skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Metagenomics uncovers gaps in amplicon-based detection of microbial diversity

Abstract

Our view of microbial diversity has expanded greatly over the past 40 years, primarily through the wide application of PCR-based surveys of the small-subunit ribosomal RNA (SSU rRNA) gene. Yet significant gaps in knowledge remain due to well-recognized limitations of this method. Here in this paper, we systematically survey primer fidelity in SSU rRNA gene sequences recovered from over 6,000 assembled metagenomes sampled globally. Our findings show that approximately 10% of environmental microbial sequences might be missed from classical PCR-based SSU rRNA gene surveys, mostly members of the Candidate Phyla Radiation (CPR) and as yet uncharacterized Archaea. In conclusion, these results underscore the extent of uncharacterized microbial diversity and provide fruitful avenues for describing additional phylogenetic lineages.

Authors:
 [1];  [1];  [1];  [1]
  1. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1379258
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Nature Microbiology
Additional Journal Information:
Journal Volume: 1; Journal Issue: 4; Journal ID: ISSN 2058-5276
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Environmental microbiology; Metagenomics; Microbial ecology; Microbiome

Citation Formats

Eloe-Fadrosh, Emiley A., Ivanova, Natalia N., Woyke, Tanja, and Kyrpides, Nikos C. Metagenomics uncovers gaps in amplicon-based detection of microbial diversity. United States: N. p., 2016. Web. https://doi.org/10.1038/NMICROBIOL.2015.32.
Eloe-Fadrosh, Emiley A., Ivanova, Natalia N., Woyke, Tanja, & Kyrpides, Nikos C. Metagenomics uncovers gaps in amplicon-based detection of microbial diversity. United States. https://doi.org/10.1038/NMICROBIOL.2015.32
Eloe-Fadrosh, Emiley A., Ivanova, Natalia N., Woyke, Tanja, and Kyrpides, Nikos C. Mon . "Metagenomics uncovers gaps in amplicon-based detection of microbial diversity". United States. https://doi.org/10.1038/NMICROBIOL.2015.32. https://www.osti.gov/servlets/purl/1379258.
@article{osti_1379258,
title = {Metagenomics uncovers gaps in amplicon-based detection of microbial diversity},
author = {Eloe-Fadrosh, Emiley A. and Ivanova, Natalia N. and Woyke, Tanja and Kyrpides, Nikos C.},
abstractNote = {Our view of microbial diversity has expanded greatly over the past 40 years, primarily through the wide application of PCR-based surveys of the small-subunit ribosomal RNA (SSU rRNA) gene. Yet significant gaps in knowledge remain due to well-recognized limitations of this method. Here in this paper, we systematically survey primer fidelity in SSU rRNA gene sequences recovered from over 6,000 assembled metagenomes sampled globally. Our findings show that approximately 10% of environmental microbial sequences might be missed from classical PCR-based SSU rRNA gene surveys, mostly members of the Candidate Phyla Radiation (CPR) and as yet uncharacterized Archaea. In conclusion, these results underscore the extent of uncharacterized microbial diversity and provide fruitful avenues for describing additional phylogenetic lineages.},
doi = {10.1038/NMICROBIOL.2015.32},
journal = {Nature Microbiology},
number = 4,
volume = 1,
place = {United States},
year = {2016},
month = {2}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 47 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

IMG/M 4 version of the integrated metagenome comparative analysis system
journal, October 2013

  • Markowitz, Victor M.; Chen, I-Min A.; Chu, Ken
  • Nucleic Acids Research, Vol. 42, Issue D1, p. D568-D573
  • DOI: 10.1093/nar/gkt919

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies
journal, August 2012

  • Klindworth, Anna; Pruesse, Elmar; Schweer, Timmy
  • Nucleic Acids Research, Vol. 41, Issue 1
  • DOI: 10.1093/nar/gks808

BLAT---The BLAST-Like Alignment Tool
journal, March 2002


Ecology and exploration of the rare biosphere
journal, March 2015

  • Lynch, Michael D. J.; Neufeld, Josh D.
  • Nature Reviews Microbiology, Vol. 13, Issue 4
  • DOI: 10.1038/nrmicro3400

PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers
journal, February 2011


Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences
journal, August 2014

  • Yarza, Pablo; Yilmaz, Pelin; Pruesse, Elmar
  • Nature Reviews Microbiology, Vol. 12, Issue 9
  • DOI: 10.1038/nrmicro3330

BLAT---The BLAST-Like Alignment Tool
journal, March 2002


Searching for new branches on the tree of life
journal, November 2014


The Earth Microbiome Project: Meeting report of the “1st EMP meeting on sample selection and acquisition” at Argonne National Laboratory October 6th 2010.
journal, January 2010

