Human-associated microbial communities are known to be highly diverse, comprising between hundreds and a thousand species, depending on the body area. The sheer numbers of species as well as the fastidious nature of most of these organisms make culture-based techniques both inefficient and challenging to study these communities. As a result, analyses of such communities are best accomplished by...

The mOTU profiler, or mOTUs for short, is a software tool that enables the profiling of microbial communities in terms their taxonomic composition, relative abundance metabolically active members, and diversity strain populations. To this end, it maintains database single-copy phylogenetic marker gene sequences, which are used as reference to short read metagenomic metatranscriptomic reads mapp...

"Phylogenetic profiling" is based on the hypothesis that during evolution functionally or physically interacting genes are likely to be inherited or eliminated in a codependent manner. Creating presence-absence profiles of orthologous genes is now a common and powerful way of identifying functionally associated genes. In this approach, correctly determining orthology, as a means of identifying ...