Human-associated Microbiota

The human body harbors an estimated ten times as many microbial cells as human cells. By studying these microbes, we can learn more about ourselves, as microbial communities may record traces of what we’ve eaten, where we’ve lived, and who we’ve been in contact with, and also influence our health. We have found that the microbial ecosystems in different parts of our bodies differ dramatically, but also demonstrate unique intra-personal signatures which develop in early life (Koenig et al., 2012) and are generally stable over time (Costello et al., 2009;Caporaso et al., 2011;Faith et al., 2013;Yatsunenko et al., 2012). However, the overall composition of our microbiota can be influenced by the way we are born (Dominguez-Bello et al., 2010) and may change in response to our diets (Manichanh et al., 2013;Wu et al., 2011) and hygiene (Fierer et al., 2008), who we live with (Song et al., 2013) and different conditions and diseases (Lozupone et al., 2013;Ley et al., 2005;Lozupone et al., 2013;Smith et al.; 2013;Koren et al., 2011;Turnbaugh et al., 2009). With various collaborators using rat and gnotobiotic mouse models, we have further investigated how we can influence the gut microbiome through dietary interventions (Ravussin et al., 2012;Turnbaugh et al., 2009;Hildebrandt et al., 2009) and antibiotic administration (Devine et al., 2013;Manichanh et al., 2010), and also how direct manipulations such as introduction of specific microbial communities can impact health — amazingly, microbial communities from individual humans can be transplanted into mice, and how the mice respond depends on whose microbes they got (Manichanh et al., 2010;Ridaura et al., 2013). Evidence for the translation of these results lies in the recently demonstrated success of human fecal transplants in treating C. difficile infections (

Building on this previous work and our involvement in the Human Microbiome Project (cite HMP papers), we launched the American Gut Project (, (contact: Daniel McDonald) in conjunction with Jeff Leach of the Human Food Project and a host of collaborators to characterize the human microbiome on a massive scale, inviting participation from the general public via a crowd-funded initiative. To our knowledge, this is the largest crowd-funded scientific effort to date. In addition to supplying samples for microbiome analysis, participants voluntarily provide information on factors which may potentially affect their gut microbes such as age, and information on exercise and dietary habits, which will allow us to further elucidate the factors driving changes in our resident microbiota.