Abstract
BackgroundThe overall metabolic/functional potential of any given environmental niche is a function of the sum total of genes/proteins/enzymes that are encoded and expressed by various interacting microbes residing in that niche. Consequently, prior (collated) information pertaining to genes, enzymes encoded by the resident microbes can aid in indirectly (re)constructing/ inferring the metabolic/ functional potential of a given microbial community (given its taxonomic abundance profile). In this study, we present Vikodak—a multi-modular package that is based on the above assumption and automates inferring and/ or comparing the functional characteristics of an environment using taxonomic abundance generated from one or more environmental sample datasets. With the underlying assumptions of co-metabolism and independent contributions of different microbes in a community, a concerted effort has been made to accommodate microbial co-existence patterns in various modules incorporated in Vikodak.ResultsValidation experiments on over 1400 metagenomic samples have confirmed the utility of Vikodak in (a) deciphering enzyme abundance profiles of any KEGG metabolic pathway, (b) functional resolution of distinct metagenomic environments, (c) inferring patterns of functional interaction between resident microbes, and (d) automating statistical comparison of functional features of studied microbiomes. Novel features incorporated in Vikodak also facilitate automatic removal of false positives and spurious functional predictions.ConclusionsWith novel provisions for comprehensive functional analysis, inclusion of microbial co-existence pattern based algorithms, automated inter-environment comparisons; in-depth analysis of individual metabolic pathways and greater flexibilities at the user end, Vikodak is expected to be an important value addition to the family of existing tools for 16S based function prediction.Availability and ImplementationA web implementation of Vikodak can be publicly accessed at: http://metagenomics.atc.tcs.com/vikodak. This web service is freely available for all categories of users (academic as well as commercial).
Highlights
The field of metagenomics has significantly improved our overall understanding of the microbial world within and around us
Prior information pertaining to genes, enzymes encoded by the resident microbes can aid in indirectlyconstructing/ inferring the metabolic/ functional potential of a given microbial community
Validation experiments on over 1400 metagenomic samples have confirmed the utility of Vikodak in (a) deciphering enzyme abundance profiles of any KEGG metabolic pathway, (b) functional resolution of distinct metagenomic environments, (c) inferring patterns of functional interaction between resident microbes, and (d) automating statistical comparison of functional features of studied microbiomes
Summary
The field of metagenomics has significantly improved our overall understanding of the microbial world within and around us. The 16S approach helps in deciphering the taxonomic/microbial composition of a given environmental sample, thereby paving the way for performing specific diversity analysis and subsequent identification of environment-specific marker microbes. Besides helping in obtaining a taxonomic profile of the environmental sample under study, computational analysis of WGS data provides information at a functional level (i.e. types and relative abundances of genes encoded by various microbes in a given environment). Given the relatively higher costs associated with WGS sequencing (and the computational complexity of handling huge volumes of WGS data), a majority of metagenomic initiatives employ 16S sequencing for obtaining a quick comparative snap-shot of microbial diversity. Prior (collated) information pertaining to genes, enzymes encoded by the resident microbes can aid in indirectly (re)constructing/ inferring the metabolic/ functional potential of a given microbial community (given its taxonomic abundance profile). With the underlying assumptions of co-metabolism and independent contributions of different microbes in a community, a concerted effort has been made to accommodate microbial co-existence patterns in various modules incorporated in Vikodak
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