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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 evolutionary divergence ofPrevotella. (A) Neighbor Joining (NJ) tree based on 28 Prevotella and E. Coli 83972 (reference) 16S rRNA sequences, was constructed using MEGA 6 after 1000 bootstrap replications, (B) NJ Tree based on the binary gene presence/absence matrix of orthologous gene families of 28 Prevotella and 3 Bacteroides strains and (C) NJ tree based on core genome using 100 bootstrap replications. The bootstrap values are marked at the root of each branch of trees. The species names are colored according to their niches (brown: GIT, green: ORAL Cavity, purple: SKIN and blue: UGT).
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Fig3: Relative evolutionary divergence ofPrevotella. (A) Neighbor Joining (NJ) tree based on 28 Prevotella and E. Coli 83972 (reference) 16S rRNA sequences, was constructed using MEGA 6 after 1000 bootstrap replications, (B) NJ Tree based on the binary gene presence/absence matrix of orthologous gene families of 28 Prevotella and 3 Bacteroides strains and (C) NJ tree based on core genome using 100 bootstrap replications. The bootstrap values are marked at the root of each branch of trees. The species names are colored according to their niches (brown: GIT, green: ORAL Cavity, purple: SKIN and blue: UGT).

Mentions: In an attempt to elucidate the relative importance of lineage-specific divergences and niche-specific selections in shaping the gene architectures of the PDGHM, we have constructed three Neighbor Joining (NJ) Trees (Figure 3). The first one is the traditional phylogenetic tree generated from 16S rRNA sequences (Figure 3A), the second tree is based on the binary gene presence/absence matrix (Figure 3B) and the third one has been constructed using concatenated alignments of core genes (Figure 3C). In all three trees, E. coli has been taken as the outgroup species and 3 GIT-derived Bacteroides genomes have been included in an attempt to see whether the GIT-derived genomes of Prevotella and Bacteroides cluster together. These 3 Bacteroides genomes are selected as they are similar in genomic properties like GC content and genome size to that of GIT derived Prevotella isolates. Bacteroides from other body sites are not included in our analysis due to unavailability of complete genome sequences. Sequences isolated from the gut, oral cavity, skin and urogenital tract are highlighted in brown, green, purple and blue color respectively.Figure 3


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 evolutionary divergence ofPrevotella. (A) Neighbor Joining (NJ) tree based on 28 Prevotella and E. Coli 83972 (reference) 16S rRNA sequences, was constructed using MEGA 6 after 1000 bootstrap replications, (B) NJ Tree based on the binary gene presence/absence matrix of orthologous gene families of 28 Prevotella and 3 Bacteroides strains and (C) NJ tree based on core genome using 100 bootstrap replications. The bootstrap values are marked at the root of each branch of trees. The species names are colored according to their niches (brown: GIT, green: ORAL Cavity, purple: SKIN and blue: UGT).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig3: Relative evolutionary divergence ofPrevotella. (A) Neighbor Joining (NJ) tree based on 28 Prevotella and E. Coli 83972 (reference) 16S rRNA sequences, was constructed using MEGA 6 after 1000 bootstrap replications, (B) NJ Tree based on the binary gene presence/absence matrix of orthologous gene families of 28 Prevotella and 3 Bacteroides strains and (C) NJ tree based on core genome using 100 bootstrap replications. The bootstrap values are marked at the root of each branch of trees. The species names are colored according to their niches (brown: GIT, green: ORAL Cavity, purple: SKIN and blue: UGT).
Mentions: In an attempt to elucidate the relative importance of lineage-specific divergences and niche-specific selections in shaping the gene architectures of the PDGHM, we have constructed three Neighbor Joining (NJ) Trees (Figure 3). The first one is the traditional phylogenetic tree generated from 16S rRNA sequences (Figure 3A), the second tree is based on the binary gene presence/absence matrix (Figure 3B) and the third one has been constructed using concatenated alignments of core genes (Figure 3C). In all three trees, E. coli has been taken as the outgroup species and 3 GIT-derived Bacteroides genomes have been included in an attempt to see whether the GIT-derived genomes of Prevotella and Bacteroides cluster together. These 3 Bacteroides genomes are selected as they are similar in genomic properties like GC content and genome size to that of GIT derived Prevotella isolates. Bacteroides from other body sites are not included in our analysis due to unavailability of complete genome sequences. Sequences isolated from the gut, oral cavity, skin and urogenital tract are highlighted in brown, green, purple and blue color respectively.Figure 3

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