Where next for microbiome research?

doi:10.1371/journal.pbio.1002050

. 2015 Jan 20;13(1):e1002050.

doi: 10.1371/journal.pbio.1002050. eCollection 2015 Jan.

Where next for microbiome research?

Affiliations

¹ Division of Infectious Diseases, Brigham and Women's Hospital, Department of Microbiology and Immunobiology Harvard Medical School and HHMI, Boston, Massachusetts, United States of America.
² Australian Centre for Ecogenomics and Advanced Water Management Centre, The University of Queensland, Brisbane, Australia.
³ Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America; Department of Computer Science and Engineering, University of Washington, Seattle, Washington, United States of America; Santa Fe Institute, Santa Fe, New Mexico, United States of America.
⁴ Department of Integrative Biology, University of Texas, Austin, Texas, United States of America.
⁵ Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America.
⁶ Michael Smith Laboratories, University of British Columbia, Vancouver, Canada.
⁷ Dermatology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America.
⁸ Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America.
⁹ J. Craig Venter Institute, Rockville, Maryland, United States of America.
¹⁰ Second Genome, Inc., South San Francisco, California, United States of America.
¹¹ J. Craig Venter Institute, La Jolla, California, United States of America.

PMID: 25602283
PMCID: PMC4300079
DOI: 10.1371/journal.pbio.1002050

Where next for microbiome research?

Matthew K Waldor et al. PLoS Biol. 2015.

. 2015 Jan 20;13(1):e1002050.

doi: 10.1371/journal.pbio.1002050. eCollection 2015 Jan.

Authors

Affiliations

¹ Division of Infectious Diseases, Brigham and Women's Hospital, Department of Microbiology and Immunobiology Harvard Medical School and HHMI, Boston, Massachusetts, United States of America.
² Australian Centre for Ecogenomics and Advanced Water Management Centre, The University of Queensland, Brisbane, Australia.
³ Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America; Department of Computer Science and Engineering, University of Washington, Seattle, Washington, United States of America; Santa Fe Institute, Santa Fe, New Mexico, United States of America.
⁴ Department of Integrative Biology, University of Texas, Austin, Texas, United States of America.
⁵ Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America.
⁶ Michael Smith Laboratories, University of British Columbia, Vancouver, Canada.
⁷ Dermatology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America.
⁸ Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America.
⁹ J. Craig Venter Institute, Rockville, Maryland, United States of America.
¹⁰ Second Genome, Inc., South San Francisco, California, United States of America.
¹¹ J. Craig Venter Institute, La Jolla, California, United States of America.

PMID: 25602283
PMCID: PMC4300079
DOI: 10.1371/journal.pbio.1002050

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.

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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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[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

[2] 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

[3] 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

[4] 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

[5] 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

[6] 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

[7] 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

[8] 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

[9] 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

[10] 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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Where next for microbiome research?

Affiliations

Where next for microbiome research?

Authors

Affiliations

Abstract

Conflict of interest statement

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References

MeSH terms

Grants and funding

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