New Science Of Metagenomics to Transform Modern Microbiology?

ScienceDaily has a look at the emerging field of metagenomics that watches the DNA of whole communities of microbes to better understand the microbial world. "Metagenomics studies begin by extracting DNA from all the microbes living in a particular environmental sample; there could be thousands or even millions of organisms in one sample. The extracted genetic material consists of millions of random fragments of DNA that can be cloned into a form capable of being maintained in laboratory bacteria. These bacteria are used to create a "library" that includes the genomes of all the microbes found in a habitat, the natural environment of the organisms. Although the genomes are fragmented, new DNA sequencing technology and more powerful computers are allowing scientists to begin making sense of these metagenomic jigsaw puzzles. They can examine gene sequences from thousands of previously unknown microorganisms, or induce the bacteria to express proteins that are screened for capabilities such as vitamin production or antibiotic resistance."

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Re:how do you...

[goombah99]

Meta genomics is usually applied to unculturable communities. As such it can only be done when the source is so abundant that one can get enough DNA to be able to sequence it.

The best this can do is tell you what genes are present in abundance. Often you may also need primers for that gene so you have to guess a portion of it before you go looking for it. Thus one has some blind spots but these are no worse perhaps than the simple reality that one must always miss some of the low concentration genomes. The presumption is that higher concentration genomes are the most important. That's debatable. If a martian sampled our planet he'd conclude we are irrelevant, and probably that nothing but the top layer of sea water was relevant, given the profile of DNA concentration. Maybe he's right, but I think he'd be missing out on using this to explain a lot of phenomena on earth. How would this explain for example high rise building, deforestation, or changes in the atmosphere, let alone nuclear explosions. For those you might need to sequence us.

Another problem with this kind of analysis is that while it tells you what is there it does not tell you how the genes interact. For that you need to measure things under varying condittions where relative abundances shift. E.g. finding conditions where nominally the same populations exist--highly coupled envirnonments in equilibrium--where there are different stresses and opportunities. Perhaps the best example of this is depth profiles in sea water. However, obtaining enough degrees of freedom in the experimental conditions, so that one can correlate DNA presence patterns is rough. These self-simmmilar variations can be factored out only under assumptions that need to be justified. Typically Linear factors are assumed and that's almost certainly not true. It certainly would be false in any situation involving either negative feedback or saturation effects. getting enough sample points of entire meta genomes is thus the limit. It's pretty heroic to do even one. And of course one replicate is not enough since one can't distinguish noise from variations one is seeking. So it's all very hard.

Thus it's sort of a race which will prove more powerful. Reductive decomposition of a population one species at a time or a discovery based meta genomic analysis.

the simple answer is we need to do both. When it works reduction is far more conclusive about interactions. But there's likely some aspects of community life that dont reside in any one geneome but are traits that float around between different "owners". Likewise, most environments like ground soils have proven to be unculturable so one is sort of stuck with metagenomics or nothing.