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Cited by 575Microbial Community Ecology and PhysiologyGenomics and Phylogenetic StudiesEnvironmental DNA in Biodiversity Studies

The Madness of Microbiome: Attempting To Find Consensus “Best Practice” for 16S Microbiome Studies

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Pollock, Jolinda, Glendinning, Laura, Wisedchanwet, Trong, Watson, Mick·2018·Applied and Environmental Microbiology
DOI 10.1128/aem.02627-17PMC PMC5861821
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Abstract

The development and continuous improvement of high-throughput sequencing platforms have stimulated interest in the study of complex microbial communities. Currently, the most popular sequencing approach to study microbial community composition and dynamics is targeted 16S rRNA gene metabarcoding. To prepare samples for sequencing, there are a variety of processing steps, each with the potential to introduce bias at the data analysis stage. In this short review, key information from the literature pertaining to each processing step is described, and consequently, general recommendations for future 16S rRNA gene metabarcoding experiments are made.

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  • Recent efforts have been made to consolidate and standardize sequencing and analysis protocols to improve overall quality and compatibility of microbiome research.

    “Recent efforts have been made to consolidate and standardize sequencing and analysis protocols, to improve overall quality and compatibility of research in the microbiome field (Knight et al., 2018;Mallick et al., 2017;Pollock et al., 2018).”

    From The Microbiota-Gut-Brain Axis (2019) · cites this paper as Pollock et al., 2018

    The Introduction says the review collates research on 16S sequencing and analysis, and the Conclusions recommend consistent methods to minimize bias. That supports an effort to improve study quality. But the Conclusions also say there is little consensus and that comparisons between studies may not be possible, so the paper does not support the claim's implication of improved compatibility across microbiome research. (LLM, conf=0.84)

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Cited by

Sorted by citations

Authors
Pollock, J., Glendinning, L., Wisedchanwet, T., & Watson, M.
Affiliations
Roslin Institute (GB)
Corresponding author
Pollock, Jolinda
ORCID
Venue
Applied and Environmental Microbiology
Publisher
American Society for Microbiology
Published
2018-04
Volume
84
Issue
7
ISSN
  • 0099-2240 (ISSN-L)
  • 1098-5336
DOI
10.1128/aem.02627-17
PMC
PMC5861821
OpenAlex
W2786335128
Cited by
575
References
4
Citations by year
2026: 57 · 2025: 41 · 2024: 47 · 2023: 59 · 2022: 69 · 2021: 119 · 2020: 94 · 2019: 66 · 2018: 22 · 2015: 1
FWCI
7.94
Type
journal article
Language
en
Open access
Licence
Locations
  • Applied and Environmental Microbiology (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, cc-by)
Funders
RCUK | Biotechnology and Biological Sciences Research Council (BB/K501591/1, BB/N016742/1, BB/J01446X/1, BB/N01720X/1)
Topics
  • Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Physical Sciences › Environmental Science › Ecology › Environmental DNA in Biodiversity Studies
Keywords
16S rRNA metabarcoding, microbiome, microbial community composition, best practices, next-generation sequencing
MeSH terms
RNA, Bacterial, RNA, Ribosomal, 16S, Guidelines as Topic, DNA Barcoding, Taxonomic, Microbiota

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