ABSTRACT
BACKGROUND: Microbially mediated oral diseases can signal underlying HIV/AIDS progression in HIV-infected adults. The role of the oral microbiota in HIV-infected youth is not known. The Adolescent Master Protocol of the Pediatric HIV/AIDS Cohort Study is a longitudinal study of perinatally HIV-infected (PHIV) and HIV-exposed, uninfected (PHEU) youth. We compared oral microbiome levels and associations with caries or periodontitis in 154 PHIV and 100 PHEU youth. RESULTS: Species richness and alpha diversity differed little between PHIV and PHEU youth. Group differences in average counts met the significance threshold for six taxa; two Corynebacterium species were lower in PHIV and met thresholds for noteworthiness. Several known periodontitis-associated organisms (Prevotella nigrescens, Tannerella forsythia, Aggregatibacter actinomycetemcomitans, and Filifactor alocis) exhibited expected associations with periodontitis in PHEU youth, associations not observed in PHIV youth. In both groups, odds of caries increased with counts of taxa in four genera, Streptococcus, Scardovia, Bifidobacterium, and Lactobacillus. CONCLUSIONS: The microbiomes of PHIV and PHEU youth were similar, although PHIV youth seemed to have fewer "health"-associated taxa such as Corynebacterium species. These results are consistent with the hypothesis that HIV infection, or its treatment, may contribute to oral dysbiosis.
Subject(s)
Bacteria/classification , Bacteria/isolation & purification , Dental Caries/microbiology , HIV Infections/pathology , Mouth Mucosa/microbiology , Periodontitis/microbiology , Saliva/microbiology , Adolescent , Adult , Bacteria/genetics , Child , Cross-Sectional Studies , Female , Humans , Longitudinal Studies , Male , Microbiota , RNA, Ribosomal, 16S/genetics , Young AdultABSTRACT
Here, we present the draft genome sequence of the actinobacterium Curtobacterium sp. strain UCD-KPL2560, which was isolated from the running surface of an indoor track field house in Medford, MA, USA (42.409716°N, -71.115169°W). The genome assembly contains 3,480,487 bp in 156 contigs.
ABSTRACT
Dental caries is a major disease of the oral cavity with profound clinical significance. Caries results from a transition of a healthy oral microbiome into an acidogenic community of decreased microbial diversity in response to excessive dietary sugar intake. Microbiological cultivation, molecular identification, gene expression and metabolomic analyses show the importance of the entire microbial community in understanding the role of the microbiome in the pathology of caries.
Subject(s)
Dental Caries/microbiology , Microbiota/physiology , Mouth/microbiology , Acids , Biofilms , Dental Enamel/microbiology , Dentin/microbiology , Humans , Hydrogen-Ion Concentration , Microbial Interactions/physiology , Root Caries/microbiologyABSTRACT
The oral microbiome, the complex ecosystem of microbes inhabiting the human mouth, harbors several thousands of bacterial types. The proliferation of pathogenic bacteria within the mouth gives rise to periodontitis, an inflammatory disease known to also constitute a risk factor for cardiovascular disease. While much is known about individual species associated with pathogenesis, the system-level mechanisms underlying the transition from health to disease are still poorly understood. Through the sequencing of the 16S rRNA gene and of whole community DNA we provide a glimpse at the global genetic, metabolic, and ecological changes associated with periodontitis in 15 subgingival plaque samples, four from each of two periodontitis patients, and the remaining samples from three healthy individuals. We also demonstrate the power of whole-metagenome sequencing approaches in characterizing the genomes of key players in the oral microbiome, including an unculturable TM7 organism. We reveal the disease microbiome to be enriched in virulence factors, and adapted to a parasitic lifestyle that takes advantage of the disrupted host homeostasis. Furthermore, diseased samples share a common structure that was not found in completely healthy samples, suggesting that the disease state may occupy a narrow region within the space of possible configurations of the oral microbiome. Our pilot study demonstrates the power of high-throughput sequencing as a tool for understanding the role of the oral microbiome in periodontal disease. Despite a modest level of sequencing (~2 lanes Illumina 76 bp PE) and high human DNA contamination (up to ~90%) we were able to partially reconstruct several oral microbes and to preliminarily characterize some systems-level differences between the healthy and diseased oral microbiomes.
Subject(s)
Gene Expression Profiling , High-Throughput Nucleotide Sequencing/methods , Metagenome/genetics , Mouth/microbiology , Periodontal Diseases/genetics , Periodontal Diseases/microbiology , Actinomyces/drug effects , Actinomyces/genetics , Adult , Drug Resistance, Bacterial/drug effects , Drug Resistance, Bacterial/genetics , Genes, Bacterial/genetics , Genetic Variation/drug effects , Genetic Variation/genetics , Health , Humans , Metabolic Networks and Pathways/drug effects , Metabolic Networks and Pathways/genetics , Metagenome/drug effects , Metagenomics , Metals/pharmacology , Middle Aged , Mouth/drug effects , Periodontitis/genetics , Periodontitis/microbiology , RNA, Ribosomal, 16S/genetics , Reference Standards , Virulence Factors/metabolismABSTRACT
COMBREX (http://combrex.bu.edu) is a project to increase the speed of the functional annotation of new bacterial and archaeal genomes. It consists of a database of functional predictions produced by computational biologists and a mechanism for experimental biochemists to bid for the validation of those predictions. Small grants are available to support successful bids.
