Novel bacterial Taxa in the human microbiome

Kristine M. Wylie, Rebecca M. Truty, Thomas J. Sharpton, Kathie A. Mihindukulasuriya, Yanjiao Zhou, Hongyu Gao, Erica Sodergren, George M. Weinstock, Katherine S. Pollard

Research output: Contribution to journalArticle

58 Citations (Scopus)

Abstract

The human gut harbors thousands of bacterial taxa. A profusion of metagenomic sequence data has been generated from human stool samples in the last few years, raising the question of whether more taxa remain to be identified. We assessed metagenomic data generated by the Human Microbiome Project Consortium to determine if novel taxa remain to be discovered in stool samples from healthy individuals. To do this, we established a rigorous bioinformatics pipeline that uses sequence data from multiple platforms (Illumina GAIIX and Roche 454 FLX Titanium) and approaches (whole-genome shotgun and 16S rDNA amplicons) to validate novel taxa. We applied this approach to stool samples from 11 healthy subjects collected as part of the Human Microbiome Project. We discovered several low-abundance, novel bacterial taxa, which span three major phyla in the bacterial tree of life. We determined that these taxa are present in a larger set of Human Microbiome Project subjects and are found in two sampling sites (Houston and St. Louis). We show that the number of false-positive novel sequences (primarily chimeric sequences) would have been two orders of magnitude higher than the true number of novel taxa without validation using multiple datasets, highlighting the importance of establishing rigorous standards for the identification of novel taxa in metagenomic data. The majority of novel sequences are related to the recently discovered genus Barnesiella, further encouraging efforts to characterize the members of this genus and to study their roles in the microbial communities of the gut. A better understanding of the effects of less-abundant bacteria is important as we seek to understand the complex gut microbiome in healthy individuals and link changes in the microbiome to disease.

Original languageEnglish (US)
Article numbere35294
JournalPLoS One
Volume7
Issue number6
DOIs
StatePublished - Jun 13 2012
Externally publishedYes

Fingerprint

Microbiota
Bioinformatics
Ports and harbors
Ribosomal DNA
Titanium
Metagenomics
Bacteria
Pipelines
Genes
Sampling
digestive system
Firearms
sampling
Computational Biology
titanium
Healthy Volunteers
bioinformatics
Genome
microbial communities
microbiome

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Wylie, K. M., Truty, R. M., Sharpton, T. J., Mihindukulasuriya, K. A., Zhou, Y., Gao, H., ... Pollard, K. S. (2012). Novel bacterial Taxa in the human microbiome. PLoS One, 7(6), [e35294]. https://doi.org/10.1371/journal.pone.0035294

Novel bacterial Taxa in the human microbiome. / Wylie, Kristine M.; Truty, Rebecca M.; Sharpton, Thomas J.; Mihindukulasuriya, Kathie A.; Zhou, Yanjiao; Gao, Hongyu; Sodergren, Erica; Weinstock, George M.; Pollard, Katherine S.

In: PLoS One, Vol. 7, No. 6, e35294, 13.06.2012.

Research output: Contribution to journalArticle

Wylie, KM, Truty, RM, Sharpton, TJ, Mihindukulasuriya, KA, Zhou, Y, Gao, H, Sodergren, E, Weinstock, GM & Pollard, KS 2012, 'Novel bacterial Taxa in the human microbiome', PLoS One, vol. 7, no. 6, e35294. https://doi.org/10.1371/journal.pone.0035294
Wylie KM, Truty RM, Sharpton TJ, Mihindukulasuriya KA, Zhou Y, Gao H et al. Novel bacterial Taxa in the human microbiome. PLoS One. 2012 Jun 13;7(6). e35294. https://doi.org/10.1371/journal.pone.0035294
Wylie, Kristine M. ; Truty, Rebecca M. ; Sharpton, Thomas J. ; Mihindukulasuriya, Kathie A. ; Zhou, Yanjiao ; Gao, Hongyu ; Sodergren, Erica ; Weinstock, George M. ; Pollard, Katherine S. / Novel bacterial Taxa in the human microbiome. In: PLoS One. 2012 ; Vol. 7, No. 6.
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