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Microbiota
Harm Caused by Medicine
The microbiota in the gut is susceptible to medical interventions:
Impact of antibiotics on the human microbiome and consequences for host health, Patangia et al 2022
Bactrim (sulfamethoxazole and trimethoprim) is a combination antibiotic. Is there a danger of making the gut microbiota less diverse? That would be detrimental to health in the long term.
Impact of Long-Term Low Dose Antibiotic Prophylaxis on Gut Microbiota in Children, Akagawa et al 2020. Sci-hub doesn't have this article and I don't know what exactly is “low dose” or “long term”.
Transient osmotic perturbation causes long-term alteration to the gut microbiota, Tropini et al 2018
Bacteria in Probiotics Are Not Adapted to Living in a Human Digestive System
https://academic.oup.com/ajcn/article/73/2/399s/4737569
“ Should it become desirable to permanently colonize the human intestinal tract with an exogenous probiotic, it is reasonable to suggest that a human-specific probiotic with potent intestinal mucosal cell adhesion properties be chosen. Selection of such strains on the basis of this criterion may be insufficient. It may be necessary to culture surgical or biopsy specimens to select suitable probiotic strains. “
” An ideal probiotic would be one that can survive passage through the gastrointestinal tract, [and] establish itself permanently in the small intestine and colon… ”
Many probiotics do survive stomach acid, and the bile salts of the small intestine, they just don't adhere to the mucosal lining of the large intestine, to take up residence with the existing bacteria. I imagine this is true of all existing probiotics on the market? Would a company sell a probiotic that only needs to be taken once?
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3337120/
Germ free mice, fed all 10 strains of *human* bacteria, did not retain all 10 strains, rather at most 3. I guess because bacteria compete with each other. The best method they found to successfully build up the full array of bacteria, was to feed individual germ free mice a single bacteria, and then mix the mice together in the same cage (since like dogs, they eat each other's poop). The idea is, that the individual human gut bacteria needed to first adapt to living in the mice. Once adapted, they could easily gain hold in other mice as well.
“ Moreover, GF animals introduced to these isolators on day 56 of the study, quickly acquired a similar bacterial community to that of the donor animals, suggesting that the transferred microbial community had achieved a significant level of stability and adaptation to the host gut environment. “
So, once the bacteria had adapted/evolved to live in mice, then they could all settle in to a new mouse, all at once, unlike before, where at mot 3 strains survived.
So are companies selling strains of probiotics that are good at colonizing a human gut? Would that be a good monetary investment for the medical industry?
Synthesized Vectors:
- Rebyota™ (RBX2660) – A standardized fecal-derived product (FDA-approved) that contains a consortium of beneficial bacteria for C. difficile infections.
- SER-109 – A purified, spore-based microbiome therapy (from donor-derived Firmicutes spores) aimed at preventing recurrent C. difficile infections.
- Lactobacillus spp. Suppositories – Some studies have tested Lactobacillus species, such as L. crispatus, L. gasseri, and L. rhamnosus, as vaginal and rectal suppositories to help restore microbiome balance.
- Escherichia coli Nissle 1917 – This probiotic strain has been studied for its potential use in treating inflammatory bowel disease (IBD) and infections.
Small Intesting Bacterial Overgrowth (SIBO)
I think IBS is often caused by bacteria growing in the small intestine, and may very well be the predominant cause, even if this doesn't come up in mainstream broadcasts.
Diversifying the microbiota is a cure:
Clinical efficacy of fecal microbiota transplantation for patients with small intestinal bacterial overgrowth: a randomized, placebo-controlled clinic study, Xu et al 2021
Other natural remedies:
https://www.verywellhealth.com/natural-remedies-for-bacterial-overgrowth-89298
Irritable Bowel Syndrome
Microbiota Dysbiosis
A microbiota test has little clinical utility. Multi-strain probiotics for IBS (with permanent strain colonization a possibility!) is a sufficiently effective treatment. While FMT and WIMT may be more effective, probiotics are safer, easy, and less costly.
https://examine.com/supplements/probiotics/
Probiotics for the management of irritable bowel syndrome: a systematic review and three-level meta-analysis, Chen et al 2023
Gut Microbiota in Patients With Irritable Bowel Syndrome—A Systematic Review, Pittayanon et al 2019
Managing IBS
Intermittent Fasting
While I practice intermittent fasting, I do not have symptoms of IBS. Intestines get to rest when there is not food going through them.
