Broadscale Ecological Patterns Are Robust to Use of Exact Sequence Variants versus Operational Taxonomic Units
Abstract
Recent discussion focuses on the best method for delineating microbial taxa, based on either exact sequence variants (ESVs) or traditional operational taxonomic units (OTUs) of marker gene sequences. We sought to test if the binning approach (ESVs versus 97% OTUs) affected the ecological conclusions of a large field study. The data set included sequences targeting all bacteria (16S rRNA) and fungi (internal transcribed spacer [ITS]), across multiple environments diverging markedly in abiotic conditions, over three collection times. Despite quantitative differences in microbial richness, we found that all α and β diversity metrics were highly positively correlated (r> 0.90) between samples analyzed with both approaches. Moreover, the community composition of the dominant taxa did not vary between approaches. Consequently, statistical inferences were nearly indistinguishable. Furthermore, ESVs only moderately increased the genetic resolution of fungal and bacterial diversity (1.3 and 2.1 times OTU richness, respectively). We conclude that for broadscale (e.g., all bacteria or all fungi) α and β diversity analyses, ESV or OTU methods will often reveal similar ecological results. Thus, while there are good reasons to employ ESVs, we need not question the validity of results based on OTUs. Microbial ecologists have made exceptional improvements in our understanding of microbiomesmore »
- Authors:
-
- Department of Ecology and Evolutionary Biology, University of California—Irvine, Irvine, California, USA, Department of Microbiology and Plant Pathology, University of California—Riverside, Riverside, California, USA
- Department of Ecology and Evolutionary Biology, University of California—Irvine, Irvine, California, USA
- Publication Date:
- Research Org.:
- Univ. of California, Irvine, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1461716
- Alternate Identifier(s):
- OSTI ID: 1511016
- Grant/Contract Number:
- SC0016410
- Resource Type:
- Published Article
- Journal Name:
- mSphere
- Additional Journal Information:
- Journal Name: mSphere Journal Volume: 3 Journal Issue: 4; Journal ID: ISSN 2379-5042
- Publisher:
- American Society for Microbiology
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Illumina MiSeq, bacteria, exact sequence variants (ESVs), fungi, microbial ecology, operational taxonomic units (OTUs)
Citation Formats
Glassman, Sydney I., Martiny, Jennifer B. H., and Tringe, ed., Susannah Green. Broadscale Ecological Patterns Are Robust to Use of Exact Sequence Variants versus Operational Taxonomic Units. United States: N. p., 2018.
Web. doi:10.1128/mSphere.00148-18.
Glassman, Sydney I., Martiny, Jennifer B. H., & Tringe, ed., Susannah Green. Broadscale Ecological Patterns Are Robust to Use of Exact Sequence Variants versus Operational Taxonomic Units. United States. https://doi.org/10.1128/mSphere.00148-18
Glassman, Sydney I., Martiny, Jennifer B. H., and Tringe, ed., Susannah Green. Wed .
"Broadscale Ecological Patterns Are Robust to Use of Exact Sequence Variants versus Operational Taxonomic Units". United States. https://doi.org/10.1128/mSphere.00148-18.
@article{osti_1461716,
title = {Broadscale Ecological Patterns Are Robust to Use of Exact Sequence Variants versus Operational Taxonomic Units},
author = {Glassman, Sydney I. and Martiny, Jennifer B. H. and Tringe, ed., Susannah Green},
abstractNote = {Recent discussion focuses on the best method for delineating microbial taxa, based on either exact sequence variants (ESVs) or traditional operational taxonomic units (OTUs) of marker gene sequences. We sought to test if the binning approach (ESVs versus 97% OTUs) affected the ecological conclusions of a large field study. The data set included sequences targeting all bacteria (16S rRNA) and fungi (internal transcribed spacer [ITS]), across multiple environments diverging markedly in abiotic conditions, over three collection times. Despite quantitative differences in microbial richness, we found that all α and β diversity metrics were highly positively correlated (r> 0.90) between samples analyzed with both approaches. Moreover, the community composition of the dominant taxa did not vary between approaches. Consequently, statistical inferences were nearly indistinguishable. Furthermore, ESVs only moderately increased the genetic resolution of fungal and bacterial diversity (1.3 and 2.1 times OTU richness, respectively). We conclude that for broadscale (e.g., all bacteria or all fungi) α and β diversity analyses, ESV or OTU methods will often reveal similar ecological results. Thus, while there are good reasons to employ ESVs, we need not question the validity of results based on OTUs. Microbial ecologists have made exceptional improvements in our understanding of microbiomes in the last decade due to breakthroughs in sequencing technologies. These advances have wide-ranging implications for fields ranging from agriculture to human health. Due to limitations in databases, the majority of microbial ecology studies use a binning approach to approximate taxonomy based on DNA sequence similarity. There remains extensive debate on the best way to bin and approximate this taxonomy. Here we examine two popular approaches using a large field-based data set examining both bacteria and fungi and conclude that there are not major differences in the ecological outcomes. Thus, it appears that standard microbial community analyses are not overly sensitive to the particulars of binning approaches.},
doi = {10.1128/mSphere.00148-18},
journal = {mSphere},
number = 4,
volume = 3,
place = {United States},
year = {2018},
month = {8}
}
https://doi.org/10.1128/mSphere.00148-18
Web of Science
Figures / Tables:

Works referenced in this record:
Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters
journal, April 2017
- Needham, David M.; Sachdeva, Rohan; Fuhrman, Jed A.
