Vast majority of sequence data has led to the emergence of new field called comparative metagenomics. This study provides an insight into the structural and functioning of microbial communities. A lot of challenges in this area have been dealt with learning algorithms known in literature. Inherent properties of the metagenomic data has not been taken into account in any of the past studies.
Tanaseichuk et. al. (2014) have proposed a new method of classification of microbial communities based on frequency of operational taxonomic units (OTUs) .Environmental specific compositional patterns have also been taken care of in the present study. They have also kept a provision for simulation of 16s ribosomal RNA readouts which will be useful for comparative metagenomic research. For more on this you can go through the following site http://www.cs.ucr.edu/tanaseio/ metaphyl.htm.
Tanaseichuk, O. (2014). Phylogeny based classification of microbial communities.Bioinformatics 30(4)449-456.