually, the term "benign bacteria" is wrong as there is no benign bacteria in our gut. There are just less or more pathogenic types. The same applies to the fungi, with Candida being an example of a highly nefarious one.
This new study finds that high-fat diet (and by extension from the above study - alcohol) causes not only an imbalance in our microbiome (with a shift towards more pathogenic bacteria and fungi) but also allows the bacteria and fungi to enter into a highly effective symbiosis. This symbiosis likely leads to developing of a number of inflammatory bowel disease (IBD) conditions like Chron's and ulcerative colitis (UC), as well as more benign (but more common) ones like IBS. The link between bacteria and Chron's is already considered highly causative and in some countries patients get treated with a high course of antibiotics.
Mycobacterium avium subspecies paratuberculosis - Wikipedia

If the findings of the study below are true then the current immunosuppressive "treatments" for IBD such as Humira or Remicade are not just ineffective - they are the exact opposite of what should be administered and possibly criminally negligent. The study below proposes instead treating such patients with an anti-fungal, which I think can be made eve more effective by combining with a non-absorbable antibiotic like Rifaximin (already approved for treating SIBO and IBS).

http://www.dldjournalonline.com/article/S1590-8658(17)31015-0/fulltext
High-Fat Diet Changes Fungal Microbiomes and Interkingdom Relationships in the Murine Gut | mSphere
Gut fungi might be linked to obesity and inflammatory bowel disorders
"...High-fat diets may alter relationships between bacteria and fungi in mice’s intestines, contributing to obesity, researchers report October 11 in mSphere. In independent work, researchers report that a fungus teams up with two types of bacteria to fuel gut inflammation in people with Crohn’s disease. That work was summarized October 4 in Digestive and Liver Disease. Together, the studies are part of a growing body of research indicating that relationships between the bacterial and fungal kingdoms can affect health, says David Andes, a fungal biologist at the University of Wisconsin School of Medicine and Public Health in Madison. Andes wasn’t involved in either study."

"...Meanwhile, other researchers are investigating how a microbial triad might contribute to an irritable bowel syndrome. People with Crohn’s disease have an overabundance of Candida tropicalis fungus along with Escherichia coli and Serratia marcescens bacteria, say Christopher Hager and Mahmoud Ghannoum of Case Western Reserve University School of Medicine in Cleveland. When grown separately in lab dishes, the organisms “grew fine,” says Hager. “They formed nice little colonies. But when you mixed all three of them together, they just grew out of control. They form these intense, large robust biofilms.” Biofilms are structured microbial communities that can shield bacteria from antibiotics, making them hard to kill."

"...By itself C. tropicalis grows as a harmless budding yeast, Hager says. But in the presence of bacteria, the fungus stretches out into long filaments. Electron microscopy showed that E. coli fuse to the fungal growths. Meanwhile S. marcescens make protein strings that somehow stabilize the biofilm. That’s good news for the microbes: Their partnership allows them to outcompete loner bacteria and fungi. But biofilms are bad news for the gut. Mice harboring the three organisms developed intestinal inflammation, a symptom of Crohn’s disease and other bowel disorders."

"...Hager and Ghannoum propose that giving Crohn’s disease patients antifungal drugs and then adding beneficial fungi, such as S. cerevisiae, could create a healthier microbe balance in the gut."
Thanks haidut. What would you consider a safe anti-fungal? MB? thx
 

Mito

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"...High-fat diets
Mice were fed either standard chow with 18% calories from fat and undetectable cholesterol (catalog no. 2018; Harlan Teklad, Madison, WI) (n = 9) or a high-fat diet with 60% calories from fat and 345 mg cholesterol/kg of body weight (catalog no. F3282; Bio-Serv, West Chester, PA) (n = 9) beginning at 8 weeks of age.

Profile of the high fat diet
12% PUFA
41% SFA
47% MUFA
17FB9821-94E7-404E-8377-BB881B79D1E8.jpeg
http://www.bio-serv.com/pdf/F3282_S3282.pdf
 

tca300

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Thanks haidut. What would you consider a safe anti-fungal? MB? thx
Medium chain triglycerides ( especially C:8 ), vinegar, garlic, raw carrots and flowers of sulfur are all pretty good.

Eating a carrot salad with mct oil, vinegar, salt, and garlic can be helpful in my experience.
 

Regina

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Medium chain triglycerides ( especially C:8 ), vinegar, garlic, raw carrots and flowers of sulfur are all pretty good.

Eating a carrot salad with mct oil, vinegar, salt, and garlic can be helpful in my experience.
:thumbsup:
 

Broken man

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So I am really lost because Its 2 months that I found higher fat intake helped my with steady blood sugar and bowel movements. Will idealabs make antibiotics like minocycline? I know that K2 mk4 should work too but I find that its not working atleast for me.
 

