title: Vikodak--A Modular Framework for Inferring Functional Potential of Microbial Communities from 16S Metagenomic Datasets.
abstract: BACKGROUND
  The 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.
  
  
  RESULTS
  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. Novel features incorporated in Vikodak also facilitate automatic removal of false positives and spurious functional predictions.
  
  
  CONCLUSIONS
  With 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.
  
  
  METHODS
  A 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).
authors: Bio-Sciences R&D Division, TCS Innovation Labs, Tata Research Development & Design Centre, 54-B, Hadapsar Industrial Estate, Pune 411 013, Maharashtra, India.
authors: Sunil
authors: S
authors: Nagpal
authors: Bio-Sciences R&D Division, TCS Innovation Labs, Tata Research Development & Design Centre, 54-B, Hadapsar Industrial Estate, Pune 411 013, Maharashtra, India.
authors: Mohammed Monzoorul
authors: MM
authors: Haque
authors: Bio-Sciences R&D Division, TCS Innovation Labs, Tata Research Development & Design Centre, 54-B, Hadapsar Industrial Estate, Pune 411 013, Maharashtra, India.
authors: Sharmila S
authors: SS
authors: Mande
mesh_terms: D000465:Algorithms; D057205:Automation, Laboratory; D053858:Metabolic Networks and Pathways / Q000235:genetics* / Q000502:physiology; D054892:Metagenome / Q000235:genetics*; D056186:Metagenomics / Q000379:methods*; D064307:Microbiota / Q000235:genetics* / Q000502:physiology; D012336:RNA, Ribosomal, 16S / Q000235:genetics
chemical_list: D012336:RNA, Ribosomal, 16S