  • Gilbert, Jack A.; Meyer, Folker; Jansson, Janet
  • Standards in Genomic Sciences, Vol. 3, Issue 3
  • DOI: 10.4056/aigs.1443528

Complex archaea that bridge the gap between prokaryotes and eukaryotes
journal, May 2015

  • Spang, Anja; Saw, Jimmy H.; Jørgensen, Steffen L.
  • Nature, Vol. 521, Issue 7551
  • DOI: 10.1038/nature14447

Mapping the Tree of Life: Progress and Prospects
journal, November 2009


RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
journal, August 2006


Unusual biology across a group comprising more than 15% of domain Bacteria
journal, June 2015

  • Brown, Christopher T.; Hug, Laura A.; Thomas, Brian C.
  • Nature, Vol. 523, Issue 7559
  • DOI: 10.1038/nature14486

Insights into the phylogeny and coding potential of microbial dark matter
journal, July 2013

  • Rinke, Christian; Schwientek, Patrick; Sczyrba, Alexander
  • Nature, Vol. 499, Issue 7459
  • DOI: 10.1038/nature12352

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
journal, March 2012

  • Caporaso, J. Gregory; Lauber, Christian L.; Walters, William A.
  • The ISME Journal, Vol. 6, Issue 8
  • DOI: 10.1038/ismej.2012.8

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes
journal, May 2013

  • Albertsen, Mads; Hugenholtz, Philip; Skarshewski, Adam
  • Nature Biotechnology, Vol. 31, Issue 6
  • DOI: 10.1038/nbt.2579

Infernal 1.1: 100-fold faster RNA homology searches
journal, September 2013


WebLogo: A Sequence Logo Generator
journal, May 2004

  • Crooks, Gavin E.; Hon, Gary; Chandonia, John-Marc
  • Genome Research, Vol. 14, Issue 6, p. 1188-1190
  • DOI: 10.1101/gr.849004

Experimental factors affecting PCR-based estimates of microbial species richness and evenness
journal, January 2010

  • Engelbrektson, Anna; Kunin, Victor; Wrighton, Kelly C.
  • The ISME Journal, Vol. 4, Issue 5
  • DOI: 10.1038/ismej.2009.153

Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling
journal, March 2015

  • Castelle, Cindy J.; Wrighton, Kelly C.; Thomas, Brian C.
  • Current Biology, Vol. 25, Issue 6
  • DOI: 10.1016/j.cub.2015.01.014

Comparison of 15 dinoflagellate genomes reveals extensive sequence and structural divergence in family Symbiodiniaceae and genus Symbiodinium
journal, April 2021


    Works referencing / citing this record:

    The bacterial community structure and functional profile in the heavy metal contaminated paddy soils, surrounding a nonferrous smelter in South Korea
    journal, May 2018

    • Tipayno, Sherlyn C.; Truu, Jaak; Samaddar, Sandipan
    • Ecology and Evolution, Vol. 8, Issue 12
    • DOI: 10.1002/ece3.4170

    The growing tree of Archaea: new perspectives on their diversity, evolution and ecology
    journal, August 2017

    • Adam, Panagiotis S.; Borrel, Guillaume; Brochier-Armanet, Céline
    • The ISME Journal, Vol. 11, Issue 11
    • DOI: 10.1038/ismej.2017.122

    Capturing the genetic makeup of the active microbiome in situ
    journal, June 2017

    • Singer, Esther; Wagner, Michael; Woyke, Tanja
    • The ISME Journal, Vol. 11, Issue 9
    • DOI: 10.1038/ismej.2017.59

    A communal catalogue reveals Earth’s multiscale microbial diversity
    journal, November 2017

    • Thompson, Luke R.; Sanders, Jon G.; McDonald, Daniel
    • Nature, Vol. 551, Issue 7681
    • DOI: 10.1038/nature24621

    Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies
    journal, July 2016

    • Gohl, Daryl M.; Vangay, Pajau; Garbe, John
    • Nature Biotechnology, Vol. 34, Issue 9
    • DOI: 10.1038/nbt.3601

    Retrieval of a million high-quality, full-length microbial 16S and 18S rRNA gene sequences without primer bias
    journal, January 2018

    • Karst, Søren M.; Dueholm, Morten S.; McIlroy, Simon J.
    • Nature Biotechnology, Vol. 36, Issue 2
    • DOI: 10.1038/nbt.4045

    The trajectory of microbial single-cell sequencing
    journal, October 2017

    • Woyke, Tanja; Doud, Devin F. R.; Schulz, Frederik
    • Nature Methods, Vol. 14, Issue 11
    • DOI: 10.1038/nmeth.4469

    Pangenomic comparison of globally distributed Poribacteria associated with sponge hosts and marine particles
    journal, October 2018


    High proportions of bacteria and archaea across most biomes remain uncultured
    journal, August 2019

