The S rDNA sequence reads were processed using
The 16S rDNA sequence reads were processed using the MOTHUR software package (Schloss et al., 2009). The quality of all the sequence reads was assessed by using the PyroNoise algorithm implemented in MOTHUR and filtered according to the following criteria: minimal length of 425 bp, an exact match to the barcode, and 1 mismatch allowed to the proximal primer. The sequences were checked for the presence of chimeric amplifications using the UCHIME algorithm (Edgar et al., 2011). The resulting read sets were compared with SB 216763 reference data set of aligned sequences of the corresponding region derived from the SILVA database of full-length rDNA sequences (http://www.arb-silva.de/) implemented in MOTHUR (Pruesse et al., 2007). The final reads were clustered into operational taxonomic units (OTU) with the nearest neighbor algorithm using MOTHUR with a 0.03 distance unit cutoff. A taxonomic identity was attributed to each OTU by comparison with the SILVA database (80% homogeneity cutoff). As MOTHUR is not dedicated to taxonomic assignment beyond the genus level, all unique sequences for each OTU were compared with the SILVA data set (version 111), using the BLASTN algorithm (https://ezproxy.student.twu.ca:5726/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome (Altschul et al., 1990)). For each OTU, a consensus detailed taxonomic identification was given based upon the identity (less than 1% of mismatches with the aligned sequence) and the metadata associates with the most frequent hits (validated bacterial species or not).