We use MEGAN6 to generate microbiome reports along with a host of other analytical and visualization tools. Here is an example of a microbiome report from MEGAN6.
Fig. 1 shows a phylogram of a human nasopharyngeal sample displayed with MEGAN6. This particular figure shows a phylogenetic tree of all organisms at the Class level. In MEGAN6 you can drill-up or drill-down in the Linnean hierarchy from the Domain level to the Species level. Below the Class level the number of organisms is too large to easily display here. This sample included 1,000+ identified species, which is far too great to show in its entirety here.
For many microbiome projects we use the NCBI non-redundant nucleotide database for species identification. This database includes taxonomic classifications down to the subspecies and strain level for many organisms. Thus, MEGAN6 can often identify organisms to this level. Fig. 2 shows a single Genus, Porphyromonas, down to the species and strain level.
As shown in Fig. 3, MEGAN6 can generate rarefaction curves to estimate species richness. Rarefaction curves plot the number of species as a function of the number of samples (i.e. reads). We expect the curve to go asymptotic if the community has been sufficiently sampled, which appears to be the case for our case study.
MEGAN6 has a rich set of functionality beyond species identification. These additional functions are too numerous to list here but you can check the Users Manual to see if any functions might be useful in your research.