Tuesday, May 29, 2007

All of us

John Dennehy, the Evilutionary biologist, put up a post last week about an article in Science News reviewing research on the abundance and diversity of microbes associated with the human body. It presents a nice summary. Some fact culled from that article and elsewhere that are worth contemplating:

> There are 10 time (TEN TIMES) as many bacterial cells as mammalian cells in your body. If you like to contemplate zeros the number is estimated to be ~ 1014 bacterial cells to a measly 1013 mammalian.

> The bulk of these microbes live in our gut where densities can reach 1011 to 1012 cells ml-1 making the gut the ecosystem with the highest density of bacterial cells yet described.

> These are diverse communities 400 or so species but with two only 2 divisions (Fermicutes and bacteroides) accounting for 98% of total population)

>As with other microbial communities a very small fraction of the total number of species present are conducive to culture so most of what we know about them is from extracting and sequencing their genetic material.

> At birth the gut is sterile and must be colonized by bacteria ingested from the environment.

I do have one nit to pick with the Science News article. In the section describing the metagenomic efforts directed at sequencing the 'community genome' this is said:

"Called metagenomics, this form of analysis doesn't produce a list of bacteria but instead describes the metabolic activities going on within a microbial community. These activities include energy conversion and the transport and break down of carbohydrates and amino acids."

Generating sequence data from the DNA present in a microbial community is useful and worth doing. It provides information about what genes are present and about the metabolic potential of the community. But in isolation, it provides no information about what metabolic activities are actually occurring. The only real way to know what activities are occurring is to measure the activity directly There are practical limitations to doing direct measurements of all enzymatic activities of potential interest so the genetic data is very valuable but its limitations are worth keeping in mind.

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