article · Microbiology and Immunology
Multilocus sequence analysis based on hypervariable housekeeping proteins provides an effective method for differentiating closely related bacterial species within the family Enterobacteriaceae. From an initial set of 150 housekeeping proteins, the 10 most hypervariable proteins were selected and concatenated to generate genetic distance data. This ten-protein approach yielded broader distance ranges and higher average bootstrap reliability than traditional 16S ribosomal RNA sequencing and four-gene multilocus sequence analysis. While most species aligned with existing classifications, the resulting phylogenetic tree indicated that several species require reassignment. Specifically, Escherichia hermannii and Salmonella subterranea clustered on an independent branch distinct from other members of the family. Based on these phylogenetic relationships, a new genus named Atlantibacter is proposed, leading to the reclassification of these two organisms as Atlantibacter hermannii and Atlantibacter subterranea.
Accurate bacterial classification is vital for correctly identifying microbes and understanding their evolutionary relationships. Standard genetic markers often lack the resolution needed to distinguish very similar species within large bacterial families. Using hypervariable protein markers resolves ambiguities in bacterial taxonomy and ensures that species with distinct genetic lineages are placed into properly defined genera.
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Multilocus sequence analysis based on hypervariable housekeeping proteins was utilized to differentiate closely related species in the family Enterobacteriaceae. Of 150 housekeeping proteins, the top 10 hypervariable proteins were selected and concatenated to obtain distance data. Distances between concatenated proteins within the family were 0.9-41.2%, whereas the 16S rRNA and atpD-gyrB-infB-rpoB concatenated sequence (4MLSA) distances were 0.8-6.0% and 0.9-22.1%, respectively. These data indicate that phylogenetic analysis by concatenation of hypervariable proteins is a powerful tool for discriminating species in the family Enterobacteriaceae. To confirm the discriminatory power of the 10 chosen concatenated hypervariable proteins (C10HKP), phylogenetic trees based on C10HKP, 4MLSA, and the 16S rRNA gene were constructed. Comparison of average bootstrap values among C10HKP, 4MLSA and 16S rRNA genes indicated that the C10HKP tree was the most reliable. Location via the C10HKP tree was consistent with existing assignments for almost all species in the family Enterobacteriaceae. However, the C10HKP tree suggested that several species (including Enterobacter massiliensis, Escherichia vulneris, Escherichia hermannii, and Salmonella subterranea) should be reassigned to different clusters than those defined in previous analyses. Furthermore, E. hermannii and S. subterranea appeared to fall onto a branch independent from those occupied by the other Enterobacteriaceae. Therefore, we propose Atlantibacter gen. nov., such that E. hermannii and S. subterranea would be transferred to genus Atlantibacter as Atlantibacter hermannii, comb. nov. and Atlantibacter subterranea. comb. nov., respectively.
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DOI: 10.1111/1348-0421.12374
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