Human gut microbial metagenome sequenced

4 March 2010

Remarkably, every human body contains ten times as many (much smaller) microbial cells as it does human cells. Interest in the role of this ‘microbiome’ in health and disease has been growing over recent years (see previous news), especially with the advent of faster genome sequencing. Now a new paper in Nature by an international team of researchers led by the Beijing Genomics Institute describes the human gut microbiome. Commensal gut microbes are important for normal nutrition and digestion, and provide protection from harmful microbes; it is thought that changes in the normal composition of gut microbes may be involved in a range of conditions such as bowel disease and obesity. 

Faecal samples from 124 Europeans from the European MetaHIT consortium were analysed for microbial genes; some people were healthy, others overweight, obese or with irritable bowel disease (IBD). Over 99% of the genes sequenced were bacterial in origin, leading the researchers to estimate that each individual had at least 160 different bacterial species present in their gut, with a collective total of more than 1000 species for the whole group [Quin J et al. (2010) Nature 464, 59-65].

A small number of species were present in most or all individuals (a conservative estimate identified 57 species that were present in90% or more of those tested), but the relative abundance of bacteria of some of even these most common species varied enormously, from 12 to over 2000-fold difference between individuals for a given bacterial species. The researchers next compared the microbial genes present between healthy individuals and those with ulcerative colitis and IBD. Statistical analysis showed very distinctive patterns of bacterial genetic profiles between these three groups

The researchers plan to extend this sort of analysis to more subjects from different countries via the International Human Microbiome Consortium, as well as sequencing of all the human associated bacterial genomes.

Comment: This research provides proof-of-concept that metagenomic sequencing is feasible, and could be useful for further study into how variation in gut microbes may playa role in certain diseases, although this work in itself does not provide any insight into how bacteria could affect these conditions beyond the observation of differences between modest numbers of healthy and diseased subjects. Co-author Professor Jeroen Raes commented:"It will allow us to understand diseases better…We know there is a microbial component but we don't know exactly how [it works]. We will use it for prognostic and diagnostic markers so we can predict disease severity or sensitivity to these diseases" (see BBC news).

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