The human body is host to a large conglomerate of microorganisms, including bacteria, archaea, viruses, and fungi, that occupy different niches and collectively known as microbiome. Bacteria form a major part of human microbiome. These microorganisms are vital for human survival and well being and play highly active and supportive role for various metabolic processes and functions that human system is unable to perform.
The figure showing major human microbiome species: The examples of highly diverse habitats are human intestines/gut showing presence of 500 to 1000 bacterial species and skin containing over 1000 bacterial species, followed by over 600 species in oral cavity and respiratory system.
The Human Microbiome Project (HMP) pioneered large scale characterization of the commensal microorganisms from all major body locations (body sites). This was immensely useful novel information and data which was helpful in various kinds of research endeavors since past decade. The metagenomic sequencing of thousands of such samples helped us to understand what is present and what are they doing inside human system.
What is Pan Genome?
Pan Genome is the complete gene repertoire, typically of a species having multiple sequenced strains. The pan genome is the non-redundant set of genes consisting of Core/Conserved Genes (shared among all the strains of a species), Accessory/Mosaic Genes (shared among more than one but not all strains) and Unique/Singleton Genes (specific to individual strains not shared elsewhere.)
A figure illustrating the pan genome concept: The schematic shows pan genome of 3 strains of a bacterial species, indicated by different colors. The core, accessory and unique sets of the pan genome are labeled with respective titles. The visible area of the circles collectively referred to as "The Pan Genome".
About PanGFR-HM Web Resource
PanGFR-HM is the resource which combines the above two contexts and provides quick estimates pan genomic and functional repertoire of the microbial strains exclusively from human microbiome. The resource can estimate pan genomes along with functional repertoire of microbial species from ~1300 Microbial Reference Genomes of strains isolated from samples among various body sites of human body, available at Human Microbiome Project - Data Analysis and Coordination Center.
The three distinct modules of PanGFR-HM provides various options to group the microbiome strains by three means i.e. taxonomy, body-site of isolation or any other grouping criterion for comparative gene and comparative function analysis among these groups.
SIGNIFICANCE & OUTCOME:
This resource will enable researchers focusing on studying the functional repertoire of microbial species within human microbiome where they can apply concepts of pan genome to understand the shared gene repertoire of human associated strains. The body site wise gene repertoire among bacterial strains may help to get crucial clues about body site specific (niche/habitat specific) adaptive evolution in terms of enzymes and metabolic pathways.
The comparative analysis might be essential to illustrate the functional cooperation among related taxa or groups by providing shared and dispensable gene content or functional and metabolic repertoire of these groups.
The in-depth studies based on whole genomes of strains of a microbiome species or genera are still very few. This resorce will encourage researchers to focus on essential and ubiquitous microbes at various taxonomic levels and enable them to look into intricate details of those microbiota.