Method

Acidobacterial sequences from silva release 119 (Quast 2012) were downloaded and mixed with sequences of 1997 in-house isolates. The sequences were de-replicated and it resulted in 12231 unique reference sequences. They were aligned with Infernal 1.1 (-notrunc -g -matchonly) (Nawrocki 2009) against its bacterial ssu model. The alignment was clustered with HPC-CLUST 1.1 (-t 0.9 -al true -dfunc nogap) (Rodrigues 2013) and it generated in total 5450 reference OTUs upon an identity cutoff of 97%. The query sequences were compared to the de-replicated reference seqeunces upon a 99% identity cutoff. Subsequently, query sequences were assigned to reference OTUs with a fractionated approach, in which each reference OTU got only a value equal to one divided by the amount of qualified hits.