Food is held for a longer period in the small intestine, if there is not more food coming along the way. This allows the small intestine to fully digest the food before releasing it to the large intestine. Unhealthy IBS small intestines tend to suffer from inflammation and digest poorly, which results in undigested food reaching the large intestine. Not fully digested food in the large intestine causes a large amount of flatulence, and an unhealthy microbiome.
Food can make it to the large intestine in as little as 6 hours after consumption. If you have two meals spaced 4 hours apart, the food from the first meal will continue to be digested in the small intestine, even after the second meal is consumed. However, waiting some hours longer may allow the first meal to travel further along the small intestine, such that the second meal may trigger the release of the first meal into the large intestine, before being fully digested. This also can happen from over-eating. There are also some other exceptions.
My experience is that an eating window of 6 hours during the day is optimal in preventing IBS. It's also important not to eat before bedtime, because your body repairs itself during sleep, especially during the deep sleep cycles that happen in the first few hours of sleep. The body can better work on repairing the small intestine if it isn't busy digesting. See the intermittent fasting article for science sources.
Staying hydrated is vitally important for bowel health, so do drink plenty of water during the fasting period.
Related reading: Carbohydrate Maldigestion and Malabsorption, Omer and Quigley 20180801.
Low FODMAPs Diet
https://www.healthline.com/nutrition/fodmaps-101
Low-FODMAP Diet for Treatment of Irritable Bowel Syndrome, Magge and Lembo 2012
https://en.wikipedia.org/wiki/Abdominal_distension
Dietary Fiber
Based on studies summarised in the article, dietary fibre shows significant clinical benefits in patients with IBD. Supplementation of some types of dietary fibre can help to maintain remission and reduce lesions of the intestinal mucosa during the course of the disease. The described effects are primarily associated with increased luminal production of SCFA after administering dietary fibre. SCFA have immunomodulatory properties, they accelerate healing and regeneration processes of the intestinal epithelium, and they lower colonic pH thereby stimulating growth of the beneficial microflora and inhibiting growth of the pathogens. The role of dietary fibre in inflammatory bowel disease, Pituch-Zdanowska et al 2015
See also: https://mekineer.com/health/fiber
Peppermint Tea and Peppermint Oil
Eight studies show that peppermint oil helps with the symptoms of IBS. See the details in the examine article. Update: they used to list all the studies, and now you need to pay subscription to access the full list 
Coconut oil pulling bites (with peppermint):
https://thehonoursystem.com/peppermint-coconut-oil-pulling-bites
Lactose Maldigestion Self-Reporting vs Breath Test Results
“Self-reported intolerance symptoms at home are not clearly related to lactose maldigestion in elderly.” Self-perceived lactose intolerance and lactose breath test in elderly, Casellas et al, 201312
“Of the maldigesters, 63% reported symptoms and 3% of the total sample reported severe symptoms.” Prevalence of lactose maldigestion. Influence and interaction of age, race, and sex, Rao et al 199407
Bismuth Subsalicylate (Pepto Bismol)
Pepto-Bismol is used to treat diarrhea and relieve the symptoms of an upset stomach. These symptoms can include:
- heartburn
- nausea
- indigestion
- gas
- belching
- a feeling of fullness
Pepto-Bismol is thought to treat diarrhea by:
- increasing the amount of fluid your intestines absorb
- reducing inflammation and overactivity of your intestines
- preventing your body’s release of a chemical called prostaglandin that causes inflammation
- blocking toxins produced by bacteria such as Escherichia coli
- killing other bacteria that cause diarrhea
The active ingredient, bismuth subsalicylate, also has antacid properties that can help decrease heartburn, upset stomach, and nausea. healthline.com
Subjects treated with bismuth subsalicylate for up to 21 days have 3.5 times greater odds of preventing travelers’ diarrhea compared with placebo (95% CI 2.1, 5.9; p < 0.001). In addition, subjects with infectious diarrhea treated with bismuth subsalicylate had 3.7 times greater odds of diarrhea relief (recorded on diaries as subjective symptomatic improvement) compared to those receiving placebo (95% CI 2.1, 6.3; p < 0.001). Systematic Review and Meta-Analyses Assessment of the Clinical Efficacy of Bismuth Subsalicylate for Prevention and Treatment of Infectious Diarrhea, Brum et al 2021
