title: Phylogenetics of family Enterobacteriaceae and proposal to reclassify Escherichia hermannii and Salmonella subterranea as Atlantibacter hermannii and Atlantibacter subterranea gen. nov., comb. nov.
abstract: 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.
authors.affiliation: Department of Microbiology, Gifu University Graduate School of Medicine.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Hata
authors.affiliation: Department of Microbiology, Gifu University Graduate School of Medicine.
authors.forename: Tatsuya
authors.initials: T
authors.lastname: Natori
authors.affiliation: Department of Microbiology, Gifu University Graduate School of Medicine.
authors.forename: Takuya
authors.initials: T
authors.lastname: Mizuno
authors.affiliation: Department of Microbiology, Gifu University Graduate School of Medicine.
authors.forename: Izumi
authors.initials: I
authors.lastname: Kanazawa
authors.affiliation: Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Kafrelsheikh University, 33516, Egypt.
authors.forename: Ibrahim
authors.initials: I
authors.lastname: Eldesouky
authors.affiliation: Division of Anaerobe Research, Life Science Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1194.
authors.forename: Masahiro
authors.initials: M
authors.lastname: Hayashi
authors.affiliation: Department of Microbiology, Gifu University Graduate School of Medicine.
authors.forename: Machiko
authors.initials: M
authors.lastname: Miyata
authors.affiliation: Department of Microbiology, Gifu University Graduate School of Medicine.
authors.forename: Hajime
authors.initials: H
authors.lastname: Fukunaga
authors.affiliation: Biological Resource Center, National Institute of Technology and Evaluation, 2-5-8, Kazusakamatari, Kisarazu-shi, Chiba 292-0818, Japan.
authors.forename: Shoko
authors.initials: S
authors.lastname: Ohji
authors.affiliation: Biological Resource Center, National Institute of Technology and Evaluation, 2-5-8, Kazusakamatari, Kisarazu-shi, Chiba 292-0818, Japan.
authors.forename: Akira
authors.initials: A
authors.lastname: Hosoyama
authors.affiliation: Biological Resource Center, National Institute of Technology and Evaluation, 2-5-8, Kazusakamatari, Kisarazu-shi, Chiba 292-0818, Japan.
authors.forename: Eiji
authors.initials: E
authors.lastname: Aono
authors.affiliation: Biological Resource Center, National Institute of Technology and Evaluation, 2-5-8, Kazusakamatari, Kisarazu-shi, Chiba 292-0818, Japan.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Yamazoe
authors.affiliation: Biological Resource Center, National Institute of Technology and Evaluation, 2-5-8, Kazusakamatari, Kisarazu-shi, Chiba 292-0818, Japan.
authors.forename: Keiko
authors.initials: K
authors.lastname: Tsuchikane
authors.affiliation: Biological Resource Center, National Institute of Technology and Evaluation, 2-5-8, Kazusakamatari, Kisarazu-shi, Chiba 292-0818, Japan.
authors.forename: Nobuyuki
authors.initials: N
authors.lastname: Fujita
authors.affiliation: Department of Microbiology, Gifu University Graduate School of Medicine.
authors.forename: Takayuki
authors.initials: T
authors.lastname: Ezaki
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D004755:Enterobacteriaceae / Q000145:classification* / Q000235:genetics*; D020043:Genes, Essential; D058885:Multilocus Sequence Typing; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S
keywords: Enterobacteriaceae; genes, essential; multilocus sequencing typing; phylogeny