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. 2015 Jan 20;13(1):e1002050.
doi: 10.1371/journal.pbio.1002050. eCollection 2015 Jan.

Where next for microbiome research?

Matthew K Waldor  1 , Gene Tyson  2 , Elhanan Borenstein  3 , Howard Ochman  4 , Andrew Moeller  5 , B Brett Finlay  6 , Heidi H Kong  7 , Jeffrey I Gordon  8 , Karen E Nelson  9 , Karim Dabbagh  10 , Hamilton Smith  11
Affiliations

Where next for microbiome research?

Matthew K Waldor et al. PLoS Biol. .

Abstract

The development of high-throughput sequencing technologies has transformed our capacity to investigate the composition and dynamics of the microbial communities that populate diverse habitats. Over the past decade, these advances have yielded an avalanche of metagenomic data. The current stage of "van Leeuwenhoek"-like cataloguing, as well as functional analyses, will likely accelerate as DNA and RNA sequencing, plus protein and metabolic profiling capacities and computational tools, continue to improve. However, it is time to consider: what's next for microbiome research? The short pieces included here briefly consider the challenges and opportunities awaiting microbiome research.

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Conflict of interest statement

The authors have declared that no competing interests exist.

References

    1. Albertsen M, Hugenholtz P, Skarshewski A, Nielsen KL, Tyson GW, et al. (2013) Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol 31: 533–538. 10.1038/nbt.2579 - DOI - PubMed
    1. Imelfort M, Parks D, Woodcroft BJ, Dennis P, Hugenholtz P, et al. (2014) GroopM: An automated tool for the recovery of population genomes from related metagenomes. PeerJ PrePrints 2:e409v1 10.7717/peerj.603 - DOI - PMC - PubMed
    1. Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, et al. (2013) Insights into the phylogeny and coding potential of microbial dark matter. Nature 499: 431–437. 10.1038/nature12352 - DOI - PubMed
    1. Greenblum S, Turnbaugh PJ, Borenstein E (2012) Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease. Proc Natl Acad Sci U S A 109: 594–599. 10.1073/pnas.1116053109 - DOI - PMC - PubMed
    1. Levy R, Borenstein E (2013) Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules. Proc Natl Acad Sci U S A 110: 12804–12809. 10.1073/pnas.1300926110 - DOI - PMC - PubMed

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