Category: NIH Human Microbiome Project (HMP)

Getting Personal with Bacteria

Microbes, including bacteria, inhabit your body in great numbers and impact many aspects of health and disease such as obesity and Crohn’s disease. Characterizing the genetic diversity of microbes that live in specific areas of the body is key to understanding the composition and dynamics of microbial communities within individuals, in transmission between individuals, and in transmission between individuals and the environment. The ability to characterize microbial diversity and transmission has been hampered in the past by a lack of high-throughput analysis tools. New computational tools being developed through the Common Fund’s Human Microbiome Project (HMP) are accelerating microbiology and biomedical research, and unexpectedly, other fields like forensics.

Dr. Rob Knight, an investigator in the HMP, is developing novel approaches to analyze human microbial communities, and recently contributed to a paper in the Proceedings of the National Academy of Science on the discovery of “microbial fingerprints”; in a person’s skin. The skin surface harbors a large number of bacteria that are highly diverse and yet personally unique from individual to individual. The bacteria are easily dislodged from the skin and transferred to objects upon contacting. By analyzing the “microbial fingerprint”; of bacteria left on computer equipment, Dr. Knight and colleagues at the University of Colorado found that the fingerprint could be traced to a specific individual with a high degree of certainty even if the objects had not been touched for two weeks. The approach could be important in forensic investigations to provide independent confirmation of forensic results obtained using more traditional methods such as human DNA analysis or fingerprinting. […]

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Microbiome Interagency Working Group Releases Interagency Strategy Plan for Microbiome Research

In 2015, the Office of Science and Technology Policy (OSTP) of the White House, chartered a committee of sixteen federal agencies that fund research to complete a survey of all federally supported microbiome research over fiscal years 2012-2014. The Fast-Track Action Committee on Mapping the Microbiome (FTAC-MM) analysis included studies of microbial communities and their ecological roles in plants, animals, and humans and in ecosystems like oceans and forests. The FTAC-MM identified an investment of $920M in both intramural and extramural microbiome research over fiscal years 2012-2014; this analysis was published in Nature Microbiology (Stulberg et al. 2016). This analysis motivated the establishment of an interagency committee, the Microbiome Interagency Working Group (MIWG), which is charged with coordination of microbiome research across the federal government. This report, the ‘Interagency Strategic Plan for Microbiome Research’, released April 19, 2018, summarizes each agency’s investments in this field, the range of current coordination activities and plans for future MIWG activities to support the needed resources for advancing this emerging field. The report also includes the representative from each agency who contributed to this report. […]

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The genome sequence of Christensenella minuta: a bacterium which is the most heritable member of the gut microbiota and which also influences host weight.

There has been considerable interest in a particular member of the gut microbiota, a bacterial species named Christensenella minuta, which is a member of the Firmicutes phylum. Three recent findings have generated this interest. First, the Christensenella genus appears to be found so far only in human hosts (link is external). Second, C. minuta was found to be the most heritable species in the human gut microbiome, meaning that it is the species whose presence or absence in our gut is mostly determined by the genes of its human host. Third, evidence suggests that the presence of C. minuta can directly affect the weight of its host by as yet unknown mechanisms. C. minuta is more likely to be present in leaner people, and adding C. minuta to the gut tracts of mice resulted in leaner mice. These findings suggest a potential use of C. minuta as a probiotic for weight control.

HMP researchers at WashU have now published the complete genome sequence of C. minuta. The availability of this genome sequence will allow future researchers to gain in depth insights into its life cycle, its metabolism and the mechanisms by which it can affect the human host in which it lives. This research highlights another way in which the HMP is supporting the larger microbiome research community.

Reference:

Genome Sequence of Christensenella minuta DSM 22607^T. Rosa BA, Hallsworth-Pepin K, Martin J, Wollam A, Mitreva M. Genome Announc. 2017 Jan 12; 5(2).

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Dramatic Fluctuations of the Gut Microbiome in Individuals with Inflammatory Bowel Disease

Inflammatory Bowel Disease (IBD) is a group of conditions caused by chronic inflammation in the digestive tract. The most common subtypes of IBD are Crohn’s disease and ulcerative colitis. iHMP researchers are generating a public database containing information collected over time from several studies of IBD patients. Along with a variety of relevant patient data, the database will contain information about both the composition of the gut microbiome over time in these patients as well as the small molecules and proteins being produced by these microbes.

It has been previously established that patients with IBD have large differences in the composition of their gut microbiome compared to heathy individuals. These findings are often based on samples obtained at a single point in time. However, the species that make up our gut microbiome can fluctuate over time based on infections, diet, antibiotics, and other factors. As part of the larger iHMP study on IBD, Dr. Jansen and colleagues determined the composition of the gut microbiomes in over 100 patients with IBD in three month intervals to determine how these microbiomes differs over time. They found that patients with IBD had much less consistency in their microbiomes when compared to healthy individuals. This information could potentially be used by doctors to monitor the health of IBD patients and their response to treatments. In addition, understanding the dynamics of the microbiome in IBD patients should help the design of future therapies that aim to restore the microbiome to a more natural state.

Reference:

Dynamics of the human gut microbiome in inflammatory bowel disease. Halfvarson J, Brislawn CJ, Lamendella R, Vázquez-Baeza Y, Walters WA, Bramer LM, D’Amato M, Bonfiglio F, McDonald D, Gonzalez A, McClure EE, Dunklebarger MF, Knight R, Jansson JK. Nat Microbiol. 2017 Feb 13; 2:17004.

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Microscopic study of the healthy human body has demonstrated that microbial cells outnumber human cells by about ten to one. Until recently though, this abundant community of human-associated microbes remained largely unstudied, leaving their influence upon human development, physiology, immunity, and nutrition almost entirely unknown. The NIH Common Fund Human Microbiome Project (HMP) was established with the mission of generating research resources enabling comprehensive characterization of the human microbiota and analysis of their role in human health and disease. The information generated by HMP is made available worldwide for use by investigators and others in efforts to understand and improve human health.