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Novel bacterial taxa in the human microbiome
Kristine M Wylie1, Rebecca M Truty, Thomas J Sharpton
1The Genome Institute, Washington University School of Medicine, St Louis, Missouri, United States of America. kwylie@genome.wustl.edu
Plos One
|June 22, 2012
Summary
Researchers discovered novel, low-abundance bacterial taxa in the human gut microbiome using advanced bioinformatics. Rigorous validation confirmed these new species, enhancing our understanding of gut microbial diversity and health.
Area of Science:
- Microbiology
- Bioinformatics
- Genomics
Background:
- The human gut microbiome contains thousands of bacterial species.
- Advances in metagenomic sequencing have generated vast amounts of data from human stool samples.
- The extent of undiscovered bacterial taxa in the gut remains an open question.
Purpose of the Study:
- To identify novel bacterial taxa in the human gut microbiome.
- To assess if new species can be discovered in existing metagenomic data from healthy individuals.
- To establish rigorous standards for identifying novel taxa in metagenomic datasets.
Main Methods:
- Utilized metagenomic data from the Human Microbiome Project (HMP).
- Developed a bioinformatics pipeline integrating data from multiple sequencing platforms (Illumina, Roche 454) and approaches (whole-genome shotgun, 16S rDNA amplicons).
- Applied the pipeline to stool samples from 11 healthy HMP subjects for validation.
Main Results:
- Discovered several novel, low-abundance bacterial taxa spanning three major bacterial phyla.
- Confirmed the presence of these taxa in a broader set of HMP subjects and across different sampling sites.
- Demonstrated that rigorous multi-dataset validation is crucial to avoid overestimating novel taxa due to chimeric sequences.
Conclusions:
- Novel bacterial taxa with low abundance exist in the human gut microbiome.
- The genus Barnesiella is a significant source of novel sequences, warranting further characterization.
- Understanding less-abundant bacteria is vital for comprehending the healthy gut microbiome and its role in disease.
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