Downloaded from www.asmscience.org by IP: 54.162.69.248 On: Thu, 11 Jun 2020 05:16:11 Dynamics of Host-Associated Microbial Communities Studying microbial communities will deepen our understanding of biology and provide tangible health benefits Stanley Maloy, Jo Handelsman, and Shiva Singh M icrobes account for more than 90% of the cells of the human maintenance of organ alloen- graftment has body, forming dis- tinctive communities at different sites. These communities affect health—pro- moting organ development, stimulating the im- mune system, providing nutrients, and exclud- ing pathogens. These communities cause pathologies, including periodontal disease, ul- cers, and secondary pneumonias, while influ- encing other conditions, including obesity and atherosclerosis. Taking that view into account, the National Institutes of Health (NIH) recently expanded the working definition of the human genome to include genomes of the microorganisms that associate with the human body and established the Human Microbiome Project (HMP) to ex- plore those relationships. In its initial phase, the HMP is focused on sequencing the metage- nomes of five major human microbiomes: the gut, mouth, skin, vagina, and nose of 250 healthy volunteers. These projects are generat- ing massive amounts of sequence information that will provide insight into the diversity and stability of these complex communities that play a fundamental role in human health. The conditions correlated with human- associated microorganisms reach into every institute at the NIH—including Tourette syndrome, sleep cycles, depression, diabe- tes, colon cancer, asthma, heart disease, and longevity. This breadth adds complexity to the traditional concept of “one microbe, one disease,” giving rise to the idea that some diseases are subject to particular com- munities instead of single species of mi- crobes. For instance, the microbial commu- nities of the gut may broadly affect health as they metabolize food and drugs, transform- ing consumed chemicals into either more or less harmful products or even beneficial products. To address these issues more fully, the National Institute of General Medical Sci- ences (NIGMS) convened a colloquium in November 2008 focused on host-associated microbial communities. Participants, in- cluding leaders in microbial ecology, mac- roecology, computational biology, micro- Summary • Initially, the Human Microbiome Project is fo- cused on sequencing the metagenomes of the gut, mouth, skin, vagina, and nose of 250 healthy volunteers. • In the future, personalized medicine and medi- cal screenings may include assessments of one’s microbial health. • Metagenomics, other comprehensive evalua- tions, and still other novel analytic approaches will help to describe the complex interactions within host-associated microbial communities. • Studies in model systems will help to decipher principles underlying microbial communities and to develop effective tools for studying those communities. • New approaches are needed to understand the physiology and ecology of microbial communi- ties • An enhanced understanding of human-associ- ated microbial communities will lead to new ways to improve human health. Stanley Maloy is Dean of the College of Sciences, San Diego State Univer- sity; Jo Handels- man is Professor of Molecular, Cellular, and Developmental Biology at the Yale School of Medicine, Yale University; and Shiva Singh is Pro- gram Director in the Division of Ge- netics and Develop- mental Biology at the National Insti- tute of General Medical Sciences, National Institutes of Health. Volume 6, Number 1, 2011 / Microbe Y 21