- The ISME Journal, Vol. 11, Issue 7
Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences
journal, October 2014
- Eren, A. Murat; Morrison, Hilary G.; Lescault, Pamela J.
- The ISME Journal, Vol. 9, Issue 4
Microdiversity of an Abundant Terrestrial Bacterium Encompasses Extensive Variation in Ecologically Relevant Traits
journal, November 2017
- Chase, Alexander B.; Karaoz, Ulas; Brodie, Eoin L.
- mBio, Vol. 8, Issue 6
Sequence clustering threshold has little effect on the recovery of microbial community structure
journal, May 2018
- Botnen, Synnøve Smebye; Davey, Marie Louise; Halvorsen, Rune
- Molecular Ecology Resources, Vol. 18, Issue 5
PCR-Induced Sequence Artifacts and Bias: Insights from Comparison of Two 16S rRNA Clone Libraries Constructed from the Same Sample
journal, December 2005
- Acinas, S. G.; Sarma-Rupavtarm, R.; Klepac-Ceraj, V.
- Applied and Environmental Microbiology, Vol. 71, Issue 12
Taxonomic Note: A Place for DNA-DNA Reassociation and 16S rRNA Sequence Analysis in the Present Species Definition in Bacteriology
journal, October 1994
- Stackebrandt, E.; Goebel, B. M.
- International Journal of Systematic and Evolutionary Microbiology, Vol. 44, Issue 4
Extracellular enzyme kinetics and thermodynamics along a climate gradient in southern California
journal, November 2017
- Baker, Nameer R.; Allison, Steven D.
- Soil Biology and Biochemistry, Vol. 114
Microdiversity shapes the traits, niche space, and biogeography of microbial taxa: The ecological function of microdiversity
journal, March 2017
- Larkin, Alyse A.; Martiny, Adam C.
- Environmental Microbiology Reports, Vol. 9, Issue 2
Quantification of Bias Related to the Extraction of DNA Directly from Soils
journal, December 1999
- Frostegård, Åsa; Courtois, Sophie; Ramisse, Vincent
- Applied and Environmental Microbiology, Vol. 65, Issue 12
Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions
journal, September 2010
- Claesson, Marcus J.; Wang, Qiong; O'Sullivan, Orla
- Nucleic Acids Research, Vol. 38, Issue 22
Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns
journal, March 2017
- Amir, Amnon; McDonald, Daniel; Navas-Molina, Jose A.
- mSystems, Vol. 2, Issue 2
A global atlas of the dominant bacteria found in soil
journal, January 2018
- Delgado-Baquerizo, Manuel; Oliverio, Angela M.; Brewer, Tess E.
- Science, Vol. 359, Issue 6373
Multilocus sequence data reveal extensive phylogenetic species diversity within the Neurospora discreta complex
journal, May 2006
- Dettman, J. R.; Jacobson, D. J.; Taylor, J. W.
- Mycologia, Vol. 98, Issue 3
Taxonomic resolution, ecotypes and the biogeography of Prochlorococcus
journal, April 2009
- Martiny, Adam C.; Tai, Amos P. K.; Veneziano, Daniele
- Environmental Microbiology, Vol. 11, Issue 4
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
journal, October 2009
- Schloss, P. D.; Westcott, S. L.; Ryabin, T.
- Applied and Environmental Microbiology, Vol. 75, Issue 23, p. 7537-7541
Exact sequence variants should replace operational taxonomic units in marker-gene data analysis
journal, July 2017
- Callahan, Benjamin J.; McMurdie, Paul J.; Holmes, Susan P.
- The ISME Journal, Vol. 11, Issue 12
QIIME allows analysis of high-throughput community sequencing data
journal, April 2010
- Caporaso, J. Gregory; Kuczynski, Justin; Stombaugh, Jesse
- Nature Methods, Vol. 7, Issue 5
UPARSE: highly accurate OTU sequences from microbial amplicon reads
journal, August 2013
- Edgar, Robert C.
- Nature Methods, Vol. 10, Issue 10
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
Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates
journal, January 2010
- Kunin, Victor; Engelbrektson, Anna; Ochman, Howard
- Environmental Microbiology, Vol. 12, Issue 1
DADA2: High-resolution sample inference from Illumina amplicon data
journal, May 2016
- Callahan, Benjamin J.; McMurdie, Paul J.; Rosen, Michael J.
- Nature Methods, Vol. 13, Issue 7