Gut microbiome composition, with exceptions that I’ll discuss below, is remarkably stable, particularly in adults. Although probiotics are expected to be a $45B business by 2018, their effects on microbiome composition are small and transient. A recent meta-analysis of seven randomized control trials found “a lack of evidence for an impact of probiotics on fecal microbiota composition in healthy adults”[1] . Perhaps more importantly, the gut metaproteome – the suite of human and bacterial proteins expressed in the gut – is also unchanged by probiotics.[2] These conclusions are somewhat surprising because there is decent evidence that that probiotics have clinical benefit in treating depression[3] .
Gastric bypass surgery has a much more profound impact on microbiome composition. Weight loss is not caused by mechanical restriction of the stomach[4] . Instead, bypass surgery causes an increase in the levels of bile acids in the upper intestine, resulting in changes in the microbiota, which (somehow, perhaps through short-chain fatty acid or trimethylamine metabolism) results in changes in feelings of satiety[5] [6] .
Antibiotics can also perturb microbiome composition, and not in a good way. C difficile-associated diarrhea, which kills 14,000 Americans per year, is almost always precipitated by antibiotic use[7] , and less-severe forms of diarrhea are also a well-known risk of antibiotic therapy[8] . However, the effects of most antibiotics on microbiome composition in adults are transient[9] . Clindamycin appears to be an exception. Microbiome composition was detectably altered for two years after a single course of treatment[10] .
The good news – if you are healthy – is that gut microbiome composition is stable and will re-establish itself after various insults. This is bad news, though, if you have a microbiome-associated disorder such as obesity or diabetes or inflammatory bowel disease. Simple fixes such as probiotics, prebiotics or antibiotics seem to have little effect. But we are still at an early stage in our understanding of what constitutes a healthy microbiome, and at an even earlier stage in trying to apply this understanding.
Footnotes
[1] Alterations in fecal microbiota composition by probiotic supplementation in healthy adults: a systematic review of randomized controlled trials
[2] Faecal Metaproteomic Analysis Reveals a Personalized and Stable Functional Microbiome and Limited Effects of a Probiotic Intervention in Adults.
[3] Effect of Probiotics on Depression: A Systematic Review and Meta-Analysis of Randomized Controlled Trials
[4] Roux-en-Y Gastric Bypass and Vertical Banded Gastroplasty Induce Long-Term Changes on the Human Gut Microbiome Contributing to Fat Mass Regulation
[5] Bile acids and the gut microbiome.
[6] Conserved Shifts in the Gut Microbiota Due to Gastric Bypass Reduce Host Weight and Adiposity
[7] What have we learned about antimicrobial use and the risks for Clostridium difficile-associated diarrhoea?
[8] Antibiotic-associated diarrhoea.
[9] Antibiotic use and microbiome function.
[10] Long-term ecological impacts of antibiotic administration on the human intestinal microbiota.