Comparative metagenomics of microbial communities Page: 4 of 46
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samples examined. Near-complete assemblies were possible for the genomes of
just three of these organisms, and nearly half of the sequences obtained could not
be assembled beyond mate-pairing of bidirectional reads from individual clones
(7).
An important unanswered question arising from these initial forays into shotgun
sequencing of environmental samples is whether whole genome shotgun sequence
data can be meaningful in the absence of significant assembly. Many microbial
communities, such as those residing in soils and sediments, are substantially more
complex than those found in the acid mine drainage biofilm or even the Sargasso
Sea and thus less amenable to genome assembly (6, 7, 9). This obstacle may in
part be offset by the high gene density of prokaryotes and improved sequence
read lengths which result in most reads containing a significant portion of at least
one gene (10, 11). While genomic sequencing goals targeting species ranging
from humans to microbes have almost exclusively focused on determining the
complete genome of a particular organism, the genetic information contained in
individual sequencing reads suggests the feasibility of a less whole genome-
oriented approach to the analysis of metagenomic data. Examination of the
proteins encoded in a community, rather than the types of organisms producing
them, could potentially distinguish samples based on the functions selected for by
the local environment and reveal insights into features of that environment.
To explore the utility of a gene-centric approach to environmental samples we
examined a number of communities of varying complexity from environments
presenting several different metabolic challenges. One sample was from soil, a4
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Tringe, Susannah Green; von Mering, Christian; Kobayashi, Arthur; Salamov, Asaf A.; Chen, Kevin; Chang, Hwai W. et al. Comparative metagenomics of microbial communities, article, December 15, 2004; Berkeley, California. (https://digital.library.unt.edu/ark:/67531/metadc783014/m1/4/: accessed April 25, 2024), University of North Texas Libraries, UNT Digital Library, https://digital.library.unt.edu; crediting UNT Libraries Government Documents Department.