PanGFR-HM: A Dynamic Web Resource for Pan-Genomic and Functional Profiling of Human Microbiome With Comparative Features.

Narendrakumar M Chaudhari,Chitra Dutta,Sandip Paul,Vinod Kumar Gupta,Gagneet Kaur,Anupam Gautam

doi:10.3389/fmicb.2018.02322

Abstract

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.

Highlights

The variety of microorganisms inhabiting different body-sites of human – is one of the key determinants of human health and disease
All 1293 strains belong to 8 major bacterial/archaeal phyla, i.e., Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, Proteobacteria, Spirochaetes, Synergistetes, and Euryarchaeota. These genomes represent 187 different defined genera. These microbes, as part of human microbiome, comprise mostly of bacteria derived from distinct body-sites of human (Detailed list of microbial species is provided in Supplementary Table S1)
Gene families generated from all annotated proteins from complete genomes of these microbes were integrated into a database, where pan-genomic details of any subset of these microbial strains belonging to specific taxonomical clade or body-site, can be dynamically retrieved

Summary

Introduction

The variety of microorganisms inhabiting different body-sites of human – is one of the key determinants of human health and disease. Various reports reveal that the comparative pan-genome analysis has tremendous potential for offering new perspective on the species diversity and adaptive strategies of human microbiome in body-site specific manner (Rasko et al, 2008; Conlan et al, 2012; Gupta et al, 2015; Bakshi et al, 2016; Duranti et al, 2016). A comprehensive resource of human microbiome providing in-depth pan-genomic analysis of strains at various taxonomic levels, with subsequent estimation of the functional repertoire from same or different body-sites along with comparative analysis approach will be of great interest

Methods

Results

Conclusion