Species-level microbiome analysis using EzBioCloud
EzBioCloud 16S database is designed to be best performed for species-level identification even though there is a clear limitation due to the lack of differences. The combination of EzBioCloud and bioinformatics pipelines allows us a species-level exploration of human microbiome data as well as environmental samples. This article is based on EzBioCloud 16S database version mtp1.5 and QIIME pipeline.
A Faecalibacterium case
Let me bring up a case the genus Faecalibacterium. This genus is known as a major player in the human gut environment. Unfortunately, there is only one species that is officially recognized, that is, Faecalibacterium prausnitzii. In EzBioCloud, this genus is further classified into 48 species on the basis of 16S and genome sequences (Explore this). Below are the comparisons of bacterial composition between EzBioCloud and one of other databases.
Below is the compositional difference of a fecal microbiome sample between EzBioCloud and other databases. The genus level compositions are very similar for Faecalibacterium.
However, species-level compositional differences are dramatic (as below chart). Using EzBioCloud, we can identify 5 different Faecalibacterium species. Genome sequence data are available for some species (Explore more).
A Bacteroides case
Another human fecal sample rich in the genus Bacteroides, also a major inhabitant of the human gut. Again, compositions at the genus level are similar.
However, species-level compositions are significantly different from results between two databases. Please note that EzBioCloud has species which are recently described as well as uncultured phylotypes such as DQ798855_s.
The current EzBioCloud 16S database, ver. mtp1.5, contains 272 species of the genus Bacteroides and 557 species of the genus Prevotella. It is far larger than any other database at the species level classification.
To obtain your copy of EzBioCloud 16S database for QIIME/MOTHUR pipelines, please visit here.
Last edited on Jan. 10 2017 (JC)