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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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Related in: MedlinePlus

Distribution of dispensable genome among 28Prevotellastrains. Colored cells indicate presence of genes in the respective Prevotella strain and orthologous gene family, while uncolored cells indicate absence of genes. The species names and cells are colored according to their niches - brown: GIT, green: ORAL Cavity, purple: SKIN and blue: UGT. Dark cell colors represent flexible genome and light cell colors represent singletons.
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Fig2: Distribution of dispensable genome among 28Prevotellastrains. Colored cells indicate presence of genes in the respective Prevotella strain and orthologous gene family, while uncolored cells indicate absence of genes. The species names and cells are colored according to their niches - brown: GIT, green: ORAL Cavity, purple: SKIN and blue: UGT. Dark cell colors represent flexible genome and light cell colors represent singletons.

Mentions: To investigate the genomic and proteomic diversity between Prevotella species adapted at different body sites of human, we have constructed the binary gene presence/absence matrices for orthologous gene families within these smaller niche-specific datasets. Interestingly enough, there are 19753 families showing habitat-specific presence, i.e., exclusive existence in the genomes isolated from a specific site of the human body (niche specific clusters). As depicted in Figure 2, there are 11798, 3673, 3348 and 934 gene clusters, which have members exclusively present in the Prevotella genomes derived from human oral cavity, GIT, UGT and skin, respectively (Table 2, Figure 2). It was not surprising to find largest number of habitat-specific gene families (11798) in oral isolates, since 17 genomes out of 28 in our study belonged to the oral cavity. A complete list of these niche-specific genes is shown in the (Additional file 4: Table S2).Figure 2


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)

Distribution of dispensable genome among 28Prevotellastrains. Colored cells indicate presence of genes in the respective Prevotella strain and orthologous gene family, while uncolored cells indicate absence of genes. The species names and cells are colored according to their niches - brown: GIT, green: ORAL Cavity, purple: SKIN and blue: UGT. Dark cell colors represent flexible genome and light cell colors represent singletons.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig2: Distribution of dispensable genome among 28Prevotellastrains. Colored cells indicate presence of genes in the respective Prevotella strain and orthologous gene family, while uncolored cells indicate absence of genes. The species names and cells are colored according to their niches - brown: GIT, green: ORAL Cavity, purple: SKIN and blue: UGT. Dark cell colors represent flexible genome and light cell colors represent singletons.
Mentions: To investigate the genomic and proteomic diversity between Prevotella species adapted at different body sites of human, we have constructed the binary gene presence/absence matrices for orthologous gene families within these smaller niche-specific datasets. Interestingly enough, there are 19753 families showing habitat-specific presence, i.e., exclusive existence in the genomes isolated from a specific site of the human body (niche specific clusters). As depicted in Figure 2, there are 11798, 3673, 3348 and 934 gene clusters, which have members exclusively present in the Prevotella genomes derived from human oral cavity, GIT, UGT and skin, respectively (Table 2, Figure 2). It was not surprising to find largest number of habitat-specific gene families (11798) in oral isolates, since 17 genomes out of 28 in our study belonged to the oral cavity. A complete list of these niche-specific genes is shown in the (Additional file 4: Table S2).Figure 2

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