Dataset Information

Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives.

ABSTRACT: The mammalian gut is an attractive model for exploring the general question of how habitat impacts the evolution of gene content. Therefore, we have characterized the relationship between 16 S rRNA gene sequence similarity and overall levels of gene conservation in four groups of species: gut specialists and cosmopolitans, each of which can be divided into pathogens and non-pathogens. At short phylogenetic distances, specialist or cosmopolitan bacteria found in the gut share fewer genes than is typical for genomes that come from non-gut environments, but at longer phylogenetic distances gut bacteria are more similar to each other than are genomes at equivalent evolutionary distances from non-gut environments, suggesting a pattern of short-term specialization but long-term convergence. Moreover, this pattern is observed in both pathogens and non-pathogens, and can even be seen in the plasmids carried by gut bacteria. This observation is consistent with the finding that, despite considerable interpersonal variation in species content, there is surprising functional convergence in the microbiome of different humans. Finally, we observe that even within bacterial species or genera 16S rRNA divergence provides useful information about average conservation of gene content. The results described here should be useful for guiding strain selection to maximize novel gene discovery in large-scale genome sequencing projects, while the approach could be applied in studies seeking to understand the effects of habitat adaptation on genome evolution across other body habitats or environment types.

SUBMITTER: Zaneveld JR

PROVIDER: S-EPMC2896507 | biostudies-literature | 2010 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives.

Zaneveld Jesse R JR Lozupone Catherine C Gordon Jeffrey I JI Knight Rob R

Nucleic acids research 20100302 12

The mammalian gut is an attractive model for exploring the general question of how habitat impacts the evolution of gene content. Therefore, we have characterized the relationship between 16 S rRNA gene sequence similarity and overall levels of gene conservation in four groups of species: gut specialists and cosmopolitans, each of which can be divided into pathogens and non-pathogens. At short phylogenetic distances, specialist or cosmopolitan bacteria found in the gut share fewer genes than is ...[more]

PMID: 20197316

Similar Datasets

Project description:BackgroundAmong the gut microbiota, sulfate-reducing bacteria (SRB) is a kind of hydrogen-utilizing functional bacteria that plays an important role in intestinal hydrogen and sulfur metabolism. However, information is lacking regarding diversity and community structure of SRB in the gut of piglets. Middle cecum contents were collected from 6 Yorkshire and 6 Meishan piglets at postnatal days (PND) 14, 28 and 49. Piglets were weaned at PND28. Real-time quantitative PCR was performed to detect the number of SRB in the cecum based on dissimilatory sulfite reductase subunit A (dsrA) gene. Prior to real-time PCR, plasmid containing the dsrA gene was constructed and used as external standard to create a standard curve, from which the gene copies of dsrA were calculated. H2S concentration in the cecal contents was measured. Illumina PE250 sequencing of dsrA gene was used to investigate SRB diversity in cecum contents.ResultsThe qPCR results showed that the number of SRB at PND49 was significantly higher than that at PND28 in Meishan piglets. The concentration of H2S has no significant difference between piglet breeds and between different ages. The Illumina sequencing analysis revealed that the Chao1 richness index was significantly higher at PND49 than that at PND14 and PND28 in Yorkshire piglets. Based on dsrA gene similarities, Proteobacteria, Actinobacteria, and Firmicutes were identified at the phylum level, and most sequences were classified as Proteobacteria. At the genus level, most of sequences were classified as Desulfovibrio. At the species level, Desulfovibrio intestinalis was the predominant SRB in the piglet cecum. The relative abundance and the inferred absolute abundance of Faecalibacterium prausnitzii at PND49 were significantly higher than that at PND14 in Yorkshire piglets. Pig breeds did not affect the dsrA gene copies of SRB, diversity index and community pattern of SRB.ConclusionsSulfate-reducing bacteria are widely colonized in the cecum of piglets and D. intestinalis is the dominant SRB. The age of piglets, but not the pig breeds affects the diversity and community pattern of SRB.

Dataset Information

Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives.

Publications

Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure