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."

Comments

New paradigm

[drooling-dog]

This is really a new paradigm for microbial ecology. Instead of worrying about how thousands of different species (most of them unknown) are interacting with each other, you can now think about what genomic and proteomic resources are present in a habitat. Think of the organisms themselves as just the bags that contain what you're really interested in looking at, and suddenly a lot of insights and high-throughput techniques open up to you.

Re:how do you...

[drooling-dog]

I always thought that DNA extraction was a manual process... or at least it required a significant amount of manpower to get. Nope. That's pretty much been automated in the laboratory, as has much of the analysis. A lot easier than sorting and isolating individual critters, anyway...

Source

[Red Flayer]

The article was taken from a National Academies press release. Here's the full report, parts of which (maybe the whole thing? I didn't check) can be previewed as a pdf if you don't want to purchase the book.

Oh, and here's a brief (4-page summary) of the report.

Woulda been nice to have the source info in the summary...

Related Resource

[Anonymous Coward]

The Craig Venter Institute's Global Ocean Sampling Expedition has been collecting Metagenomic samples for the past couple of years. Among other things the expedition has doubled the number of putative proteins. An excellent video from the expedition is available at http://plos.cnpg.com/lsca/webinar/venter/20070306/ index.html and a set of recently published papers from the expedition are available for free at http://collections.plos.org/plosbiology/gos-2007.p hp

A website hosting the data from the expedition catered towards use on metagenomic samples has been developed by the Venter institute and is available at http://camera.calit2.net/

Re:any biologists in the room..ermm...slashdot?

[Anonymous Coward]

Basically, from an evolutionary standpoint, the colony is a single organism, and the worker bees are just appendages if you will. The Queens have normal heredity, and pass down genes for pumping out lots of sterile worker bees. Genes for producing more/better workers help her survive and have more queen offspring that can do the same. The workers get to evolve as well, but only indirectly - in that a queen which randomly makes better-suited workers will tend to survive/thrive and pass down the genes to make better workers.

Sad tendency

[mapkinase]

The advent of metagenomics is accentuating a sad trend in science: less lab work, more computers. Do not get me wrong, I feed my kids from the computer desk and I have never touched an "Eppendorf" or "Pipetteman" (not sure about spelling). In the race for grants we are chasing aggrandisement of the projects we are applying to NSF and DOE. More computers, more modeling instead of experimenting.

I have been reading scientific literature for almost 25 years and the tendency is clear: the results of "computer experemints" (read, modeling) are trusted more and more without any experimental verification. The procentage of sequences in GenBank and Refseq which function is determined only by homology to existing proteins grows. That means we are guessing the function of new proteins by comparing them to the proteins which function we also guessed by comparing to earlier proteins, etc...

Number of protein folds is limited: 700, 1000, 30000, does not matter: it is limited, but it does not mean the functions are limited in the same way. How on earth are we going to find out the function of completely new protein that have not enough similarity to anything in the database? We cannot do it on computers.

And obviously we do not have resources to research experimentally 1.5M genes in Refseq. So instead of blindly pumping more and more raw data into our RAID arrays, we need to be more focused on researching the genes, proteins, pathways that have a direct impact on medicine. You know, "stuff that matters".