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Updated: May 17, 2026
11:22
Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
Published on: October 15, 2019
Species-level analysis of DNA sequence data from the NIH Human Microbiome Project
Sean Conlan1, Heidi H Kong, Julia A Segre
1Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America.
Plos One
|October 17, 2012
Summary
Genomic sequencing of the 16S rRNA gene from the Human Microbiome Project (HMP) accurately identified Staphylococcus aureus in healthy volunteers. This supports using genomic data for bacterial surveillance and infection control.
Area of Science:
- Microbiology
- Genomics
- Epidemiology
Background:
- Antibiotic-resistant bacterial infections necessitate robust surveillance of pathogenic bacteria.
- Genomic sequencing of clinical samples enhances the study of diverse bacterial communities, including uncultivable species.
- The study compares data from the National Institutes of Health's Human Microbiome Project (HMP) with existing Staphylococcus aureus surveillance data.
Purpose of the Study:
- To evaluate the utility of HMP 16S ribosomal RNA (rRNA) gene sequencing data for bacterial surveillance.
- To compare genomic surveillance findings with traditional culture-based epidemiological data for Staphylococcus aureus.
- To assess the species distribution of key bacterial genera (Staphylococcus, Klebsiella, Enterococcus) in healthy individuals.
Main Methods:
- Utilized deep sequencing of the 16S rRNA gene from the HMP dataset, encompassing samples from 242 healthy volunteers across five body regions.
- Developed a reference database and employed phylogenetic placement with most recent common ancestor classification for species-level identification.
- Compared HMP genomic data with published culture-based epidemiological surveillance data for Staphylococcus aureus.
Main Results:
- Accurate selection of 16S rRNA gene regions is crucial for distinguishing closely related bacterial species, similar to optimizing culture conditions.
- Staphylococcus aureus was detected in the nares of 36% of healthy volunteers, aligning with culture-based epidemiological findings.
- Klebsiella pneumoniae and Enterococcus faecalis were identified less frequently but were present across multiple body habitats.
Conclusions:
- Large-scale 16S rRNA gene sequencing studies can effectively support epidemiological surveillance goals.
- Genomic techniques are vital for understanding microbial evolution within complex communities and for implementing hospital infection control strategies.
- This research highlights the potential of genomic data to augment traditional methods in tracking bacterial pathogens.
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