Recovering complete and draft population genomes from metagenome datasets

doi:10.1186/s40168-016-0154-5

Review

. 2016 Mar 8:4:8.

doi: 10.1186/s40168-016-0154-5.

Recovering complete and draft population genomes from metagenome datasets

Naseer Sangwan^{1

2}, Fangfang Xia³, Jack A Gilbert^{4

5

6

7}

Affiliations

¹ Biosciences Division (BIO), Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA. nikki1018sangwan@gmail.com.
² Department of Surgery, University of Chicago, 5841 South Maryland Avenue, MC 5029, Chicago, IL, 60637, USA. nikki1018sangwan@gmail.com.
³ Computing, Environment and Life Sciences, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA. fangfang@anl.gov.
⁴ Biosciences Division (BIO), Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA. gilbertjack@gmail.com.
⁵ Department of Ecology and Evolution, University of Chicago, 1101 E 57th Street, Chicago, IL, 60637, USA. gilbertjack@gmail.com.
⁶ Department of Surgery, University of Chicago, 5841 South Maryland Avenue, MC 5029, Chicago, IL, 60637, USA. gilbertjack@gmail.com.
⁷ Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 02543, USA. gilbertjack@gmail.com.

PMID: 26951112
PMCID: PMC4782286
DOI: 10.1186/s40168-016-0154-5

Review

Recovering complete and draft population genomes from metagenome datasets

Naseer Sangwan et al. Microbiome. 2016.

. 2016 Mar 8:4:8.

doi: 10.1186/s40168-016-0154-5.

Authors

Naseer Sangwan^{1

2}, Fangfang Xia³, Jack A Gilbert^{4

5

6

7}

Affiliations

¹ Biosciences Division (BIO), Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA. nikki1018sangwan@gmail.com.
² Department of Surgery, University of Chicago, 5841 South Maryland Avenue, MC 5029, Chicago, IL, 60637, USA. nikki1018sangwan@gmail.com.
³ Computing, Environment and Life Sciences, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA. fangfang@anl.gov.
⁴ Biosciences Division (BIO), Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA. gilbertjack@gmail.com.
⁵ Department of Ecology and Evolution, University of Chicago, 1101 E 57th Street, Chicago, IL, 60637, USA. gilbertjack@gmail.com.
⁶ Department of Surgery, University of Chicago, 5841 South Maryland Avenue, MC 5029, Chicago, IL, 60637, USA. gilbertjack@gmail.com.
⁷ Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 02543, USA. gilbertjack@gmail.com.

PMID: 26951112
PMCID: PMC4782286
DOI: 10.1186/s40168-016-0154-5

Abstract

Assembly of metagenomic sequence data into microbial genomes is of fundamental value to improving our understanding of microbial ecology and metabolism by elucidating the functional potential of hard-to-culture microorganisms. Here, we provide a synthesis of available methods to bin metagenomic contigs into species-level groups and highlight how genetic diversity, sequencing depth, and coverage influence binning success. Despite the computational cost on application to deeply sequenced complex metagenomes (e.g., soil), covarying patterns of contig coverage across multiple datasets significantly improves the binning process. We also discuss and compare current genome validation methods and reveal how these methods tackle the problem of chimeric genome bins i.e., sequences from multiple species. Finally, we explore how population genome assembly can be used to uncover biogeographic trends and to characterize the effect of in situ functional constraints on the genome-wide evolution.

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Figures

**Fig. 1**
Workflow and overview for recovering population genomes from shotgun metagenomics data

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References

1. Ramette A, Tiedje JM. Biogeography: an emerging cornerstone for understanding prokaryotic diversity, ecology, and evolution. Microb Ecol. 2007;53:197–207. doi: 10.1007/s00248-005-5010-2. - DOI - PubMed
1. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, et al. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature. 2004;428:37–43. doi: 10.1038/nature02340. - DOI - PubMed
1. Hua Z-S, Han Y-J, Chen L-X, Liu J, Hu M, Li S-J, et al. Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics. ISME J. 2015;9(6):1280–94. doi: 10.1038/ismej.2014.212. - DOI - PMC - PubMed
1. Sharon I, Morowitz MJ, Thomas BC, Costello EK, Relman DA, Banfield JF. Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization. Genome Res. 2013;23:111–120. doi: 10.1101/gr.142315.112. - DOI - PMC - PubMed
1. Hess M, Sczyrba A, Egan R, Kim T-W, Chokhawala H, Schroth G, et al. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science. 2011;331:463–467. doi: 10.1126/science.1200387. - DOI - PubMed

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[1] Ramette A, Tiedje JM. Biogeography: an emerging cornerstone for understanding prokaryotic diversity, ecology, and evolution. Microb Ecol. 2007;53:197–207. doi: 10.1007/s00248-005-5010-2. - DOI - PubMed

[2] Ramette A, Tiedje JM. Biogeography: an emerging cornerstone for understanding prokaryotic diversity, ecology, and evolution. Microb Ecol. 2007;53:197–207. doi: 10.1007/s00248-005-5010-2. - DOI - PubMed

[3] Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, et al. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature. 2004;428:37–43. doi: 10.1038/nature02340. - DOI - PubMed

[4] Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, et al. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature. 2004;428:37–43. doi: 10.1038/nature02340. - DOI - PubMed

[5] Hua Z-S, Han Y-J, Chen L-X, Liu J, Hu M, Li S-J, et al. Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics. ISME J. 2015;9(6):1280–94. doi: 10.1038/ismej.2014.212. - DOI - PMC - PubMed

[6] Hua Z-S, Han Y-J, Chen L-X, Liu J, Hu M, Li S-J, et al. Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics. ISME J. 2015;9(6):1280–94. doi: 10.1038/ismej.2014.212. - DOI - PMC - PubMed

[7] Sharon I, Morowitz MJ, Thomas BC, Costello EK, Relman DA, Banfield JF. Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization. Genome Res. 2013;23:111–120. doi: 10.1101/gr.142315.112. - DOI - PMC - PubMed

[8] Sharon I, Morowitz MJ, Thomas BC, Costello EK, Relman DA, Banfield JF. Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization. Genome Res. 2013;23:111–120. doi: 10.1101/gr.142315.112. - DOI - PMC - PubMed

[9] Hess M, Sczyrba A, Egan R, Kim T-W, Chokhawala H, Schroth G, et al. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science. 2011;331:463–467. doi: 10.1126/science.1200387. - DOI - PubMed

[10] Hess M, Sczyrba A, Egan R, Kim T-W, Chokhawala H, Schroth G, et al. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science. 2011;331:463–467. doi: 10.1126/science.1200387. - DOI - PubMed

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Recovering complete and draft population genomes from metagenome datasets

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Recovering complete and draft population genomes from metagenome datasets

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