Big data from world's largest citizen science microbiome project

Researchers at University of California San Diego School of Medicine and collaborators have published the first major results from the American Gut Project, a crowdsourced, global citizen science effort. The project, described May 15 in mSystems, is the largest published study to date of the human microbiome -- the unique microbial communities that inhabit our bodies.

This publication provides the largest public reference database of the human gut microbiome, which may help drive many future microbiome studies. What's more, according to the research team, the success of the American Gut Project validates citizen science as a practical model for engaging the public in research.

Here are a few observations that have emerged so far:

Diet. The number of plant types in a person's diet plays a role in the diversity of his or her gut microbiome -- the number of different types of bacteria living there. No matter the diet they prescribed to (vegetarian, vegan, etc.), participants who ate more than 30 different plant types per week (41 people) had gut microbiomes that were more diverse than those who ate 10 or fewer types of plants per week (44 people). The gut samples of these two groups also differed in the types of molecules present.

Antibiotics. The gut microbiomes of American Gut Project participants who reported that they took antibiotics in the past month (139 people) were, as predicted, less diverse than people who reported that they had not taken antibiotics in the last year (117 people). But, paradoxically, people who had taken antibiotics recently had significantly greater diversity in the types of chemicals in their gut samples than those who had not taken antibiotics in the past year.

The participants who ate more than 30 plants per week also had fewer antibiotic resistance genes in their gut microbiomes than people who ate 10 or fewer plants. In other words, the bacteria living in the guts of the plant-lovers had fewer genes that encode the molecular pumps that help the bacteria avoid antibiotics. This study didn't address why this might be the case, but the researchers think it could be because people who eat fewer plants may instead be eating more meat from antibiotic-treated animals or processed foods with antibiotics added as a preservative, which may favor the survival of antibiotic-resistant bacteria.

Mental health. The American Gut Project researchers also examined the gut microbiomes of 125 people who reported having a mental health disorder, such as depression, schizophrenia, post-traumatic stress disorder (PTSD) or bipolar disorder. They matched each of these participants to individuals who did not have a mental health disorder, but did have other major factors in common, such as country, age, gender and body mass index. The team found that people with a mental disorder had more in common with other people with mental disorders, in terms of the bacteria makeup of their gut microbiomes, than they did with their mentally healthy pairs. The observation held true in both U.S. and U.K. populations, in males and females, and across age groups. In addition, the research team found some indications that specific bacteria types may be more common in people with depression than people who do not have the condition.

See:

Daniel McDonald et al. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems, 2018; 3 (3): e00031-18 DOI: 10.1128/mSystems.00031-18

Posted by Dr. Tim Sandle