    • Steen, Andrew D.; Crits-Christoph, Alexander; Carini, Paul
    • The ISME Journal, Vol. 13, Issue 12
    • DOI: 10.1038/s41396-019-0484-y

    Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny
    journal, November 2018


    A great-ape view of the gut microbiome
    journal, January 2019


    Occurrence and expression of novel methyl-coenzyme M reductase gene (mcrA) variants in hot spring sediments
    journal, August 2017


    The impact of immigration on microbial community composition in full-scale anaerobic digesters
    journal, August 2017

    • Kirkegaard, Rasmus H.; McIlroy, Simon J.; Kristensen, Jannie M.
    • Scientific Reports, Vol. 7, Issue 1
    • DOI: 10.1038/s41598-017-09303-0

    Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia
    journal, February 2019

    • Wilkins, Laetitia G. E.; Ettinger, Cassandra L.; Jospin, Guillaume
    • Scientific Reports, Vol. 9, Issue 1
    • DOI: 10.1038/s41598-019-39576-6

    Uncovering the hidden marine sponge microbiome by applying a multi-primer approach
    journal, April 2019


    Co-cultivation of the marine sponge Halichondria panicea and its associated microorganisms
    journal, July 2019


    Genome size evolution in the Archaea
    journal, November 2018

    • Kellner, Siri; Spang, Anja; Offre, Pierre
    • Emerging Topics in Life Sciences, Vol. 2, Issue 4
    • DOI: 10.1042/etls20180021

    Field sampling of indoor bioaerosols
    journal, November 2019


    A review of methods and databases for metagenomic classification and assembly
    journal, September 2017

    • Breitwieser, Florian P.; Lu, Jennifer; Salzberg, Steven L.
    • Briefings in Bioinformatics, Vol. 20, Issue 4
    • DOI: 10.1093/bib/bbx120

    IMG/M: integrated genome and metagenome comparative data analysis system
    journal, October 2016

    • Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken
    • Nucleic Acids Research, Vol. 45, Issue D1
    • DOI: 10.1093/nar/gkw929

    Genome‐inferred spatio‐temporal resolution of an uncultivated Roizmanbacterium reveals its ecological preferences in groundwater
    journal, December 2019

    • Geesink, Patricia; Wegner, Carl‐Eric; Probst, Alexander J.
    • Environmental Microbiology, Vol. 22, Issue 2
    • DOI: 10.1111/1462-2920.14865

    Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment
    journal, September 2018

    • Bahram, Mohammad; Anslan, Sten; Hildebrand, Falk
    • Environmental Microbiology Reports, Vol. 11, Issue 4
    • DOI: 10.1111/1758-2229.12684

    Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life
    journal, August 2017


    Status of the Archaeal and Bacterial Census: an Update
    journal, May 2016


    Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons
    journal, October 2019

    • Brewer, Tess E.; Aronson, Emma L.; Arogyaswamy, Keshav
    • mBio, Vol. 10, Issue 5
    • DOI: 10.1128/mbio.01318-19

    Unexplored Archaeal Diversity in the Great Ape Gut Microbiome
    journal, February 2017


    Phylogenetically Novel Uncultured Microbial Cells Dominate Earth Microbiomes
    journal, September 2018


    Metagenomic Approaches for Understanding New Concepts in Microbial Science
    journal, August 2018

    • Alves, Luana de Fátima; Westmann, Cauã Antunes; Lovate, Gabriel Lencioni
    • International Journal of Genomics, Vol. 2018
    • DOI: 10.1155/2018/2312987

    Changes in microbiota composition, bile and fatty acid metabolism, in successful faecal microbiota transplantation for Clostridioides difficile infection
    journal, August 2018

    • Brown, Jillian R. -M.; Flemer, Burkhardt; Joyce, Susan A.
    • BMC Gastroenterology, Vol. 18, Issue 1
    • DOI: 10.1186/s12876-018-0860-5

    Towards a balanced view of the bacterial tree of life
    journal, October 2017


    Do you cov me? Effect of coverage reduction on metagenome shotgun sequencing studies
    journal, January 2018


    A census-based estimate of Earth's bacterial and archaeal diversity
    journal, February 2019


    Genomic Insight Into the Predominance of Candidate Phylum Atribacteria JS1 Lineage in Marine Sediments
    journal, November 2018


    Uncovering the Uncultivated Majority in Antarctic Soils: Toward a Synergistic Approach
    journal, February 2019


    Exploring the Archaeome: Detection of Archaeal Signatures in the Human Body
    journal, December 2019


    Bioinformatic Analysis Reveals Archaeal tRNATyr and tRNATrp Identities in Bacteria
    journal, February 2017

    • Mukai, Takahito; Reynolds, Noah; Crnković, Ana
    • Life, Vol. 7, Issue 1
    • DOI: 10.3390/life7010008