The American Gut Project: Some Initial Findings

In 2012, 3 scientists from the University of California, San Diego, started The American Gut Project, the largest crowd funded “citizen science project in existence.”[i]  Ordinary people can send in a stool sample along with a questionnaire (about diet and lifestyle choices), and $99 USD, and receive back an analysis of their bacterial microbiomes – while at the same time, providing valuable data to the team of researchers involved.  To date, they have analyzed the microbiomes of more than 11,300 (anonymous) people from the USA, UK, Australia, and 42 other countries around the world.

Some results were just published in their new study[ii]:

  1. Those who eat plenty of plant-based foods (more than 30 types per week) have more diverse microbiomes than those who eat 10 or fewer.  It didn’t matter if they ate meat or were vegetarian, as long as the plant-based food level was high enough.
  2. This one’s kind of scary! The former group (high plant-based food consumption) had fewer drug-resistant genes in their bacterial microbiomes than the latter.  One theory proposed to explain this:  those who eat fewer plant-based options may eat more meat from animals treated with antibiotics, or processed foods with antibiotic preservatives.
  3. Those individuals who had used antibiotics within the last month had less bacterial diversity.
  4. Here’s a big one: those individuals who reported “mental” illnesses like depression, bipolar disorder, PTSD or schizophrenia had bacterial microbiomes more like each other than like those without such psychological issues.[iii]

None of this is a huge surprise, except maybe the information about the antibiotic- resistant bacteria differences, which I found particularly interesting. I remember sitting at the 1st International Symposium on the Microbiome in Health and Disease with a special Focus on Autism, at Arkansas Children’s Hospital in Little Rock, listening to Dr. Carl Cerneglia, of the FDA, explaining to us that “antimicrobial residues in foods makeup a small fraction of total antimicrobials to which persons are exposed to in terms of either frequency or dose.”[iv] He went on to conclude, “An extensive literature review DID NOT reveal reports of human health effects from exposure to antimicrobial drug residues that could result in changes in the proportion of antimicrobial resistant bacteria in the normal human intestinal microbiota.”


I think I will personally continue to buy only meat that is antibiotic free.  Call me crazy….



[ii] McDonald, D. et. al. American Gut: an Open Platform for Citizen Science. mSystems. 2018. DOI: 10.1128/mSystems.00031-18




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