Evaluation of 16S rDNA-Based Community Profiling for Human Microbiome Research
Open accessAbstract
The Human Microbiome Project will establish a reference data set for analysis of the microbiome of healthy adults by surveying multiple body sites from 300 people and generating data from over 12,000 samples. To characterize these samples, the participating sequencing centers evaluated and adopted 16S rDNA community profiling protocols for ABI 3730 and 454 FLX Titanium sequencing. In the course of establishing protocols, we examined the performance and error characteristics of each technology, and the relationship of sequence error to the utility of 16S rDNA regions for classification- and OTU-based analysis of community structure. The data production protocols used for this work are those used by the participating centers to produce 16S rDNA sequence for the Human Microbiome Project. Thus, these results can be informative for interpreting the large body of clinical 16S rDNA data produced for this project.
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Technical variability between studies in microbiome measurements can sometimes exceed biological effects.
“Inter-study technical variability in microbiome measurements can sometimes, for example, outweigh biological effects6–9.”
From Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium (2017) · cites this paper as [7]
DNA extraction protocols are a known source of variation in microbial community characterization experiments.
“DNA extraction protocols are a known source of variation between microbial community characterization experiments7–9.”
From Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium (2017) · cites this paper as [7]
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Bacterial Communities of the Coronal Sulcus and Distal Urethra of Adolescent Males
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Analysis of soil microbial communities based on amplicon sequencing of marker genes
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Performing Skin Microbiome Research: A Method to the Madness
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Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling
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“All species were detected in both regions, apart from Methanobrevibacter which neither regions amplified [34].”
BackgroundThe Dental Plaque Microbiome in Health and Disease
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“This composition is consistent with data generated as part of the HMP consortium surveys [34–36].”
ResultReference standards for next-generation sequencing
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Capturing the diversity of the human gut microbiota through culture-enriched molecular profiling
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Tick microbiome and pathogen acquisition altered by host blood meal
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The antipsychotic olanzapine interacts with the gut microbiome to cause weight gain in mouse
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Pregnancy's Stronghold on the Vaginal Microbiome
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MixMC: A Multivariate Statistical Framework to Gain Insight into Microbial Communities
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“While many published analyses have focused on the main microbial habitats (gut, oral cavity, skin and vagina from the [24, 47]), little has been done to comprehensively characterise multiple sites within a single habitat.”
BackgroundMeta'omic Analytic Techniques for Studying the Intestinal Microbiome
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Survival in hostile territory: the microbiota of the stomach
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SPINGO: a rapid species-classifier for microbial amplicon sequences
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“Variable regions V1-V3 (6,046 sequences), V3-V5 (5,860) and V6-V9 (5,241) were extracted from the SILVA database using previously described primers [11] with the V-ripper script and subsequently classified using the evaluation database not containing the 9,607 test sequences.”
MethodMicrobial phylogenetic profiling with the Pacific Biosciences sequencing platform
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Kubinak, J. L., Stephens, W. Z., Soto, R., Petersen, C., Chiaro, T. R., Gogokhia, L., Bell, R. S., Ajami, N. J., Petrosino, J. F., Morrison, L. C., et al. (2015) · Nature Communications · doi:10.1038/ncomms9642 · Cited by 158 · see citing works
“The 16S rRNA gene libraries were generated by the Center for Metagenomics and Microbiome Research at Baylor College of Medicine, using the V3-V5 (357F/926R) primer in accordance with standard HMP protocols 50 .”
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Modulation of the faecal microbiome of healthy adult dogs by inclusion of potato fibre in the diet
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Impact of Preservation Method and 16S rRNA Hypervariable Region on Gut Microbiota Profiling
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Tiny microbes, enormous impacts: what matters in gut microbiome studies?
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Ancient DNA analysis of dental calculus
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Urinary Microbiome and Cytokine Levels in Women With Interstitial Cystitis
Abernethy, M., Rosenfeld, A. B., White, J. R., Mueller, M. G., Lewicky‐Gaupp, C., & Kenton, K. S. (2017) · Obstetrics and Gynecology · doi:10.1097/aog.0000000000001892 · Cited by 135 · see citing works
The Perinatal Microbiome and Pregnancy: Moving Beyond the Vaginal MicrobiomePreprint
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“This can result in differences in taxonomic resolution (Ward et al., 2012).”
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Fecal Microbiota Analysis: An Overview of Sample Collection Methods and Sequencing Strategies
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Next generation sequencing data of a defined microbial mock community
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Metagenomic Surveys of Gut Microbiota
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What Is Metagenomics Teaching Us, and What Is Missed?
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Oral Microbiome of Deep and Shallow Dental Pockets In Chronic Periodontitis
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Wind and sunlight shape microbial diversity in surface waters of the North Pacific Subtropical Gyre
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Bioinformatics for the Human Microbiome Project
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The vaginal eukaryotic DNA virome and preterm birth
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- Authors
- Jumpstart Consortium Human Microbiome Project Data Generation Working Group
- Affiliations
- University of Maryland, Baltimore (US)
- Corresponding author
- Jumpstart Consortium Human Microbiome Project Data Generation Working Group
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2012-06-13
- Volume
- 7
- Issue
- 6
- Pages
- e39315
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC3374619
- OpenAlex
- W2319405466
- Cited by
- 297
- References
- 38
- Citations by year
- 2026: 2 · 2025: 5 · 2024: 5 · 2023: 8 · 2022: 6 · 2021: 22 · 2020: 17 · 2019: 27 · 2018: 22 · 2017: 35 · 2016: 31 · 2015: 39 · 2014: 31 · 2013: 34 · 2012: 12
- FWCI
- 14.90
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS ONE (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Figshare (submittedVersion, cc-by)
- Funders
- Broad Institute
- National Institutes of Health
- U.S. Public Health Service (HHSN2722009000018C)
- National Human Genome Research Institute (U54HG004969, U54HG003079, U01HG004866, U54HG003273, U54HG004968, U54HG004973)
- National Institute of Allergy and Infectious Diseases (HHSN272200900018C, HHSN272200900001C, HHSN272200900008C, U54AI084844)
- 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
- 16S rRNA gene, human microbiome, Human Microbiome Project, sequencing errors, community structure, reference dataset
- MeSH terms
- Bacteria, Bayes Theorem, Humans, RNA, Ribosomal, 16S, Metagenome
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