Phylogenetic Analysis of Campylobacter Species

The phylogenetic analysis was performed using BEAST v2.6.4 of partial 16S rRNA sequence [30 (link)]. A ~649bp (final size after quality trim) sequences from the NCBI Genbank database was obtained of all known Campylobacter species [31 (link)]. Along with the sequences obtained from the NCBI database, 13 sequences (Genbank acc: MZ06810 to MZ068112) obtained from this study was also included to form a dataset of 16S rRNA partial sequences (S2 Table in S1 File). All the sequences were aligned using MUSCLE v3.8.425 [32 (link)] and was visualized in AliView v1.27 [33 (link)]. Model test for BEAST analysis was performed using Bmodel test v1.2.1 [34 (link)] for substitution model for 10 million iterations. The phylogenetic tree was prepared on BEAST v2.6.4 with HKY substitution model and YuleModel with 100 million iterations, every 1000 trees subsampling and discarding 25% of samples as burn-in. The log file from BEAST was analyzed using Tracer v1.7.2 [35 (link)] to verify all the parameter has effective sampling size (ESS) above 200 and tree was visualized/edited using Figtree v 1.4.4 [36 ]. Further, the mean genetic distance between our 13 unknown Campylobacter spp. samples and other Campylobacter spp. found in the neighboring clades from the phylogenetic analysis, were estimated through the Kimura 2-parameter (K2P) distance measure using MEGA 11 v11.0.10 [37 (link)].