Construction of aligned database of dsrA, a gene encoding dissimilatory sulfite reductase alpha subunit, for metagenomic studies of sulfate-reducing bacteria

A sulfite reductase gene sequence database, which could facilitate analysis of metagenomic data of a functional gene from sulfate-reducing bacteria, is described. The database contains 127 aligned nucleotide sequences of a gene (dsrA), encoding a dissimilatory sulfite reductase alpha subunit, retrieved from Reference Sequence of GenBank that provides only well-annotated genome sequences. The dsrA gene sequences were screened for length and aligned using four multiple sequencing alignment programs, Mafft, Muscle, Mothur, and Clustal Omega. In addition to the dsrA gene sequences, 16S ribosomal RNA (rRNA) gene sequences for the bacterial species appearing in the database were also retrieved from the GenBank and aligned by a public database of SILVA in Mothur to examine any potential relationship between taxonomy of the bacteria and distribution of a functional gene. The aligned dsrA and 16S rRNA gene sequences were used to construct neighbor-joining phylogenetic trees for comparison of the alignments for relative agreement among the aligned sequence databases. This method of aligned reference database construction using public database can help provide better insight into microbial communities by suggesting an alternative approach of studying metagenomic analysis of functional genes involved in important ecological processes.