Bacterial genomes from the human microbiome

23 May 2010

The human microbiome refers to the enormous collective community of different micro-organisms living in and on the human body, such as viruses, bacteria, and forms of fungi. The composition of the microbiome appears to vary between different individuals. The Human Microbiome Project was launched in 2008 (see previous news) in order to explore the function of these microbes in human health and disease, and one component of the project was attempts to produce reference genome sequences for at least 900 bacterial, viral and fungal species from different key sites within the human body: the gut (digestive tract), mouth, skin, nose and vagina.
 
Whilst most of the huge numbers of bacteria present in the human body at any one time are ‘commensal’ bacteria – that is, non-pathogenic – their role is nevertheless thought to be important for health, not least because they may be beneficial for normal processes such as digestion. Sequences from the human gut microbiome were described earlier this year (see previous news). Now a new paper in Science reports on 178 microbial genome sequences from a range of body sites, and analysis of their possible protein products and functions [The Human Microbiome Jumpstart Reference Strains Consortium. Science 2010 328(5981): 994-999]. This included construction of a ‘pan-genome’, being the ‘sum of the core genes shared among all sequenced members of the species and the dispensable genes, or those genes unique to one or more strains studied’ for a few bacterial species for which multiple sequences were available
 
The analysis identified nearly 31,000 unique peptides (short proteins) of which just under 30,000 were previously unknown. Comparative analysis of previously sequenced, publicly available microbial data allowed identification of fewer than half this number. The function of most of the novel bacterial genes and gene products has yet to be investigated, but the researchers reportedly found that some peptides produced by gut bacteria might be involved in the formation of gastric ulcers, whilst others could be linked to metabolic processing of food components (see press release).
 
Comment: Although the results presented in this paper do not reveal much about the role of the microbiome in health and disease, they represent important ground work (including the development of methods, standards and infrastructure) needed to allow the next stages of research, including into links between the presence or absence of specific microbial species in certain locations and particular states of health or disease. Samples will also be taken from additional locations within the body, the blood and male urethra. The growing collection of reference genomes from the human microbiome will allow researchers to compare microbial sequence data to identify genuinely novel microbial genes more easily than at present.
 
An even larger group, the International Human Microbiome Consortium (IHMC), which includes the US HMP centers as well as other efforts including the EU MetaHIT project, is collectively seeking to sequence a total of more than 1000 bacterial reference genomes from the human microbiome.

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