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Ecological patterns are robust to use of exact sequence variants versus operational taxonomic units

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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ggplot2: Elegant Graphics for Data Analysis

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Extracellular enzyme kinetics and thermodynamics along a climate gradient in southern California

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Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

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Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences

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Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

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Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters

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A communal catalogue reveals Earth’s multiscale microbial diversity

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UPARSE: highly accurate OTU sequences from microbial amplicon reads

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DADA2: High-resolution sample inference from Illumina amplicon data

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QIIME allows analysis of high-throughput community sequencing data

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Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions

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Taxonomic Note: A Place for DNA-DNA Reassociation and 16S rRNA Sequence Analysis in the Present Species Definition in Bacteriology

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UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing

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Microdiversity shapes the traits, niche space, and biogeography of microbial taxa

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Taxonomic resolution, ecotypes and the biogeography of Prochlorococcus

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Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates

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UNITE: a database providing web‐based methods for the molecular identification of ectomycorrhizal fungi

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New primers to amplify the fungal ITS2 region - evaluation by 454-sequencing of artificial and natural communities

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A global atlas of the dominant bacteria found in soil

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Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

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Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB

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Estimation of diversity and community structure through restriction fragment length polymorphism distribution analysis of bacterial 16S rRNA genes from a microbial mat at an active, hydrothermal vent system, Loihi Seamount, Hawaii

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Quantification of Bias Related to the Extraction of DNA Directly from Soils

inferredcites →https://doi.org/10.1128/aem.71.12.8966-8969.2005openalex-snapshot

PCR-Induced Sequence Artifacts and Bias: Insights from Comparison of Two 16S rRNA Clone Libraries Constructed from the Same Sample

inferredcites →https://doi.org/10.1128/mbio.01809-17openalex-snapshot

Microdiversity of an Abundant Terrestrial Bacterium Encompasses Extensive Variation in Ecologically Relevant Traits

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Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns

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Microbial abundance and composition influence litter decomposition response to environmental change

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vegan: Community Ecology Package

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R: A Language and Environment for Statistical Computing

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Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton

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Primer and platform effects on 16S rRNA tag sequencing

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Evidence for Ecological Flexibility in the Cosmopolitan Genus Curtobacterium

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Multilocus sequence data reveal extensive phylogenetic species diversity within the Neurospora discreta complex

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Wetland soil history shapes microbial community composition, while hydrologic disturbance alters greenhouse gas fluxes

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Variations in terrestrial arthropod DNA metabarcoding methods recovers robust beta diversity but variable richness and site indicators

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The Effects of Social Experience on Host Gut Microbiome in Male Zebrafish ( Danio rerio )

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A rarefaction-without-resampling extension of PERMANOVA for testing presence–absence associations in the microbiome

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Dadasnake, a Snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology

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Functional traits of ectomycorrhizal trees influence their effects on surrounding soil organic matter properties

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Investigating microbiota differences across chronic pancreatitis, influenced by lifestyle and genetic determinants

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Arrive and wait: Inactive bacterial taxa contribute to perceived soil microbiome resilience after a multidecadal press disturbance

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Ectomycorrhizal fungi are influenced by ecoregion boundaries across Europe

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Over 2.5 million COI sequences in GenBank and growing

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Alpha-, beta-, and gamma-diversity of bacteria varies across habitats

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MetaWorks: A flexible, scalable bioinformatic pipeline for high-throughput multi-marker biodiversity assessments

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Fungal Endophytes in a Seed-Free Host: New Species That Demonstrate Unique Community Dynamics

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Comparison of metabarcoding taxonomic markers to describe fungal communities in fermented foods

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Family life and cadmium ingestion independently shape offspring microbiomes in a subsocial insect

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Putting COI Metabarcoding in Context: The Utility of Exact Sequence Variants (ESVs) in Biodiversity Analysis

inferred← citeshttps://doi.org/10.3389/fmicb.2023.1217750openalex-snapshot

Predicting environmental stressor levels with machine learning: a comparison between amplicon sequencing, metagenomics, and total RNA sequencing based on taxonomically assigned data

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