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:
-
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (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. doi: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 = {Mon Feb 01 00:00:00 EST 2016},
month = {Mon Feb 01 00:00:00 EST 2016}
}
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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
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
BLAT---The BLAST-Like Alignment Tool
journal, March 2002
- Kent, W. J.
- Genome Research, Vol. 12, Issue 4
Ecology and exploration of the rare biosphere
journal, March 2015
- Lynch, Michael D. J.; Neufeld, Josh D.
- Nature Reviews Microbiology, Vol. 13, Issue 4
PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers
journal, February 2011
- Walters, William A.; Caporaso, J. Gregory; Lauber, Christian L.
- Bioinformatics, Vol. 27, Issue 8
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
BLAT---The BLAST-Like Alignment Tool
journal, March 2002
- Kent, W. J.
- Genome Research, Vol. 12, Issue 4
Searching for new branches on the tree of life
journal, November 2014
- Woyke, T.; Rubin, E. M.
- Science, Vol. 346, Issue 6210
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
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
Mapping the Tree of Life: Progress and Prospects
journal, November 2009
- Pace, N. R.
- Microbiology and Molecular Biology Reviews, Vol. 73, Issue 4
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
journal, August 2006
- Stamatakis, Alexandros
- Bioinformatics, Vol. 22, Issue 21
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
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
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
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
Infernal 1.1: 100-fold faster RNA homology searches
journal, September 2013
- Nawrocki, E. P.; Eddy, S. R.
- Bioinformatics, Vol. 29, Issue 22
Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples: Primers for marine microbiome studies
journal, October 2015
- Parada, Alma E.; Needham, David M.; Fuhrman, Jed A.
- Environmental Microbiology, Vol. 18, Issue 5
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
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
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
Comparison of 15 dinoflagellate genomes reveals extensive sequence and structural divergence in family Symbiodiniaceae and genus Symbiodinium
journal, April 2021
- González-Pech, Raúl A.; Stephens, Timothy G.; Chen, Yibi
- BMC Biology, Vol. 19, Issue 1
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
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
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
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
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
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
The trajectory of microbial single-cell sequencing
journal, October 2017
- Woyke, Tanja; Doud, Devin F. R.; Schulz, Frederik
- Nature Methods, Vol. 14, Issue 11
Pangenomic comparison of globally distributed Poribacteria associated with sponge hosts and marine particles
journal, October 2018
- Podell, Sheila; Blanton, Jessica M.; Neu, Alexander
- The ISME Journal, Vol. 13, Issue 2
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
Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny
journal, November 2018
- Pollock, F. Joseph; McMinds, Ryan; Smith, Styles
- Nature Communications, Vol. 9, Issue 1
A great-ape view of the gut microbiome
journal, January 2019
- Nishida, Alex H.; Ochman, Howard
- Nature Reviews Genetics, Vol. 20, Issue 4
Occurrence and expression of novel methyl-coenzyme M reductase gene (mcrA) variants in hot spring sediments
journal, August 2017
- McKay, Luke J.; Hatzenpichler, Roland; Inskeep, William P.
- Scientific Reports, Vol. 7, Issue 1
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
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
Uncovering the hidden marine sponge microbiome by applying a multi-primer approach
journal, April 2019
- Yang, Qi; Franco, Christopher M. M.; Zhang, Wei
- Scientific Reports, Vol. 9, Issue 1
Co-cultivation of the marine sponge Halichondria panicea and its associated microorganisms
journal, July 2019
- Knobloch, Stephen; Jóhannsson, Ragnar; Marteinsson, Viggó
- Scientific Reports, Vol. 9, Issue 1
Field sampling of indoor bioaerosols
journal, November 2019
- Cox, Jennie; Mbareche, Hamza; Lindsley, William G.
- Aerosol Science and Technology, Vol. 54, Issue 5
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
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
Thousands of primer-free, high-quality, full-length SSU rRNA sequences from all domains of life
journal, August 2016
- Karst, Søren M.; Dueholm, Morten S.; McIlroy, Simon J.
- Nature Biotechnology
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
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
Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life
journal, August 2017
- Spang, Anja; Caceres, Eva F.; Ettema, Thijs J. G.
- Science, Vol. 357, Issue 6351
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
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
Towards a balanced view of the bacterial tree of life
journal, October 2017
- Schulz, Frederik; Eloe-Fadrosh, Emiley A.; Bowers, Robert M.
- Microbiome, Vol. 5, Issue 1
Do you cov me? Effect of coverage reduction on species identification and genome reconstruction in complex biological matrices by metagenome shotgun high-throughput sequencing
journal, January 2018
- Cattonaro, Federica; Spadotto, Alessandro; Radovic, Slobodanka
- F1000Research, Vol. 7
Do you cov me? Effect of coverage reduction on metagenome shotgun sequencing studies
journal, January 2018
- Cattonaro, Federica; Spadotto, Alessandro; Radovic, Slobodanka
- F1000Research, Vol. 7
A census-based estimate of Earth's bacterial and archaeal diversity
journal, February 2019
- Louca, Stilianos; Mazel, Florent; Doebeli, Michael
- PLOS Biology, Vol. 17, Issue 2
Genomic Insight Into the Predominance of Candidate Phylum Atribacteria JS1 Lineage in Marine Sediments
journal, November 2018
- Lee, Yung Mi; Hwang, Kyuin; Lee, Jae Il
- Frontiers in Microbiology, Vol. 9
Uncovering the Uncultivated Majority in Antarctic Soils: Toward a Synergistic Approach
journal, February 2019
- Lambrechts, Sam; Willems, Anne; Tahon, Guillaume
- Frontiers in Microbiology, Vol. 10
Exploring the Archaeome: Detection of Archaeal Signatures in the Human Body
journal, December 2019
- Pausan, Manuela R.; Csorba, Cintia; Singer, Georg
- Frontiers in Microbiology, Vol. 10
Bioinformatic Analysis Reveals Archaeal tRNATyr and tRNATrp Identities in Bacteria
journal, February 2017
- Mukai, Takahito; Reynolds, Noah; Crnković, Ana
- Life, Vol. 7, Issue 1
Do you cov me? Effect of coverage reduction on species identification and genome reconstruction in complex biological matrices by metagenome shotgun high-throughput sequencing
journal, January 2018
- Cattonaro, Federica; Spadotto, Alessandro; Radovic, Slobodanka
- F1000Research, Vol. 7
Do you cov me? Effect of coverage reduction on species identification and genome reconstruction in complex biological matrices by metagenome shotgun high-throughput sequencing
journal, January 2018
- Cattonaro, Federica; Spadotto, Alessandro; Radovic, Slobodanka
- F1000Research, Vol. 7
A communal catalogue reveals Earths multiscale microbial diversity
text, January 2017
- Thompson, Luke R.; Sanders, Jon G.; McDonald, Daniel
- ETH Zurich
A communal catalogue reveals Earth's multiscale microbial diversity
dataset, November 2017
- Thompson, Luke; Sanders, Jon; McDonald, Daniel
- Zenodo, 33 files (CSV, TSV, BIOM, TXT, GZ, RDB); 47.3 GB