Alphaproteobacteria accounted for 12% in colonised ACs which was four times more than in uncolonised ACs. Similar trends were seen in Pseudomonadales which accounted for 6.6% in colonised ACs and only 1.69% in uncolonised ACs. Colonised ACs contained more Betaproteobacteria/Burkholderiales (14.07%) than uncolonised ACs (8.99%). Similar proportions of Enterobacteriales, GSK2126458 Xanthomonadales and unclassified bacteria were observed in both groups. The difference between the overall
distributions of the taxonomic groups in colonised and uncolonised ACs was not statistically Sirtuin activator significant (p = 0.976). Figure 1 Division level distribution of 16S rRNA gene clone sequences in uncolonised and colonised ACs. OTU distribution among colonised and uncolonised ACs All of 417 sequences were grouped into OTUs based on their genetic distance in a neighbour-joining tree with the DOTUR program. Using the furthest-neighbour method of calculation and a similarity threshold of 97%, DOTUR assigned the 417 sequences into 79 OTUs. There is an average of 20 OTUs from each ACs including uncolonised and colonised devices. Approximately one quarter of the OTUs (21) were composed of a single sequence. However, three OTUs contained 30 or more sequences. The majority of OTUs and sequences
belong to the division Proteobacteria with 86.1% and 95.9%, respectively for colonised and uncolonised ACs. The largest three OTUs, a member of the division Gammaproteobacteria and family Xanthomonadaceae, contained 191 sequences (45.8%). Other common Proteobacteria OTUs indentified included filipin Enterobacteriaceae,
Pseudomonadaceae, Sphingomonadaceae, Comamonadaceae, Burkholderiaceae, Oxalobacteraceae, selleck kinase inhibitor Caulobacteraceae, Phyllobacteriaceae, and Bradyrhizobiaceae (Figure 2). OTUs and sequences were also identified from the division Firmicutes (11.4% and 4%, between colonised and uncolonised ACs respectively) including species of the family Veillonellaceae, Staphylococcaceae, and Streptococcaceae. We also identified two novel OTUs that were < 93% similar to any sequences in GenBank. These two OTUs were 92% and 91% similar to unknown clones from environmental samples. Overall there were 51 OTUs for colonised ACs and 44 OTUs uncolonised ACs. There were 33 and 27 single- and double-sequence OTUs for colonised and uncolonised ACs. Of the 79 OTUs identified in the two sets of samples, 40 (50.6%) were identified in both groups. However, these 40 OTUs represent 339 of 417 sequences (81.5%) of the clones. There was no significant difference between the distribution of sequences generated from colonised and uncolonised ACs in OTUs (p = 0.316). Figure 2 Diversity of OTUs and their abundances in 16S rRNA gene clone libraries. The taxonomic identity of each OTU was identified by phylogenetic analyses of the partial 16S rRNA gene sequences after separating them into the major bacterial phyla. A total of 79 OTUs were shown but not all the species names were labelled.