Phylogenetic and Genomic Analyses of Bacterial Strains

For phylogenetic and sequence analyses, nucleotide sequences obtained from PCR products were corrected and assembled if necessary with SerialCloner2-6 (http://serialbasics.free.fr/Serial_Cloner.html) and 4peaks (http://nucleobytes.com/4peaks/). Sequences were aligned with the ClustalW algorithm (Chenna et al., 2003 (link)) in MEGA 6.0 (Tamura et al., 2013 (link)). Randomized Axelerated Maximum Likelihood (RAxML) (Stamatakis, 2014 (link)) or MEGA 6.0 (Tamura et al., 2013 (link)) were used for the construction of phylogenetic trees. Phylogenetic trees were visualized with FigTree v.1.4.3 (http://tree.bio.ed.ac.uk/software/figtree/) and edited with Adobe Illustrator CS5 (Adobe Systems, San José, CA, USA). In order to study genomic identity among strains, Average Nucleotide Identity (either based on MUMmer alignments, ANIm, or based on BLAST alignments, ANIb) was calculated with the JSpeciesWS online server (Richter et al., 2016 (link)). A distance dendrogram was generated by hierarchical cluster analysis of 100−% ANI matrices (Chan et al., 2012 (link)) with StataSE v.14.0 (StataCorp, College Station, TX, USA) after computation of Euclidean distances with the Average Linked method.