I want to compare our strains VGH107 with other S. marcescen strains phylogenetic relationship. This selection contained both nonpathogenic (environmental, agricultural, and industrial) as well as pathogenic strains of various pathotypes.
From my understanding, 16S sequences are not suitable to analyze inter-strain relationships within a species or between closely related species. Therefore, I used the Multi-Virulence-Locus Sequence Typing (MVLST) method to discriminate species.
For the phylogenomic analysis, the combination of nine virulence gene fragments (aprA, hlyA, hlyB, hlyIII, luxS, phoP, phoQ, shlA, and shlB) were selected. Subsequently, tree was reconstructed using the Maximum Likelihood (ML) method (MEGA 7) based on Tamura-Nei model with concatenated nucleotide sequences of nine virulence genes.
I expected to divide nonpathogenic and pathogenic group. Apparently, the results show nonpathogenic and pathogenic strains mixed together. How do I effectively separated two group?
Circle color refers to nonpathogenic. Green indicates environmental S. marcescens strains. Blue indicates agricultural strains. The industrial strains are marked pink. Besides, unmarked indicate human pathogen strains.