such as "Introduction", "Conclusion"..etc
Mostly hidden from the scrutiny of the naked eye, microbes have been
said to run the world. The challenge is how best to characterize them
given that less than one percent of the estimated hundreds of millions
of microbial species can be cultured in the laboratory. The answer is
metagenomics—an increasingly popular approach for extracting the
genomes of uncultured microorganisms and discerning their specific
metabolic capabilities directly from environmental samples. Now, some
ten years after the term was coined, metagenomics is going mainstream
and already paying provocative dividends according to a "Q&A," News
and Views by the U.S. Department of Energy Joint Genome Institute (DOE
JGI) microbial ecology program head Philip Hugenholtz and MIT
researcher Gene Tyson, published in the 25 September edition of the
"By employing the techniques of metagenomics we can go beyond the
identification of specific players to creating an inventory of the
genes in that environment," said Hugenholtz. "We find that genes
occurring more frequently in a particular community seem to confer
attributes beneficial for maintenance of the function of that
particular ecological niche."
Hugenholtz and Tyson were part of the team assembled by University
of California, Berkeley geochemist Jillian Banfield to investigate
microbial communities associated with the acid mine drainage of Iron
Mountain in far Northern California in 2004. In the dank recesses of
the mine, protected by moon suits from the highly acidic effluent, the
researchers scooped up pink biofilm growing on the surface of acid mine
drainage streams. Extracting the nucleic acid from the sample and
directing DOE JGI's powerful DNA sequencing resource on them, the
Banfield team was able to reconstruct the metabolic profiles of the
organisms living under such inhospitable conditions—like putting many
Humpty-Dumpties back together again. Their findings, published in Nature
428, 37 - 43 (01 Feb 2004), showed that reconstructing the genomes of
dominant populations from the environment was feasible and that the
imprints of evolutionary selection could be discerned in these genomes.
Since this pioneering work, DOE JGI has gone on to characterize many
other metagenomes with other newly selected targets in the sequencing
queue at the Walnut Creek, Calif. Production Genomics Facility. These
range from the hindguts of termites, to plumb for microbes producing
cellulose-degrading enzymes, likewise to microbial communities in the
cow rumen, foregut of the Tammar Wallaby, and the crop of the Hoatzin,
the Amazon stinkbird. Beyond guts, the DOE JGI, through its Community
Sequencing Program (CSP) http://www.jgi.doe.gov/CSP/overview.html
is enabling metagenomic explorations of Lake Washington near Seattle,
Antarctica's Lake Vostok, and the Great Salt Lake, in addition to the
hypersaline mats at Guerrero Negro, Baja California. A video podcast of
the Lake Vostok CSP project is featured on the DOE JGI site < http://www.jgi.doe.gov/News/Lake_Vostok.mp4>. Nature features an audio podcast which includes an interview with Hugenholtz on their site <http://nature.edgeboss.net/download/nature/nature/podcast/v455/n7212/nature-2008-09-25.mp3?ewk13=1>.
Responding to the steadily increasing need to manage and interpret
the terabases and terabytes of metagenomic data now bubbling up into
the public domain, DOE JGI launched the Integrated Microbial Genomes
with Microbiome Samples (IMG/M: http://img.jgi.doe.gov/m)
data management and analysis system. IMG/M provides tools for analyzing
the functional capability of microbial communities based on the DNA
sequence of the metagenome in question.
"Metagenomic tools are becoming more widely available and improving
at a steady pace," said Hugenholtz. "But, there are still computational
and other bottlenecks to be addressed, such as the high percentage of
uncharacterized genes emerging from metagenomic studies."
In the Nature piece, Hugenholtz and Tyson go on to cite the
emergence of next generation sequencing technologies that are already
creating a deluge of data that has outstripped the computational power
available to cope with it.
"Nevertheless, it's not necessary to compare all the data to glean
useful biological insights," Hugenholtz said. "What we can capture will
help steer the direction toward a relevant data subset to investigate.
At least with metagenomics, we have the environmental genetic
blueprints awaiting our interpretation. We are still far from capturing
and characterizing the dazzling diversity of the microbial life on
earth—but at least we have hit upon the gold standard for scratching
Source : DOE/Joint Genome Institute. September 2008.
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