Recovering complete and draft population genomes from metagenome datasets

Sangwan, Naseer; Xia, Fangfang; Gilbert, Jack A.

doi:10.1186/s40168-016-0154-5

Title: Recovering complete and draft population genomes from metagenome datasets

Journal Article · Tue Mar 08 00:00:00 EST 2016 · Microbiome

DOI:https://doi.org/10.1186/s40168-016-0154-5· OSTI ID:1258642

^[1]; Xia, Fangfang ^[2]; Gilbert, Jack A. ^[3]

Argonne National Lab. (ANL), Argonne, IL (United States); Univ. of Chicago, IL (United States)
Argonne National Lab. (ANL), Argonne, IL (United States)
Argonne National Lab. (ANL), Argonne, IL (United States); Univ. of Chicago, IL (United States); Marine Biological Lab., Woods Hole, MA (United States)

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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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1258642

Journal Information:: Microbiome, Vol. 4, Issue 1; ISSN 2049-2618

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 143 works

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Untangling Genomes of Novel Planctomycetal and Verrucomicrobial Species from Monterey Bay Kelp Forest Metagenomes by Refined Binning Vollmers, John; Frentrup, Martinique; Rast, Patrick Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.00472	journal	March 2017
Genome-Centric Analysis of a Thermophilic and Cellulolytic Bacterial Consortium Derived from Composting Lemos, Leandro N.; Pereira, Roberta V.; Quaggio, Ronaldo B. Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.00644	journal	April 2017
Evolutionary Biology Needs Wild Microbiomes Hird, Sarah M. Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.00725	journal	April 2017
Overview of Virus Metagenomic Classification Methods and Their Biological Applications Nooij, Sam; Schmitz, Dennis; Vennema, Harry Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.00749	journal	April 2018
New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes Kroeger, Marie E.; Delmont, Tom O.; Eren, A. M. Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.01635	journal	July 2018
Bacterial and Archaeal Viruses of Himalayan Hot Springs at Manikaran Modulate Host Genomes Sharma, Anukriti; Schmidt, Matthias; Kiesel, Bärbel Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.03095	journal	December 2018
Applying Genome-Resolved Metagenomics to Deconvolute the Halophilic Microbiome Uritskiy, Gherman; DiRuggiero, Jocelyne Genes, Vol. 10, Issue 3 https://doi.org/10.3390/genes10030220	journal	March 2019
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Interpreting Microbial Biosynthesis in the Genomic Age: Biological and Practical Considerations Miller, Ian; Chevrette, Marc; Kwan, Jason Marine Drugs, Vol. 15, Issue 6 https://doi.org/10.3390/md15060165	journal	June 2017
Metagenome to phenome approach enables isolation and genomics characterization of Kalamiella piersonii gen. nov., sp. nov. from the International Space Station Singh, Nitin Kumar; Wood, Jason M.; Mhatre, Snehit S. Applied Microbiology and Biotechnology, Vol. 103, Issue 11 https://doi.org/10.1007/s00253-019-09813-z	journal	April 2019
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Surveillance of Foodborne Pathogens: Towards Diagnostic Metagenomics of Fecal Samples Andersen, Sandra; Hoorfar, Jeffrey Genes, Vol. 9, Issue 1, p. 14 https://doi.org/10.3390/genes9010014	journal	January 2018
Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity Roux, Simon; Emerson, Joanne B.; Eloe-Fadrosh, Emiley A. PeerJ, Vol. 5 https://doi.org/10.7717/peerj.3817	journal	January 2017
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metaVaR: Introducing metavariant species models for reference-free metagenomic-based population genomics Laso-Jadart, Romuald; Ambroise, Christophe; Peterlongo, Pierre PLOS ONE, Vol. 15, Issue 12 https://doi.org/10.1371/journal.pone.0244637	journal	December 2020
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Accurate and complete genomes from metagenomes Chen, Lin-Xing; Anantharaman, Karthik; Shaiber, Alon Genome Research, Vol. 30, Issue 3 https://doi.org/10.1101/gr.258640.119	journal	March 2020
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Translational metagenomics and the human resistome: confronting the menace of the new millennium Willmann, Matthias; Peter, Silke Journal of Molecular Medicine, Vol. 95, Issue 1 https://doi.org/10.1007/s00109-016-1478-0	journal	October 2016
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A Metagenomic Approach to Cyanobacterial Genomics Alvarenga, Danillo O.; Fiore, Marli F.; Varani, Alessandro M. Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.00809	journal	May 2017
Benefits of Genomic Insights and CRISPR-Cas Signatures to Monitor Potential Pathogens across Drinking Water Production and Distribution Systems Zhang, Ya; Kitajima, Masaaki; Whittle, Andrew J. Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.02036	journal	October 2017
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