The path of US microbiome research

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With the advent of DNA sequencing and other genome-enabled technologies for studying microbial communities, countries around the world have identified microbiome research as a way to address some of their pressing problems, from food production to human health. The US government is pursuing this research in earnest, as laid out in a new report in Nature Microbiology.

The 2016 report by US government scientists (Stulberg, et al.) offered an analysis of federally funded microbiome research between 2012 and 2014. The report defined a ‘microbiome’ as, “a multi-species community of microorganisms in a specific environment (that is, host, habitat or ecosystem)” and ‘microbiome research’ as, “those studies that emphasize community-level analyses with data derived from genome-enabled technologies.” The analysis focused on studies of complete microbial communities and did not include research on specific strains or pathogens.

A reported total of USD $920 million funded the microbiome research initiatives of participating organizations during the three fiscal years. This money supported some major projects such as the National Institutes of Health (NIH) ‘Human Microbiome Project’ (HMP) and the National Science Foundation (NSF) ‘Microbial Observatories (MO) and Microbial Interactions and Processes (MIP)’ programme.

The analysis classified microbiome studies into three research themes: (1) Tools/Resource Development, (2) Basic Biology, and (3) Applied Studies. Of these, the basic biology theme comprised half of all the research activities. This theme included studies on microbial community structure and function, the role of the microbiome in the health of a host, habitat, or ecosystem, and how microbiome properties relate to the properties of its environment. Applied studies made up 28% of all research activities, and the development of tools and resources made up 21%.

Research activities were also divided into eight microbiome environments: (1) Agriculture, (2) Aquatic, (3) Atmosphere, (4) Built environment, (5) Human, (6) Non-agricultural plants for energy production, (7) Non-human laboratory studies, and (8) Terrestrial. Perhaps not surprisingly, humans were the most studied ‘environment’.

Finally, the analysis included eight microbial categories: (1) Bacteria, (2) Archaea, (3) Microeukaryotes (fungi, protists, diatoms), (4) Phytoplankton, (5) Mobile genetic elements, (6) Viruses (eukaryotic viruses and bacteriophage), (7) Microbial communities, and (8) Other microbial components of the microbiome. The analysis made it clear that relatively few studies investigated the non-bacterial components of the microbiome such as viruses.

The report identified some future needs for the field of microbiome research. Respondents cited improved infrastructure and human resource development in computational biology and bioinformatics as a top priority, in addition to standardized protocols, improved reference databases and biorepositories, and better high-throughput tools. Participants emphasized that the way forward will be through longitudinal and functional microbiome studies, and more interdisciplinary research.

No comprehensive summary is available on microbiome research elsewhere in the world, but this table lists a number of large microbiome research initiatives specific to humans. The Europe-based MetaHIT project received EUR €21.2 million in funding over a period of four years, for example, while the ongoing gut microbiome research initiative MyNewGut has a budget of EUR €13 million.




Stulberg E, et al. (2016) An assessment of US microbiome research. Nature Microbiology 15015 doi:10.1038/nmicrobiol.2015.15

Kristina Campbell
Kristina Campbell
Science writer Kristina Campbell (M.Sc.), from British Columbia (Canada), specializes in communicating about the gut microbiota, digestive health, and nutrition. Author of the best selling Well-Fed Microbiome Cookbook, her freelance work has appeared in publications around the world. Kristina joined the Gut Microbiota for Health publishing team in 2014.  Find her on: GoogleTwitter