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Cited by 981Genomics and Phylogenetic StudiesGut microbiota and healthMicrobial Community Ecology and Physiology

Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing

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Ranjan, Ravi, Rani, Asha, Metwally, Ahmed, McGee, Halvor S., Perkins, David L.·2016·Biochemical and Biophysical Research Communications
DOI 10.1016/j.bbrc.2015.12.083PMC PMC4830092
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Abstract

The human microbiome has emerged as a major player in regulating human health and disease. Translational studies of the microbiome have the potential to indicate clinical applications such as fecal transplants and probiotics. However, one major issue is accurate identification of microbes constituting the microbiota. Studies of the microbiome have frequently utilized sequencing of the conserved 16S ribosomal RNA (rRNA) gene. We present a comparative study of an alternative approach using whole genome shotgun sequencing (WGS). In the present study, we analyzed the human fecal microbiome compiling a total of 194.1 × 10(6) reads from a single sample using multiple sequencing methods and platforms. Specifically, after establishing the reproducibility of our methods with extensive multiplexing, we compared: 1) The 16S rRNA amplicon versus the WGS method, 2) the Illumina HiSeq versus MiSeq platforms, 3) the analysis of reads versus de novo assembled contigs, and 4) the effect of shorter versus longer reads. Our study demonstrates that whole genome shotgun sequencing has multiple advantages compared with the 16S amplicon method including enhanced detection of bacterial species, increased detection of diversity and increased prediction of genes. In addition, increased length, either due to longer reads or the assembly of contigs, improved the accuracy of species detection.

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  • These methodologies diverge substantially when characterizing fine-scale diversity patterns and community structural attributes, with shotgun metagenomic approaches offering enhanced taxonomic resolution, sensitivity, and specificity at species-level identification.

    “However, these methodologies diverge substantially when characterizing fine-scale diversity patterns and community structural attributes, with shotgun metagenomic approaches offering enhanced taxonomic resolution, sensitivity, and specificity at species-level identification149.”

    From Microbiome meets immunotherapy: unlocking the hidden predictors of immune checkpoint inhibitors (2025) · cites this paper as [149]

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Sorted by citations

Authors
Ranjan, R., Rani, A., Metwally, A., McGee, H. S., & Perkins, D. L.
Affiliations
University of Illinois Chicago (US)
Corresponding author
Perkins, David L.
ORCID
Venue
Biochemical and Biophysical Research Communications
Publisher
Elsevier BV
Published
2016-01
Volume
469
Issue
4
Pages
967-977
ISSN
0006-291X (ISSN-L)
DOI
10.1016/j.bbrc.2015.12.083
PMC
PMC4830092
OpenAlex
W2207819727
Cited by
981
References
3
Citations by year
2026: 82 · 2025: 112 · 2024: 125 · 2023: 91 · 2022: 119 · 2021: 143 · 2020: 132 · 2019: 85 · 2018: 50 · 2017: 29 · 2016: 12
FWCI
13.18
Type
journal article
Language
en
Open access
Licence
www.elsevier.com/tdm/userlicense/1.0/ (tdm)
Locations
  • Biochemical and Biophysical Research Communications (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
Funders
  • University of Illinois at Chicago
  • National Heart, Lung, and Blood Institute (R01HL081663)
  • National Institute of Allergy and Infectious Diseases (R01AI053878)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
  • Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Keywords
human microbiome, fecal microbiota, whole genome shotgun sequencing, 16S rRNA amplicon sequencing, species detection, microbial diversity, gene prediction, de novo assembly, read length, sequencing platform comparison, Illumina HiSeq, Illumina MiSeq, multiplexing
MeSH terms
Bacteria, Base Sequence, Chromosome Mapping, DNA, Bacterial, Humans, Molecular Sequence Data, RNA, Ribosomal, 16S, Sensitivity and Specificity, Reproducibility of Results, Sequence Analysis, DNA, Metagenome, Microbiota

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