Millions of new genes in human microbiome

The study, from researchers at the University of Maryland School of Medicine (UM SOM), Harvard T.H. Chan School of Public Health, the Broad Institute of MIT and Harvard, and the University of California San Diego, triples the amount of data previously analyzed in this project, and is the largest human microbiome study ever.

This work appears on September 20, 2017 in the journal Nature.

The results are a significant jump in the amount of information available to scientists. This publication provides new insight into the changes in our microbiome over time and could lead to a greater understanding of the genetic differences that are unique to an individual's microbes.

"This new data really expands our appreciation for the fingerprint created by microorganisms that make up each human's microbiome," says Owen White, professor of epidemiology and public health and associate director at the Institute for Genome Sciences (IGS) at UM SOM. "These organisms play a crucial role in many key aspects of our health. The more we know about them and their role, the more likely it is that we will be able to manipulate them to improve our health."

This study is part of the National Institutes of Health Human Microbiome Project, launched in 2008 to identify and characterize human microbes, explore microbes' relationship to health and disease, and develop computational tools to analyze the microbes. The microbiome has been linked to various aspects of human health including the robustness of our immune system and our susceptibility to chronic illnesses such as Crohn's disease and cancer.

This work is a continuation of work published in Nature in 2012. In the new study, the researchers analyzed an additional 1,635 new microbiome samples, for a total of 2,355 sampled from 265 people over time. The scientists used DNA sequence analysis tools to identify which organisms are present in various body sites, determine whether they change or stay relatively stable over time, and explore their function. This study also provides one of the largest profiles of non-bacterial members -- viruses and fungi -- of the microbiome. In addition, it unraveled some of the biochemical activity that allows microbes to play a role in human health.

Although the new study illuminates a great deal about the microbiome, an enormous amount remains unknown. Learning more about it will take time, said Anup Mahurkar, the executive director of software engineering & information technology at IGS. "These communities of organisms are tremendously complex. In one sense, this study is a great advancement for the research community," he said. Mahurkar was responsible for the months of intensive computations required to process the data. However, he was also cautious, saying "On the other hand, it still just moves the needle. There will always be more we can learn." Mahurkar is confident that the work will provide a large data resource for other scientists to use in their future research.

Support for the study came from National Institutes of Health and the Crohn's & Colitis Foundation of America.