The microbiome , that is the pool of micro-organism living in our bodies generally live harmoniously with us, and form a second genome. Reports in Science, a team from the International Human Microbiome Consortium (Nelson et al. and Qin et al describe the genome sequence of the bacterial species from the human microbiome.
The contribution made by microorganisms to the human body is very important. Some 1.5 kilograms of bacteria colonize the human gut, with others inhabiting the external and internal surfaces of the body. Only only 10% of the total number of cells in the human body consists of human cells, with the rest coming from symbiotic bacterial cells.
Molecules produced by the gut bacteria can enter the bloodstream via either a normal anatomical route, the enterohepatic circulation or through a partially damaged gut barrier. Beneficial gut bacteria can produce anti-inflammatory factors, pain-relieving compounds, antioxidants and vitamins to pro¬tect and nurture the body. Conversely, harmful bacteria may deregulate genes mediating energy metabolism, and can produce toxins that mutate DNA, affecting the nervous and immune systems. The outcome is various forms of chronic disease, including obesity, diabetes and even cancers. This exchanging of nutrients and metabolic wastes, makes symbiotic bacteria a human organ and their collective genomes our second genome.
The human gut micro¬biome contains around 1,000 bacterial species.
Nelson et al. of the Human Microbiome Jumpstart Reference Strains Consortium report an initial reference-genome sequencing for 178 microbial species. These are mostly from the gut, but also from the oral cavity, urogenital/vaginal tract, skin, respi¬ratory tract and even blood.
The ultimate test of the The International Human Microbiome Con¬sortium is to capture the diversity of the microbiome relevant to human health.
The gut microbiome may vary extensively among people from different ethnic groups.
Individual strains of a bacterial species can differ by up to 30% in terms of genetic sequence. The genomes of human and mouse differ by only 10%, the genetic and functional diversity within the same bacterial species can be over¬whelmingly high. Nelson et al. show that sequencing different strains of the same species may greatly increase the discovery of new genes
In sequencing one genomically distant strain of the bacterium Bifidobacterium iongum, the authors added 640 new genes to the pan-genome of this species, Four sequenced strains (the pan-genome is all the genes found in the sequenced strains of one species). By comparison, the core genome of these strains contains just 1,430 genes (the core genome is the genes shared by all sequenced strains in a species). For many gut bacterial species, therefore, more strains must be sequenced before we can decipher their pan-genome.
Another obstacle to completing the reference-genome set is that some strains that are relevant to hwnan health and disease cannot be maintained in culture.
A complex business. Not yet open to quick judgements. Of great interest to nutritionists. But not obligatory. We can live very well without a colon.
Zhao 2010 The tale of our other gneome nature vol 465 pp 879-90

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