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Open Access Highly Accessed Research article

Microbiota diversity and gene expression dynamics in human oral biofilms

Alfonso Benítez-Páez12*, Pedro Belda-Ferre1, Aurea Simón-Soro1 and Alex Mira1*

Author Affiliations

1 Oral Microbiome Group – Department of Health and Genomics, Center for Advanced Research in Public Health (CSISP-FISABIO), Avda. Catalunya 21, 46020 Valencia, Spain

2 Bioinformatics Analysis Group – GABi. Centro de Investigación y Desarrollo en Biotecnología (CIDBIO), Bogotá, D.C 111221, Colombia

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BMC Genomics 2014, 15:311  doi:10.1186/1471-2164-15-311

Published: 27 April 2014

Abstract

Background

Micro-organisms inhabiting teeth surfaces grow on biofilms where a specific and complex succession of bacteria has been described by co-aggregation tests and DNA-based studies. Although the composition of oral biofilms is well established, the active portion of the bacterial community and the patterns of gene expression in vivo have not been studied.

Results

Using RNA-sequencing technologies, we present the first metatranscriptomic study of human dental plaque, performed by two different approaches: (1) A short-reads, high-coverage approach by Illumina sequencing to characterize the gene activity repertoire of the microbial community during biofilm development; (2) A long-reads, lower-coverage approach by pyrosequencing to determine the taxonomic identity of the active microbiome before and after a meal ingestion. The high-coverage approach allowed us to analyze over 398 million reads, revealing that microbial communities are individual-specific and no bacterial species was detected as key player at any time during biofilm formation. We could identify some gene expression patterns characteristic for early and mature oral biofilms. The transcriptomic profile of several adhesion genes was confirmed through qPCR by measuring expression of fimbriae-associated genes. In addition to the specific set of gene functions overexpressed in early and mature oral biofilms, as detected through the short-reads dataset, the long-reads approach detected specific changes when comparing the metatranscriptome of the same individual before and after a meal, which can narrow down the list of organisms responsible for acid production and therefore potentially involved in dental caries.

Conclusions

The bacteria changing activity during biofilm formation and after meal ingestion were person-specific. Interestingly, some individuals showed extreme homeostasis with virtually no changes in the active bacterial population after food ingestion, suggesting the presence of a microbial community which could be associated to dental health.

Keywords:
Dental plaque; Metatranscriptomics; Biofilm formation; Human microbiome; RT-qPCR; RNAseq