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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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COG distribution patterns of the niche-specific orthologous gene families.
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Fig7: COG distribution patterns of the niche-specific orthologous gene families.

Mentions: COG distribution patterns of the niche specific genes are presented in Figure 7. Certain COG categories like Transcription (K), Replication, recombination and repair (L), Cell wall/ membrane/ envelope biogenesis (M), are found in relatively higher frequencies (Figure 7), as compared to all other categories, among all habitats. Among the gene families found exclusively in the skin isolate, genes involved in Signal transduction mechanisms (T), Carbohydrate transport and metabolism (G) and Inorganic ion transport and metabolism (P) have significantly high frequencies (9.5%, p = 0.034, 11.6%, p = 0.007 & 10.2%, p = 0.016 respectively). GIT-specific gene families are significantly enriched in genes involved Signal transduction mechanisms (T, 7.5%, p = 0.106), Replication, recombination and repair (L, 12%, p = 0.007), Cell wall/membrane/envelope biogenesis (M, 10.3%, p = 0.016) and Transcription (K, 11.8%, p = 0.007), while genes under the category Cell wall/membrane/envelop biogenesis (M, 13.6%, p = 0.001) and Replication, recombination and repair are significantly (L, 11.6%, p = 0.007) more frequent among oral isolates (Figure 7). Interestingly enough, genes associated with Defense mechanisms (V, 0.7%, p = 0.005) are significantly underrepresented in the skin-specific families, as compared to those in exclusively present in GIT (4.4%, p = 0.178), oral cavity (4.4%, p = 0.178) and UGT isolates (5.5%, p = 0.180).Figure 7


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)

COG distribution patterns of the niche-specific orthologous gene families.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig7: COG distribution patterns of the niche-specific orthologous gene families.
Mentions: COG distribution patterns of the niche specific genes are presented in Figure 7. Certain COG categories like Transcription (K), Replication, recombination and repair (L), Cell wall/ membrane/ envelope biogenesis (M), are found in relatively higher frequencies (Figure 7), as compared to all other categories, among all habitats. Among the gene families found exclusively in the skin isolate, genes involved in Signal transduction mechanisms (T), Carbohydrate transport and metabolism (G) and Inorganic ion transport and metabolism (P) have significantly high frequencies (9.5%, p = 0.034, 11.6%, p = 0.007 & 10.2%, p = 0.016 respectively). GIT-specific gene families are significantly enriched in genes involved Signal transduction mechanisms (T, 7.5%, p = 0.106), Replication, recombination and repair (L, 12%, p = 0.007), Cell wall/membrane/envelope biogenesis (M, 10.3%, p = 0.016) and Transcription (K, 11.8%, p = 0.007), while genes under the category Cell wall/membrane/envelop biogenesis (M, 13.6%, p = 0.001) and Replication, recombination and repair are significantly (L, 11.6%, p = 0.007) more frequent among oral isolates (Figure 7). Interestingly enough, genes associated with Defense mechanisms (V, 0.7%, p = 0.005) are significantly underrepresented in the skin-specific families, as compared to those in exclusively present in GIT (4.4%, p = 0.178), oral cavity (4.4%, p = 0.178) and UGT isolates (5.5%, p = 0.180).Figure 7

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