Microbial Eukaryotes

Characterization of fungal communities, in particular, is an active research area. In principle, the bioinformatics pipeline is the same for eukaryotic marker genes as for bacterial marker genes (Iliev et al., 2012). However, the lack of a standard marker gene and reference database means that the bioinformatics protocols are not standardized for 16S rRNA gene analysis. Although several marker gene options exist for fungi, the internal transcribed spacer (ITS) region of the 16S rRNA gene is generally preferred for obtaining high taxonomic resolution. The UNITE database (Abarenkov et al., 2010) is often used for ITS sequence-based analyses of fungal sequences. However, the ITS region is not amenable to alignments across distinct fungal taxa, so ITS-based fungal community studies frequently do not use phylogene…