What constitutes good gut bacteria? What’s their benchmark? We have no clue. Economics of gene sequencing technology means fecal microbiome sequencing costs (1) a fraction of what it did just a few years back. Predictably, companies offering to sequence them have mushroomed, for a price of course. Anyone with a handful of disposable US dollars can get their poop bacteria sequenced but what do those results even mean?

  • Should poop contain ~55% Firmicutes, apparently the same as Michael Pollan or 74%, same as the author of this Newsweek piece (2)?
  • What’s the value of a one-time poop bacteria sequencing? Isn’t that just a snapshot?
  • Studies show poop bacterial composition changes rapidly not just with diet (3) but also seasonally (4) so what’s the predictive value of such a snapshot anyway?
  • What does poop bacteria even represent?
    • Isn’t poop bacteria sequenced so much just because it’s easier to access?
    • Doesn’t it really only represent distal colon bacteria supported by current diet?
    • What about what’s in the stomach, duodenum, jejunum, ileum, and proximal and transverse colon, and how they relate to gut and overall health? Don’t we need invasive biopsies to accurately access bacteria in other GI tract compartments?
    • What can we extrapolate from what’s in poop to what should be in other parts of the GI tract? Anything? Nothing?

All this to say a lot of data on poop microbiome’s being generated simply because it can be, not because anyone has a clue what any of it means nor a clue what constitutes good gut bacteria.

To top this litany of shortcomings and dubious value of current attempts to benchmark gut bacteria using fecal microbiome sequencing, at least one randomized placebo-controlled study (5, 6) not only reveals novel, incalculable curative powers of Placebo but also casts doubt on currently accepted notions of ‘good’ and ‘bad’ gut bacteria.

  • A study across two US academic medical centers, Montefiore Medical Center in the Bronx, New York and the Miriam Hospital, Providence, Rhode Island, both well-known for their expertise in Fecal microbiota transplant (FMT) (5, 6).
  • 46 patients with recurrent Clostridium difficile infection (CDI) were randomly assigned to receive either donor or autologous (their own) poop microbiota, i.e., Placebo.
  • 91% (20/22) of those who got donor poop were durably cured based on a standard definition. Expected so no surprise.
  • The absolute shocker? 63% (15/24) who got their own poop microbiota transplanted back also had durable cure. Rub eyes and read again. What? Patients with a serious GI tract infection were given back their own presumably disease-associated gut bacteria and they got cured?
  • Though there were striking inter-center differences in this Placebo effect, 9/10 (90%) placebo cases in the New York center cured versus only 6/14 (~43%) in the Rhode Island center, and perhaps associated patient population differences between these two centers, those aren’t germane to the central issue, namely, a GI tract disease cured from simply taking out and putting fecal bacteria back into C.diff patients.

Thus, even so-called ‘bad’ gut bacteria turn out to be not so cut and dry, a result that only underlines how little we currently know about gut bacteria, good, bad or anything in between. Best one could then say is absence of persistent and serious health problems, especially gastrointestinal, is evidence of having good gut bacteria. Absence of skin problems, no autoimmunities or mental health issues would be icing on the cake.


1. 16S rRNA sequencing

2. Newsweek, Roxane Khamsi, July 17, 2014. Gut Check

3. David, Lawrence A., et al. “Diet rapidly and reproducibly alters the human gut microbiome.” Nature 505.7484 (2014): 559-563. Diet rapidly and reproducibly alters the human gut

4. Davenport, Emily R., et al. “Seasonal variation in human gut microbiome composition.” PloS one 9.3 (2014): e90731. http://www.plosone.org/article/f…

5. Kelly, Colleen R., et al. “Effect of Fecal Microbiota Transplantation on Recurrence in Multiply Recurrent Clostridium difficile Infection: A Randomized Trial.” Annals of Internal Medicine (2016).

6. Fecal Transplant for Relapsing C. Difficile Infection