Wilfrid

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There were recents very promising trials made with the use of specific bacterial strains of phages for IBD, and crohn's disease in particular.
 

Wagner83

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I've seen a few people report they've been doing great for years on a ketogenic diet, many don't and crash, not sure what the differences between those are.
 

haidut

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Thanks haidut. What would you consider a safe anti-fungal? MB? thx

MB, niacinamide, aspirin, emodin, MCT, etc. But MB, emodin and MCT are probably the ones that would be most effective in doses people commonly use.
 

haidut

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So I am really lost because Its 2 months that I found higher fat intake helped my with steady blood sugar and bowel movements. Will idealabs make antibiotics like minocycline? I know that K2 mk4 should work too but I find that its not working atleast for me.

The minocycline will not help with the fungal infections. So, a combination of minocycline and MB (or another antifungal) would be needed.
 

raypeatclips

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I am not sure if I am missing something here. But in the mouse obesity study, are the two mices diets equal calorie wise? When I ctrl + F "calorie" it just says about 60% of the diet was fat and 18%. I assume the two diets would have to be equal calories to be taken seriously, but I can't actually find it saying that anywhere?



Medium chain triglycerides ( especially C:8 ), vinegar, garlic, raw carrots and flowers of sulfur are all pretty good.

Eating a carrot salad with mct oil, vinegar, salt, and garlic can be helpful in my experience.

Do you eat the garlic raw, or cooked?
 

tca300

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I am not sure if I am missing something here. But in the mouse obesity study, are the two mices diets equal calorie wise? When I ctrl + F "calorie" it just says about 60% of the diet was fat and 18%. I assume the two diets would have to be equal calories to be taken seriously, but I can't actually find it saying that anywhere?





Do you eat the garlic raw, or cooked?
I dont currently eat garlic, but when I did it was raw.
 

mipp

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I've seen a few people report they've been doing great for years on a ketogenic diet, many don't and crash, not sure what the differences between those are.
Many do well on keto and I've never heard of it causing a substantial weight gain in people. I was on a high fat low carb myself for almost a decade. It wasn't perfect and I problably wouldnt do it again but it didnt cause obesity, digestive desease or other serious health problems that I'm aware of.
 

Wagner83

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Many do well on keto and I've never heard of it causing a substantial weight gain in people. I was on a high fat low carb myself for almost a decade. It wasn't perfect and I problably wouldnt do it again but it didnt cause obesity, digestive desease or other serious health problems that I'm aware of.
My gess would be that in the context of non optimal digestion and with fermentable fibers, whole grains, resistant starch or even starch ingested then high fat may be bad. If one achieves 2-3 BM a day with a higher fat intake then the pros may (should?) outweigh any potential/theoretical cons. Similarly if a low fat intake means poor BM then it's doing damage.
 

mipp

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My gess would be that in the context of non optimal digestion and with fermentable fibers, whole grains, resistant starch or even starch ingested then high fat may be bad. If one achieves 2-3 BM a day with a higher fat intake then the pros may (should?) outweigh any potential/theoretical cons. Similarly if a low fat intake means poor BM then it's doing damage.
This is an overlooked factor in low carb diets. When I did LC I had no idea about endotoxin. It was all about macros, so I only watched my carb intake. And since sucrose and especially fructose was supposed to be 'toxic' I would get my daily carbs mostly from veggies or grains. Perhaps even small amount of fermentable stuff is enough to cause problems when combined with high saturated fat. Especially when digestion is slow or there is constipation caused by other things like low physcial activity, dehydration etc. That's why some people have problems. Interesting... If I ever switch back to LCHF I have to try a 'clean' zero starch/fiber version. This could be the key to make it work really well
 

Kray

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What is the definition of high-fat diet from a Peat perspective? After reading about high fat, I'm always left wondering if I'm doing things wrong. If you are going to discuss the dangers, how about giving some guidelines, or pointing out some links for practical purposes, that would be really helpful.
 
J

jb116

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What is the definition of high-fat diet from a Peat perspective? After reading about high fat, I'm always left wondering if I'm doing things wrong. If you are going to discuss the dangers, how about giving some guidelines, or pointing out some links for practical purposes, that would be really helpful.
Deduction is useful here. Since high carbers typically go around 60% of calories from carbs and Peat has indicated 1 : 1 : 1 ratio, I think any where in between there gives enough play to adjust to the individual. So the base is the 1 : 1 : 1. If you drop carbs below that, assuming protein is kept the same, you start entering high fat territory.
 