Several studies have documented the efficacy of bismuth subsalicylate (BSS) for the prophylaxis and treatment of bacterial diarrhea. It is not known what effect, if any, BSS has on the normal bowel flora. We quantitated the fecal flora in healthy volunteers before and after they took BSS. In the first group, 8 ounces of BSS was given on two successive days. In the second group, a standard oral intestinal lavage preparation (GoLYTELY) was used to clean the colon and then 8 ounces of BSS was given during a 4-hour period. There were no changes in total microbial counts or in counts of individual groups such as enteric bacteria, Pseudomonas, Staphylococcus, Bacteroides, or Clostridium difficile. On day 2 the yeast counts rose 2.4 log10 colony-forming units/g in the group taking 16 ounces of BSS but did not increase in the group taking 8 ounces of BSS plus GoLYTELY. The counts returned to pretreatment levels by day 7. These results show that a 1- or 2-day course of BSS, even with an oral intestinal lavage preparation, did not have significant effects on the normal microbial populations in the fecal microflora. Effect of bismuth subsalicylate on fecal microflora, Gorbach, Cornick and Silva 1990
Microbial methylation of bismuth by the human gut microbiota has recently been reported. As the lipophilicity and thus the membrane permeability of bismuth are increased by these methylation processes, the toxic effects on human cells and on members of the beneficial “physiological” gut microbiota must be considered in medical application of bismuth-containing drugs. Medical Use of Bismuth: the Two Sides of the Coin, Frank Thomas Beatrix Bialek 2011
Bismuth subsalicylate treatment for 8 weeks (eight 262mg chewable tablets per day) is safe and well tolerated. This regimen appears to be efficacious for the treatment of microscopic colitis and is worthy of further study in a controlled trial. Efficacy of open-label bismuth subsalicylate for the treatment of microscopic colitis, Fine and Lee 1998
The present review examines the hypothesis that the mechanism of action of topical salicylates may involve protection of epithelial surfaces from colonization by certain microbes. Salicylates and the Microbiota: A New Mechanistic Understanding of an Ancient Drug's Role in Dermatological and Gastrointestinal Disease, Dammam 2013
Food Combinations
There is some speculation that combining certain foods will cause maldigestion. The hypothesis is that different foods require different digestive processes, and a combination results in poor digestion, resulting in gas. I haven't looked into the science much, but found this article that makes a full attempt to answer this question:
https://www.healthline.com/nutrition/food-combining
Managing Flatulence
Effective Management of Flatulence, Bailey et al 2009
https://essentialstacks.com/blogs/gut-health/flatulence
https://www.healthline.com/health/immediate-relief-for-trapped-gas-home-remedies-and-prevention-tips
https://pubmed.ncbi.nlm.nih.gov/32016519/
Simethicone
While it doesn't decrease volume, it can decrease the bloated feeling, especially when the discomfort is compounded by IBS. Need to read up on the studies in the following review to conclude this: A review of the therapeutic uses of simethicone in gastroenterology, Meier and Steuerwald 2010
Diversifying the Microbiota can treat Diabetes
… The modulation and targeting of the intestinal microbiota in the treatment of T2DM is a relatively new concept of primary scientific interest propelling research in this field not only in the prevention and control of diabetes and obesity but also of other pathologies.
Table of effects for herbs (see pdf)
… In recent studies, Rhodiola rosea has gained attention for its potential effects on diabetes, specifically its interaction with the gut microbiome. Salidroside, one of its bioactive molecules, has been shown to significantly impact glucose and insulin tolerance in obese mice. The compound aids in preventing hyperglycemia and enhances insulin signaling.
… Several Herbal Medicines (HMs), such as Scutellaria Radix and Coptidis, were noted for their anti-diabetic and anti-inflammatory properties. Importantly, their therapeutic effects appear to be mediated by interactions with gut microbiota. The gut microbiota is increasingly recognized as a crucial mediator in the pathogenesis of T2DM, particularly through its influence on short-chain fatty acid (SCFA) production, which impacts metabolic inflammation and insulin resistance. … Our review identifies a clear gap in the regulatory approval of HMs for treating T2DM, pointing to an urgent need for standardized clinical trials. Moreover, the existing studies have largely focused on the therapeutic impact of individual HMs, leaving the interactive effects of multiple herbs largely unexplored.
… Gut microbiota may be essential in the etiology of diabetes mellitus, according to an increasing body of research. … Controlling the gut microbiome, however, may be a viable treatment for type 2 diabetes, according to a better knowledge of the disease’s root causes. In treating type 2 diabetes, the analogs of plants, particularly therapeutic and functional foods, are of great interest, because they may be given orally, are effective, non-toxic, and have few adverse effects. … Gut Microbiota Targeted Approach by Natural Products in Diabetes Management: An Overview, Sati et al 2024 (pdf)
health/microbiota.txt · Last modified: 2025/08/28 02:42 by marcos
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