Microbial abundance analysis and phylogenetic adoption in functional metagenomics

Metagenomics is an unobtrusive science of studying uncultivated microbes sampled directly from an environment, e.g. soil, ocean, air, human body, or animals, etc. Functional metagenomics particularly deals with linking microbes to environmental derivations, such as classifying the role of human gut microbiome into a diseased or non-diseased state. Ongoing research in this area includes analyzing the structure of microbial communities, and relate it to functional analysis. We present an integrative experimental framework for functional metagenomics, including data driven (abundance count of microbial species) and knowledge driven (phylogenetic tree structure) contexts. Our related experiments, indicate that i) feature selection improves the performance of classifying human microbiome samples, ii) the classification of human microbiome remains a challenging problem while incorporating phylogenetic structures. For example, our best accuracy attained on the Costello body site (CBH) dataset with forehead and external ear as body sites, is 89.13 % with a non-phylogenetic model, and 78.26 % with a phylogenetic model. This forms a potential research direction of further exploration of space for incorporating phylogeny in microbial analysis and hence developing integrative computational models for deriving functional phenotypes, based on metagenomic sequencing data.