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Title: Broadscale Ecological Patterns Are Robust to Use of Exact Sequence Variants versus Operational Taxonomic Units

Abstract

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. IMPORTANCE Microbial ecologists have made exceptional improvements inmore » 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.« less

Authors:
 [1];  [2];  [3]
  1. Univ. of California, Irvine, CA (United States). Dept. of Ecology and Evolutionary Biology; Univ. of California, Riverside, CA (United States). Dept. of Microbiology and Plant Pathology
  2. Univ. of California, Irvine, CA (United States). Dept. of Ecology and Evolutionary Biology
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Publication Date:
Research Org.:
Univ. of California, Irvine, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1461716
Alternate Identifier(s):
OSTI ID: 1511016
Grant/Contract Number:  
SC0016410
Resource Type:
Journal Article: Published Article
Journal Name:
mSphere
Additional Journal Information:
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, 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, Susannah Green. Broadscale Ecological Patterns Are Robust to Use of Exact Sequence Variants versus Operational Taxonomic Units. United States. doi:10.1128/msphere.00148-18.
Glassman, Sydney I., Martiny, Jennifer B. H., and Tringe, Susannah Green. Wed . "Broadscale Ecological Patterns Are Robust to Use of Exact Sequence Variants versus Operational Taxonomic Units". United States. doi: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, Susannah Green},
abstractNote = {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. IMPORTANCE 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},
issn = {2379-5042},
number = 4,
volume = 3,
place = {United States},
year = {2018},
month = {7}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at 10.1128/msphere.00148-18

Citation Metrics:
Cited by: 6 works
Citation information provided by
Web of Science

Figures / Tables:

FIG 1 FIG 1: (A and B) Comparison of observed diversity for (A) bacteria and (B) fungi as assayed by the richness of 97% similar operational taxonomic units (OTUs) versus exact sequence variants (ESVs). Numbers are total observed richness after normalizing to 10,000 sequences per sample from three time points (16, 12,more » and 18 months). (C and D) Comparison of observed β diversity for (C) bacteria and (D) fungi as assayed by the Bray-Curtis dissimilarity for OTUs versus ESVs from three time points (16, 12, 18 months).« less

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Works referenced in this record:

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
  • DOI: 10.1128/AEM.01541-09

    Figures / Tables found in this record:

      Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.