the all-powerful, yet oh-so-mysterious microbiome

Lynch SV, Pedersen O. N   Engl   J Med 2016;375:2369-2379

Lynch SV, Pedersen O. N Engl J Med 2016;375:2369-2379

Our colons are home to 100 trillion bacteria, representing some 1,200 different species. Scientists today believe that the root of many Western diseases can be traced to our ailing guts. The American diet is high in processed foods digested in the stomach and small intestine, leaving little fuel for the microbes in our large intestine. The result, they say, has been a “mass extinction event,” in which species of bacteria that have lived in our bodies for most of human history have died off, making it harder for our microbiota to perform its role in tuning our immune system and regulating inflammation


Your mission, should you choose to accept it: diversify your microbiome & nurture a thriving community of bacteria to keep you healthy:

(1) Stop trying to sterilize your home, which kills off more good bacteria than bad, see “Some of My Best Friends Are Germs” by my food idol Michael Pollan

(2) eat lots and lots and lots of fiber, which is digested in the lower intestine.

(3) get a dog

(4) avoid antibiotics unless absolutely necessary (i.e. fight through that viral URI on your own!)

(5) have a vaginal delivery so your baby is exposed to all the vaginal canal flora 

(6) breast feed: breast milk is both a “prebiotic” — a food for microbes — and a “probiotic,” a population of beneficial microbes introduced into the body.

(7) eat probiotic foods: fermented pickles (if they’re not refrigerated, they’re not fermented), kimchee, yogurt, kefir 


and the million dollar question... which probiotic should I take?

None! Stop right there. Do NOT spend that $50 on a fancy probiotic at Whole Foods.

The enthusiasm for probiotics has outpaced the scientific evidence.

1. Honestly we just don’t know enough about probiotics yet and the studies that have been done to look at probiotics in most GI diseases were small and inconclusive.

2. The FDA doesn’t regulate OTC supplements so WHO KNOWS what’s inside that pill. Plus the commercial preparations available to the public are so different in type of bug, quantity of bug and biologic activity that its impossible to say what the effect will be.

3. Probiotics are transient — they can’t meaningfully repopulate a broken gut


The ONLY fields where probiotics currently have strong evidence recommending their use is:

(1.) VSL#3 in the primary and secondary prevention of pouchitis (ulcerative colitis)

(2.) Probiotics as prevention for patients taking antibiotics who are at increased risk to develop Clostridium difficile diarrhea

 L. acidophilus and L. case ("Bio-K" lactobacilli-fermented milk 25 x 109 CFU/day for 2 days, then 50 x 109 CFU/day for duration of the antibiotic course) 

L. casei (19 x 109 CFU/day), L. bulgaris (1.9 x 109 CFU/day), and S. thermophiles (19 x 109 CFU/day) or "Actimel" within 48 hours of starting antibiotic therapy until 7 days after discontinuation 

(3.) Lactobacillus GG and S. boulardii for adults and children with presumed infectious diarrheal illness

That’s it folks! So if you’re considering the use of probiotics for “digestive wellness” and non-specific GI symptoms, save your money and focus on the microbiome-diversifying tips we can depend on (above).


Don't forget about PREbiotics!

 Prebiotic carbohydrates are nondigestible but fermentable foods, a major substrate for bacterial growth, selectively stimulating the growth and/or activity of beneficial members of the gut microbiota, particularly lactobacilli and bifidobacteria. Thus, probiotics could have more global effects on colonization than adding a single probiotic strain. A second, more direct immune effect appears to be mediated by the fermentation products of prebiotics. Gut micro-organisms ferment prebiotics to produce short-chain fatty acids (SCFAs) that have direct anti-inflammatory effects. SCFAs also promote intestinal integrity through effects on epithelial cell proliferation and differentiation. Prebiotics may directly affect both mucosal and systemic immunity

Best Food Sources of Prebiotics

  • Bananas, berries, and legumes (fructooligosaccharide sources)
  • Garlic, onions, Jerusalem artichokes, and leeks (inulin sources)
  • Whole grains (wheat dextrin source)
  • Nuts and seeds (arabinose sources)