PanGFR-HM: A Dynamic Web Resource for Pan-Genomic and Functional Profiling of Human Microbiome With Comparative Features
The conglomerate of microorganisms inhabiting various body-sites of human, known as the human microbiome, is one of the key determinants of human health and disease. Comprehensive pan-genomic and functional analysis approach for human microbiome components can enrich our understanding about impact o...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2018-10-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fmicb.2018.02322/full |
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| author | Narendrakumar M. Chaudhari Anupam Gautam Anupam Gautam Vinod Kumar Gupta Gagneet Kaur Gagneet Kaur Chitra Dutta Sandip Paul |
| author_facet | Narendrakumar M. Chaudhari Anupam Gautam Anupam Gautam Vinod Kumar Gupta Gagneet Kaur Gagneet Kaur Chitra Dutta Sandip Paul |
| author_sort | Narendrakumar M. Chaudhari |
| collection | DOAJ |
| description | The conglomerate of microorganisms inhabiting various body-sites of human, known as the human microbiome, is one of the key determinants of human health and disease. Comprehensive pan-genomic and functional analysis approach for human microbiome components can enrich our understanding about impact of microbiome on human health. By utilizing this approach we developed PanGFR-HM (http://www.bioinfo.iicb.res.in/pangfr-hm/) – a novel dynamic web-resource that integrates genomic and functional characteristics of 1293 complete microbial genomes available from Human Microbiome Project. The resource allows users to explore genomic/functional diversity and genome-based phylogenetic relationships between human associated microbial genomes, not provided by any other resource. The key features implemented here include pan-genome and functional analysis of organisms based on taxonomy or body-site, and comparative analysis between groups of organisms. The first feature can also identify probable gene-loss events and significantly over/under represented KEGG/COG categories within pan-genome. The unique second feature can perform comparative genomic, functional and pathways analysis between 4 groups of microbes. The dynamic nature of this resource enables users to define parameters for orthologous clustering and to select any set of organisms for analysis. As an application for comparative feature of PanGFR-HM, we performed a comparative analysis with 67 Lactobacillus genomes isolated from human gut, oral cavity and urogenital tract, and therefore characterized the body-site specific genes, enzymes and pathways. Altogether, PanGFR-HM, being unique in its content and functionality, is expected to provide a platform for microbiome-based comparative functional and evolutionary genomics. |
| first_indexed | 2024-12-22T05:18:42Z |
| format | Article |
| id | doaj.art-70a33034f03347eb994f9d00b95d4580 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-22T05:18:42Z |
| publishDate | 2018-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-70a33034f03347eb994f9d00b95d45802022-12-21T18:37:47ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2018-10-01910.3389/fmicb.2018.02322393468PanGFR-HM: A Dynamic Web Resource for Pan-Genomic and Functional Profiling of Human Microbiome With Comparative FeaturesNarendrakumar M. Chaudhari0Anupam Gautam1Anupam Gautam2Vinod Kumar Gupta3Gagneet Kaur4Gagneet Kaur5Chitra Dutta6Sandip Paul7Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, IndiaStructural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, IndiaDepartment of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Kolkata, IndiaStructural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, IndiaStructural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, IndiaDepartment of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Kolkata, IndiaStructural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, IndiaStructural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, IndiaThe conglomerate of microorganisms inhabiting various body-sites of human, known as the human microbiome, is one of the key determinants of human health and disease. Comprehensive pan-genomic and functional analysis approach for human microbiome components can enrich our understanding about impact of microbiome on human health. By utilizing this approach we developed PanGFR-HM (http://www.bioinfo.iicb.res.in/pangfr-hm/) – a novel dynamic web-resource that integrates genomic and functional characteristics of 1293 complete microbial genomes available from Human Microbiome Project. The resource allows users to explore genomic/functional diversity and genome-based phylogenetic relationships between human associated microbial genomes, not provided by any other resource. The key features implemented here include pan-genome and functional analysis of organisms based on taxonomy or body-site, and comparative analysis between groups of organisms. The first feature can also identify probable gene-loss events and significantly over/under represented KEGG/COG categories within pan-genome. The unique second feature can perform comparative genomic, functional and pathways analysis between 4 groups of microbes. The dynamic nature of this resource enables users to define parameters for orthologous clustering and to select any set of organisms for analysis. As an application for comparative feature of PanGFR-HM, we performed a comparative analysis with 67 Lactobacillus genomes isolated from human gut, oral cavity and urogenital tract, and therefore characterized the body-site specific genes, enzymes and pathways. Altogether, PanGFR-HM, being unique in its content and functionality, is expected to provide a platform for microbiome-based comparative functional and evolutionary genomics.https://www.frontiersin.org/article/10.3389/fmicb.2018.02322/fullcomparative genomicsdatabasefunctional profilehuman microbiomepan genomeweb resource |
| spellingShingle | Narendrakumar M. Chaudhari Anupam Gautam Anupam Gautam Vinod Kumar Gupta Gagneet Kaur Gagneet Kaur Chitra Dutta Sandip Paul PanGFR-HM: A Dynamic Web Resource for Pan-Genomic and Functional Profiling of Human Microbiome With Comparative Features Frontiers in Microbiology comparative genomics database functional profile human microbiome pan genome web resource |
| title | PanGFR-HM: A Dynamic Web Resource for Pan-Genomic and Functional Profiling of Human Microbiome With Comparative Features |
| title_full | PanGFR-HM: A Dynamic Web Resource for Pan-Genomic and Functional Profiling of Human Microbiome With Comparative Features |
| title_fullStr | PanGFR-HM: A Dynamic Web Resource for Pan-Genomic and Functional Profiling of Human Microbiome With Comparative Features |
| title_full_unstemmed | PanGFR-HM: A Dynamic Web Resource for Pan-Genomic and Functional Profiling of Human Microbiome With Comparative Features |
| title_short | PanGFR-HM: A Dynamic Web Resource for Pan-Genomic and Functional Profiling of Human Microbiome With Comparative Features |
| title_sort | pangfr hm a dynamic web resource for pan genomic and functional profiling of human microbiome with comparative features |
| topic | comparative genomics database functional profile human microbiome pan genome web resource |
| url | https://www.frontiersin.org/article/10.3389/fmicb.2018.02322/full |
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