Functional metagenomic profiling of nine biomes

Department of Biology, San Diego State University, San Diego, California 92182, USA.
Nature (Impact Factor: 42.35). 11/2008; 455(7214):830. DOI: 10.1038/nature07346
Source: PubMed

ABSTRACT Microbial activities shape the biogeochemistry of the planet and macroorganism health. Determining the metabolic processes performed by microbes is important both for understanding and for manipulating ecosystems (for example, disruption of key processes that lead to disease, conservation of environmental services, and so on). Describing microbial function is hampered by the inability to culture most microbes and by high levels of genomic plasticity. Metagenomic approaches analyse microbial communities to determine the metabolic processes that are important for growth and survival in any given environment. Here we conduct a metagenomic comparison of almost 15 million sequences from 45 distinct microbiomes and, for the first time, 42 distinct viromes and show that there are strongly discriminatory metabolic profiles across environments. Most of the functional diversity was maintained in all of the communities, but the relative occurrence of metabolisms varied, and the differences between metagenomes predicted the biogeochemical conditions of each environment. The magnitude of the microbial metabolic capabilities encoded by the viromes was extensive, suggesting that they serve as a repository for storing and sharing genes among their microbial hosts and influence global evolutionary and metabolic processes.

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Available from: Brandon K. Swan, Aug 25, 2015
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    • "The vast sequence diversity in environmental metagenomes suggests a similar magnitude of metabolic and biochemical diversity (Dinsdale et al. 2008; Yooseph et al. 2007), but the latter is impossible to comprehensively describe based only on sequence analysis due to the presence of the large number of unknown or poorly characterized genes. This necessitates the development of experimental approaches for metagenome research including new cultivation technologies, meta-transcriptomics, meta-proteomics and activity-based screening methods (Ferrer et al. 2007; Giovannoni and Stingl 2007; Ram et al. 2005; Simon and Daniel 2011; Uchiyama and Miyazaki 2009). "
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    Applied Microbiology and Biotechnology 09/2014; 99(5). DOI:10.1007/s00253-014-6038-3 · 3.81 Impact Factor
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    • "If we assume that a single genome encodes 4000 proteins (as is the case for the typical bacteria Escherichia coli), then 4 × 10 8 potential proteins might be expected in just 1 g of soil. Supposing that 40% of these proteins display catalytic activity (Dinsdale et al., 2008), we might expect to find 1.6 × 10 8 biocatalysts, which highlights the vast inventory of biological functions available in nature. Metagenomics avoids the necessity of isolation and laboratory cultivation of individual microorganisms, and has become a powerful tool for accessing and exploring the biological and molecular biodiversity present in different natural environments . "
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    • "AMGs have also been 60 observed in other cultivated viral isolates including genes for sugar metabolism, lipid- 61 fatty acid metabolism, and signaling (Derelle et al 2008). Further, culture-independent 62 metagenomic surveys have identified additional AMGs involved in motility, anti- 63 oxidation, photosystem I, energy metabolism, and iron-sulfur clusters (Dinsdale et al 64 2008, Sharon et al 2009, Sharon et al 2011, Yooseph et al 2007), with recent, focused 65 pathway analysis expanding these ocean virus-encoded AMG lists to include nearly all of 66 central carbon metabolism (Hurwitz et al 2013). "
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