Oral spirochetes implicated in dental diseases are widespread in normal human subjects and carry extremely diverse integron gene cassettes

Yu Wei Wu, Mina Rho, Thomas G. Doak, Yuzhen Ye

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

The NIH Human Microbiome Project (HMP) has produced several hundred metagenomic data sets, allowing studies of the many functional elements in human-associated microbial communities. Here, we survey the distribution of oral spirochetes implicated in dental diseases in normal human individuals, using recombination sites associated with the chromosomal integron in Treponema genomes, taking advantage of the multiple copies of the integron recombination sites (repeats) in the genomes, and using a targeted assembly approach thatwe have developed. We find that integron-containing Treponema species are present in 80%of the normal human subjects included in the HMP. Further, we are able to de novo assemble the integron gene cassettes using our constrained assembly approach, which employs a unique application of the de Bruijn graph assembly information;most of these cassette genes were not assembled in whole-metagenome assemblies and could not be identified by mapping sequencing reads onto the known reference Treponema genomes due to the dynamic nature of integron gene cassettes. Our studysignificantly enriches the gene pool known to be carried by Treponema chromosomal integrons, totaling 826 (598 97% nonredundant) enes. We characterize the functions of these gene cassettes: many of these genes have unknown functions. The integron gene cassette arrays found in the human microbiome are extraordinarily dynamic, with different microbial communities sharing only a small number of common genes.

Original languageEnglish
Pages (from-to)5288-5296
Number of pages9
JournalApplied and Environmental Microbiology
Volume78
Issue number15
DOIs
Publication statusPublished - Aug 2012
Externally publishedYes

Fingerprint

Integrons
Stomatognathic Diseases
Spirochaetales
Treponema
mouth
teeth
gene
Microbiota
Genes
genes
Genome
genome
Genetic Recombination
microbial communities
recombination
microbial community
Metagenome
Gene Pool
Metagenomics
Spirochaetes

ASJC Scopus subject areas

  • Applied Microbiology and Biotechnology
  • Food Science
  • Biotechnology
  • Ecology

Cite this

Oral spirochetes implicated in dental diseases are widespread in normal human subjects and carry extremely diverse integron gene cassettes. / Wu, Yu Wei; Rho, Mina; Doak, Thomas G.; Ye, Yuzhen.

In: Applied and Environmental Microbiology, Vol. 78, No. 15, 08.2012, p. 5288-5296.

Research output: Contribution to journalArticle

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