Gut check: Population diversity in humans is tallied

Gut microbiota census

What’s inside? Across many populations, new research has found a core population of bacteria populate human guts.

(Anacleto Rapping / Los Angeles Times)

Taking a census of the microbes that live in the human gut is not glamorous work, but it’s important, given our new understanding of the gut microbiome’s role in human health. And a full picture of humanity’s microbial gut population has been a mystery. Until now.

After combing through thousands of human fecal samples, two sets of researchers have cataloged the microorganisms that colonize the human digestive system. Their findings reveal the various strains that live in the guts of those who are healthy and those who are sick, allowing scientists to make some preliminary observations about how and why the mix of strains is different in each.

In one of several microbiome studies published Thursday in the journal Science, researchers identified species of microorganisms from at least 664 different genera in the guts of close to 4,000 adults from the U.S., the United Kingdom, Belgium and the Netherlands. And they’re pretty sure there are more.

When they expanded their collection of stool samples to include a small number of people from Papua New Guinea, Peru and Tanzania, the researchers detected a core group of 14 genera of microbes that were just about universally present.


These 14 genera were common to 95% of the humans sampled, and the species within these groups accounted for about 72% of their total gut microbiome. The main difference between individual people was the relative abundance of microbes from these core groups, including species of Ruminococcicea, Bacteroides, Prevotella, Faecalibacterium and Roseburia.

The researchers found several links between the diversity of gut flora and various aspects of biological function. For instance, people who reported looser stools were more likely to have a rich garden of microflora than those whose stools were harder and dryer.

The researchers also found significant associations between people’s genus abundance and their hip circumference, history of taking the antibiotic amoxicillin, uric acid concentrations (a factor in gout) and their preference for eating dark chocolate.

The older people got, the more diverse their gut microbes became, according to the study. Also, the collection microbiota in men and women diverged more with age.


More than any single factor, the use of a wide range of drugs influenced microbiome variation among the people in this study. The clearest patterns emerged in those who had a recent history of taking antibiotics, osmotic laxatives, medications for inflammatory bowel disease, benzodiazepines, antidepressants, antihistamines or hormones used for birth control or to alleviate symptoms of menopause.

But contrary to some expectations, the data did not show that the abundance of microbes in the adult gut was influenced by whether the person was born in a vaginal delivery or by C-section. Nor did researchers find any evidence that those who were breast-fed as babies had more diverse microbiomes when they grew up.

Some of these findings were echoed and amplified in a second study, also published Thursday in Science. After sequencing the genomes of gut microbes from 1,135 people in the Netherlands, researchers confirmed that antibiotics cause certain species to decline in numbers. Several other drug categories — including metformin, statins, laxatives and particularly proton-pump inhibitors — also had a strong effect on the gut microbiome.

The second study also found many links between diet and the denizens of the gut. Many eating habits that are widespread in America — including snacking, eating lots of foods high in dairy fats and carbohydrates, and drinking sugar-sweetened soda — were associated with less microbiome diversity. However, those who drank wine, coffee or tea had richer populations of gut microbes.

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