Fisherman94

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In my case escherichia coli is low, Serratia marcescens is normal as well as candida tropicalis. Im rather missing gut bacteria.
And antibiotics messed ***t up big time.

I dont think excess fungi/bacteria is the cause of UC / Crohns at all. Maybe IBS and SIBO.
 
Last edited:

raypeatclips

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What is the definition of high-fat diet from a Peat perspective? After reading about high fat, I'm always left wondering if I'm doing things wrong. If you are going to discuss the dangers, how about giving some guidelines, or pointing out some links for practical purposes, that would be really helpful.

How do you feel? There are many things I have read in here such as studies about supplements that I have reacted very negatively too. If you are eating higher fat and feeling better, I wouldn't worry about it. If things start to go wrong then reassess what's going on.

High fat probably 50-60% or higher of calories.

I have seen Peat quoted as saying up to 50 percent of the diet could be from fat but I'm not sure I've seen this said by him directly so take with a grain of salt.
 

CLASH

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Bacteria cause autoimmunity. But theres no difference between this and inflammation. Just another term really. The regulation of your immune systek via t regulatory cells is dependent upon the bacteria in your colon. The question isnt quantity of bacteria as much as it is what types and the relationships. I am not saying that anyone is being reductionistic here in this thread, But I would like to say that often people look at things very simply and reductionistic in general. People think that the gut should be sterile, which part of the gut? What is sterile? The small intestine and stomach are relatively sterile compared to the colon but they still have bacteria, so sterile is relative. There are bacteria in the placenta and the brain and the baby before birth. Becoming "sterile" is irrelevant, the idea doesnt make any sense. The colon is not sterile and will never be sterile in a real life situation realistically. The goal is not a sterile large intestine or a sterile anything. It is one with the right type and ecosystem of bacteria created by the correct terrain and environment. Antibiotics, formula feeding, alcohol, grains, maybe vegetables, pasteurized milk, c sections and starch create a negative ecosystem for our immune function. Utilizing these drugs and protocols, in my experience dont help. You can take every biofilm disruptor you want but if u put meat in the zoo your going to get lions. Antibiotics dont cure anything, they get rid of symptoms for a while. The change should be gradual and with diet. I have done many protocols to solve my gut issues only to make things worse for myself in the long run. The paleo people and gut microbiome people use these protocols to get people to eat foods that arent ideal i.e. A bunch of vegetables and starch (because sugar is bad of course....), this is why people have a difficult time healing. Using antibiotics and antifungals and all these herbs and biofilm disruptors to create an ecosystem without focusing on diet, microbial balance etc. Is like trying visualize CGI graphics of a movie by listening to the radio. The thought process is outdated. The anti-germ theory at this point is as realistic as the "bad air" theory for malaria...

Also, high fat diets may cause issues through bile acids sterilization effect on the gut in excess and promoting bacteria that utilize bile acids as substrate. They produce secondary bile acids that are irritating to the colon.




"Foxp3+ regulatory T cells (Tregs) are key suppressive cell types that regulate autoimmune inflammation in the body (23). In the gut, Tregs accumulate under steady-state conditions where they play an important role in the regulation ofinflammation against microbialstimuli."

"Tregs are critical for the prevention of spontaneous inflammation against commensal microbes (Fig. 1). In antibiotic-treated mice or GF mice, Tregs remain detectable, but their numbers are significantly decreased in the intestinal LP, suggesting that the microbiota promotes the differentiation and/or maintenance of Tregs (26, 27). Colonization of GF mice with 46 strains of Clostridium(26), or with a cocktail of 8 defined commensals, called altered Schaedler flora (ASF) is sufficient to induce Tregs in the gut (26, 27). "

"Treg development is largely dependent on the microbiota in the colon, but not in the small intestine."

Role of the Gut Microbiota in the Development and Function of Lymphoid Cells




"Human regulatory T cells (Tregs) play a critical role in preventing autoimmunity, and their failure contributes to autoimmune diseases. "

"Thus, Tregs exhibit multiple differences from healthy controls that are likely to play roles in the complex pathogenesis of RRMS; these include reduced thymic output of naïve Tregs, impaired naïve Treg suppression, and distinct impairments in at least two subsets of memory Tregs."

"Defects in the in vitrosuppressive function of Tregs occur in patients with numerous autoimmune diseases, including relapsing-remitting multiple sclerosis (RRMS), type 1 diabetes (T1D), psoriasis, myasthenia gravis, and rheumatoid arthritis (RA) [7]. Moreover, Tregs play increasingly recognized roles in a wide variety of human diseases that involve inflammation, notably cancers and infectious diseases"

Human Regulatory T Cells in Autoimmune Diseases
 
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