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Divergences in gene repertoire among the reference Prevotella genomes derived from distinct body sites of human.

Gupta VK, Chaudhari NM, Iskepalli S, Dutta C - BMC Genomics (2015)

Bottom Line: Distribution of various functional COG categories differs significantly among the habitat-specific genes.Prevotella genomes derived from different body sites differ appreciably in gene repertoire, suggesting that these microbiome components might have developed distinct genetic strategies for niche adaptation within the host.Each individual microbe might also have a component of its own genetic machinery for host adaptation, as appeared from the huge number of singletons.

View Article: PubMed Central - PubMed

Affiliation: Structural Biology & Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata, 700032, India. vinodgupta299@gmail.com.

ABSTRACT

Background: The community composition of the human microbiome is known to vary at distinct anatomical niches. But little is known about the nature of variations, if any, at the genome/sub-genome levels of a specific microbial community across different niches. The present report aims to explore, as a case study, the variations in gene repertoire of 28 Prevotella reference genomes derived from different body-sites of human, as reported earlier by the Human Microbiome Consortium.

Results: The pan-genome for Prevotella remains "open". On an average, 17% of predicted protein-coding genes of any particular Prevotella genome represent the conserved core genes, while the remaining 83% contribute to the flexible and singletons. The study reveals exclusive presence of 11798, 3673, 3348 and 934 gene families and exclusive absence of 17, 221, 115 and 645 gene families in Prevotella genomes derived from human oral cavity, gastro-intestinal tracts (GIT), urogenital tract (UGT) and skin, respectively. Distribution of various functional COG categories differs significantly among the habitat-specific genes. No niche-specific variations could be observed in distribution of KEGG pathways.

Conclusions: Prevotella genomes derived from different body sites differ appreciably in gene repertoire, suggesting that these microbiome components might have developed distinct genetic strategies for niche adaptation within the host. Each individual microbe might also have a component of its own genetic machinery for host adaptation, as appeared from the huge number of singletons.

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Relative abundance and distribution of COG categories between core genome (blue bars), accessory genome (red bars) and singletons (green bars) ofPrevotella. (A) General COG categories, (B) Functional COG categories. Only orthologous gene families assigned by WebMGA server were used for analysis.
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Fig6: Relative abundance and distribution of COG categories between core genome (blue bars), accessory genome (red bars) and singletons (green bars) ofPrevotella. (A) General COG categories, (B) Functional COG categories. Only orthologous gene families assigned by WebMGA server were used for analysis.

Mentions: Our next objective was to assign core, accessory and unique genes of the PDGHM dataset to different functional categories, taking one representative sequence from each gene family. FigureĀ 6A shows the distribution of the major COG categories in these three groups of genes. Majority of the core genes belong to the Information storage and processing (34%) and Metabolism (36%) categories. On the contrary, a major portion (29%) of the singletons belongs to the category of Cellular processes and signaling.Figure 6


Divergences in gene repertoire among the reference Prevotella genomes derived from distinct body sites of human.

Gupta VK, Chaudhari NM, Iskepalli S, Dutta C - BMC Genomics (2015)

Relative abundance and distribution of COG categories between core genome (blue bars), accessory genome (red bars) and singletons (green bars) ofPrevotella. (A) General COG categories, (B) Functional COG categories. Only orthologous gene families assigned by WebMGA server were used for analysis.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4359502&req=5

Fig6: Relative abundance and distribution of COG categories between core genome (blue bars), accessory genome (red bars) and singletons (green bars) ofPrevotella. (A) General COG categories, (B) Functional COG categories. Only orthologous gene families assigned by WebMGA server were used for analysis.
Mentions: Our next objective was to assign core, accessory and unique genes of the PDGHM dataset to different functional categories, taking one representative sequence from each gene family. FigureĀ 6A shows the distribution of the major COG categories in these three groups of genes. Majority of the core genes belong to the Information storage and processing (34%) and Metabolism (36%) categories. On the contrary, a major portion (29%) of the singletons belongs to the category of Cellular processes and signaling.Figure 6

Bottom Line: Distribution of various functional COG categories differs significantly among the habitat-specific genes.Prevotella genomes derived from different body sites differ appreciably in gene repertoire, suggesting that these microbiome components might have developed distinct genetic strategies for niche adaptation within the host.Each individual microbe might also have a component of its own genetic machinery for host adaptation, as appeared from the huge number of singletons.

View Article: PubMed Central - PubMed

Affiliation: Structural Biology & Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata, 700032, India. vinodgupta299@gmail.com.

ABSTRACT

Background: The community composition of the human microbiome is known to vary at distinct anatomical niches. But little is known about the nature of variations, if any, at the genome/sub-genome levels of a specific microbial community across different niches. The present report aims to explore, as a case study, the variations in gene repertoire of 28 Prevotella reference genomes derived from different body-sites of human, as reported earlier by the Human Microbiome Consortium.

Results: The pan-genome for Prevotella remains "open". On an average, 17% of predicted protein-coding genes of any particular Prevotella genome represent the conserved core genes, while the remaining 83% contribute to the flexible and singletons. The study reveals exclusive presence of 11798, 3673, 3348 and 934 gene families and exclusive absence of 17, 221, 115 and 645 gene families in Prevotella genomes derived from human oral cavity, gastro-intestinal tracts (GIT), urogenital tract (UGT) and skin, respectively. Distribution of various functional COG categories differs significantly among the habitat-specific genes. No niche-specific variations could be observed in distribution of KEGG pathways.

Conclusions: Prevotella genomes derived from different body sites differ appreciably in gene repertoire, suggesting that these microbiome components might have developed distinct genetic strategies for niche adaptation within the host. Each individual microbe might also have a component of its own genetic machinery for host adaptation, as appeared from the huge number of singletons.

Show MeSH
Related in: MedlinePlus