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Title: Community-wide analysis of microbial genome sequence signatures

Abstract

Background: Analyses of DNA sequences from cultivated microorganisms have revealed genome-wide, taxa-specific nucleotide compositional characteristics, referred to as genome signatures. These signatures have far-reaching implications for understanding genome evolution and potential application in classification of metagenomic sequence fragments. However, little is known regarding the distribution of genome signatures in natural microbial communities or the extent to which environmental factors shape them. Results: We analyzed metagenomic sequence data from two acidophilic biofilm communities, including composite genomes reconstructed for nine archaea, three bacteria, and numerous associated viruses, as well as thousands of unassigned fragments from strain variants and low abundance organisms. Genome signatures, in the form of tetranucleotide frequencies analyzed by emergent self-organizing maps, segregated sequences from all known populations sharing < 50 to 60% average amino acid identity and revealed previously unknown genomic clusters corresponding to low-abundance organisms and a putative plasmid. Signatures were pervasive genome-wide. Clusters were resolved because intra-genome differences resulting from translational selection or protein adaptation to the intracellular (pH ~5) versus extracellular (pH ~1) environment were small relative to inter-genome differences. We found that these genome signatures stem from multiple influences but are primarily manifested through codon composition, which we propose is the result of genome-specific mutationalmore » biases. Conclusions: An important conclusion is that shared environmental pressures and interactions among coevolving organisms do not obscure genome signatures in acid mine drainage communities. Thus, genome signatures can be used to assign sequence fragments to populations, an essential prerequisite if metagenomics is to provide ecological and biochemical insights into the functioning of microbial communities.« less

Authors:
 [1];  [1];  [1];  [1];  [1];  [1];  [2]
+ Show Author Affiliations
  1. Univ. of California, Berkeley, CA (United States). Dept. of Earth and Planetary Science
  2. Univ. of California, Berkeley, CA (United States). Dept. of Earth and Planetary Science; Univ. of California, Berkeley, CA (United States). Dept. of Environmental Science, Policy, and Management
Publication Date:
Research Org.:
Univ. of California, Oakland, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Earth and Environmental Systems Science Division
OSTI Identifier:
1626734
Grant/Contract Number:  
FG02-05ER64134
Resource Type:
Accepted Manuscript
Journal Name:
GenomeBiology.com
Additional Journal Information:
Journal Volume: 10; Journal Issue: 8; Journal ID: ISSN 1465-6906
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Biotechnology & Applied Microbiology; Genetics & Heredity

Citation Formats

Dick, Gregory J., Andersson, Anders F., Baker, Brett J., Simmons, Sheri L., Thomas, Brian C., Yelton, A. Pepper, and Banfield, Jillian F. Community-wide analysis of microbial genome sequence signatures. United States: N. p., 2009. Web. doi:10.1186/gb-2009-10-8-r85.
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Dick, Gregory J., Andersson, Anders F., Baker, Brett J., Simmons, Sheri L., Thomas, Brian C., Yelton, A. Pepper, & Banfield, Jillian F. Community-wide analysis of microbial genome sequence signatures. United States. https://doi.org/10.1186/gb-2009-10-8-r85
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Dick, Gregory J., Andersson, Anders F., Baker, Brett J., Simmons, Sheri L., Thomas, Brian C., Yelton, A. Pepper, and Banfield, Jillian F. Thu . "Community-wide analysis of microbial genome sequence signatures". United States. https://doi.org/10.1186/gb-2009-10-8-r85. https://www.osti.gov/servlets/purl/1626734.
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@article{osti_1626734,
title = {Community-wide analysis of microbial genome sequence signatures},
author = {Dick, Gregory J. and Andersson, Anders F. and Baker, Brett J. and Simmons, Sheri L. and Thomas, Brian C. and Yelton, A. Pepper and Banfield, Jillian F.},
abstractNote = {Background: Analyses of DNA sequences from cultivated microorganisms have revealed genome-wide, taxa-specific nucleotide compositional characteristics, referred to as genome signatures. These signatures have far-reaching implications for understanding genome evolution and potential application in classification of metagenomic sequence fragments. However, little is known regarding the distribution of genome signatures in natural microbial communities or the extent to which environmental factors shape them. Results: We analyzed metagenomic sequence data from two acidophilic biofilm communities, including composite genomes reconstructed for nine archaea, three bacteria, and numerous associated viruses, as well as thousands of unassigned fragments from strain variants and low abundance organisms. Genome signatures, in the form of tetranucleotide frequencies analyzed by emergent self-organizing maps, segregated sequences from all known populations sharing < 50 to 60% average amino acid identity and revealed previously unknown genomic clusters corresponding to low-abundance organisms and a putative plasmid. Signatures were pervasive genome-wide. Clusters were resolved because intra-genome differences resulting from translational selection or protein adaptation to the intracellular (pH ~5) versus extracellular (pH ~1) environment were small relative to inter-genome differences. We found that these genome signatures stem from multiple influences but are primarily manifested through codon composition, which we propose is the result of genome-specific mutational biases. Conclusions: An important conclusion is that shared environmental pressures and interactions among coevolving organisms do not obscure genome signatures in acid mine drainage communities. Thus, genome signatures can be used to assign sequence fragments to populations, an essential prerequisite if metagenomics is to provide ecological and biochemical insights into the functioning of microbial communities.},
doi = {10.1186/gb-2009-10-8-r85},
journal = {GenomeBiology.com},
number = 8,
volume = 10,
place = {United States},
year = {Thu Jan 01 00:00:00 EST 2009},
month = {Thu Jan 01 00:00:00 EST 2009}
}
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Works referenced in this record:

Deciphering the evolution and metabolism of an anammox bacterium from a community genome
journal, April 2006

  • Strous, Marc; Pelletier, Eric; Mangenot, Sophie
  • Nature, Vol. 440, Issue 7085
  • DOI: 10.1038/nature04647

Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum
journal, November 2006

  • Hallam, S. J.; Konstantinidis, K. T.; Putnam, N.
  • Proceedings of the National Academy of Sciences, Vol. 103, Issue 48
  • DOI: 10.1073/pnas.0608549103

Variation in the strength of selected codon usage bias among bacteria
journal, February 2005

Capturing Whole-Genome Characteristics in Short Sequences Using a Naive Bayesian Classifier
journal, August 2001

Community Genomics Among Stratified Microbial Assemblages in the Ocean's Interior
journal, January 2006

Phylogenetic Classification and the Universal Tree
journal, June 1999

The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families
journal, March 2007

    Sort by:
    [ × clear filter / sort ]

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    Impact of single-cell genomics and metagenomics on the emerging view of extremophile “microbial dark matter”
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    journal, November 2015

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    journal, May 2018

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    • DOI: 10.1038/s41564-018-0171-1

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    journal, January 2018

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    • Nucleic Acids Research, Vol. 46, Issue 6
    • DOI: 10.1093/nar/gkx1321

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    • The ISME Journal, Vol. 11, Issue 9
    • DOI: 10.1038/ismej.2017.72

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    • DOI: 10.1093/bib/bbs039

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    • Saw, Jimmy H.; Spang, Anja; Zaremba-Niedzwiedzka, Katarzyna
    • Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 370, Issue 1678
    • DOI: 10.1098/rstb.2014.0328

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    • Goltsman, Daniela S. Aliaga; Dasari, Mauna; Thomas, Brian C.
    • Applied and Environmental Microbiology, Vol. 79, Issue 17
    • DOI: 10.1128/aem.00202-13

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    • Genome Biology, Vol. 12, Issue 5
    • DOI: 10.1186/gb-2011-12-5-r44

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    • DOI: 10.1038/ismej.2017.39

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    • DOI: 10.1038/ncomms3420

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    • Wideman, Jeremy G.; Lax, Gordon; Leonard, Guy
    • Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 374, Issue 1786
    • DOI: 10.1098/rstb.2019.0100

    The future is now: single-cell genomics of bacteria and archaea
    journal, May 2013

    Genome sequences of lower Great Lakes Microcystis sp. reveal strain-specific genes that are present and expressed in western Lake Erie blooms
    journal, October 2017

    Ecogenomics and genome landscapes of marine Pseudoalteromonas phage H105/1
    journal, July 2010

    • Duhaime, Melissa Beth; Wichels, Antje; Waldmann, Jost
    • The ISME Journal, Vol. 5, Issue 1
    • DOI: 10.1038/ismej.2010.94

    Shotgun metagenomics, from sampling to analysis
    journal, September 2017

    • Quince, Christopher; Walker, Alan W.; Simpson, Jared T.
    • Nature Biotechnology, Vol. 35, Issue 9
    • DOI: 10.1038/nbt.3935

    Unusual respiratory capacity and nitrogen metabolism in a Parcubacterium (OD1) of the Candidate Phyla Radiation
    journal, January 2017

    • Castelle, Cindy J.; Brown, Christopher T.; Thomas, Brian C.
    • Scientific Reports, Vol. 7, Issue 1
    • DOI: 10.1038/srep40101

    Erratum: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
    journal, July 2018

    • Bowers, Robert M.; Kyrpides, Nikos C.; Stepanauskas, Ramunas
    • Nature Biotechnology, Vol. 36, Issue 7
    • DOI: 10.1038/nbt0718-660a

    Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea
    journal, October 2019

    Decontaminating eukaryotic genome assemblies with machine learning
    journal, December 2017

    Genome of a Low-Salinity Ammonia-Oxidizing Archaeon Determined by Single-Cell and Metagenomic Analysis
    journal, February 2011

    Prevalence and Implications of Contamination in Public Genomic Resources: A Case Study of 43 Reference Arthropod Assemblies
    journal, December 2019

    • Francois, Clementine M.; Durand, Faustine; Figuet, Emeric
    • G3: Genes|Genomes|Genetics, Vol. 10, Issue 2
    • DOI: 10.1534/g3.119.400758

    Comparative Metagenomics of the Polymicrobial Black Band Disease of Corals
    journal, April 2017

    • Meyer, Julie L.; Paul, Valerie J.; Raymundo, Laurie J.
    • Frontiers in Microbiology, Vol. 8
    • DOI: 10.3389/fmicb.2017.00618

    Fe–S Cluster Assembly In Oxymonads And Related Protists
    text, January 2018

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