The first major data of the human microbiome was generated from the American Gut project (AGP). The project included microbial data from 15,096 samples that were collected from 11,336 participants, primarily resident in the United States, United Kingdom, Australia and other 42 countries. Participants in this project were also asked to answer a voluntary survey about the general health status, disease history, lifestyle, and diet. Researchers of this project at University of California San Diego School of Medicine and collaborators have reported very interesting findings about the role of diet and antibiotic exposure on gut microbiota.

Data from the self-reported food frequency questionnaire suggested that the gut microbiota diversity of the participants was associated with the number of unique species of consumed plants rather than a specific dietary habits or regime such as “vegan” or “omnivore”. Eating 30 or more types of plants was found to be associated with increased abundance of Short Chain Fatty Acid (SCFA) fermenting bacteria such as the species Faecalibacterium prausnitzii and of the genus Oscillospira. Additionally, data showed that the higher abundance of Conjugated Linoleic Acid (CLA) was associated with people who were consuming 30 types of plant or higher and those consuming more fruits and vegetables. CLA is the end-product of Linoleic Acid conversion by lactic acid bacteria in the gut, such as Lactobacillus plantarum and Bifidobacterium spp. This indicated that the fermentation of undigested plant played a significant role in the change of gut microbial community.

Data also showed that, microbiota was less diverse in people who reported that they received antibiotics in the past month compared with those who reported received antibiotics in the past year. However, paradoxically, people who reported recent antibiotics exposure had significantly greater diversity in the types of chemicals in their gut samples than those who had not taken antibiotics in the past year. A significant reduction in antibiotic resistance genes was noticed in people who consumed more than 30 type of plants per week compared with people who consumed 10 or less plants per week.

The gut microbiome of 125 participants who reported having mental health diseases such as depression, schizophrenia, post-traumatic stress disorder (PTSD) or bipolar disorder was matched with other participants who did not report any mental health issues but did have other major factors in common, such as country, age, sex, and body mass index. Data from this comparison showed that people with a mental disorder had more in common with other people with mental disorders, in terms of the gut microbiota makeup, than they did with their mentally healthy pairs.