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. 2020 Sep 16;11:579306. doi: 10.3389/fmicb.2020.579306

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Copyright © 2020 Liu, Feng, Wei, Qiao and Zong.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Maximum-likelihood phylogenomic tree of Kluyvera sichuanensis 090646^T and other species in the family Enterobacteriaceae based on the core genome. The four Kluyvera species known before this study are highlighted in red, while K. sichuanensis is shown in blue. Genera comprising multiple species are depicted in green with the number of species shown in parentheses. There are two clades for the genera Cedecea, Citrobacter, and Klebsiella. Cedecea colo belongs to a separate clade, while the remaining three Cedecea species (Supplementary Table S1) form Cedecea spp. clade 1. Citrobacter spp. clade 1 comprises Citrobacter amalonaticus, Citrobacter rodentium, and Citrobacter sedlakii, while the remaining 10 Citrobacter species (Supplementary Table S1) belong to Citrobacter spp. clade 2. Klebsiella spp. clade 1 comprises Klebsiella aerogenes, Klebsiella africana, Klebsiella pneumoniae, Klebsiella quasipneumoniae, Klebsiella quasivariicola, and Klebsiella variicola, while the remaining six Klebsiella species belongs to Klebsiella spp. clade 2. For genera or clade comprising only one species and Kluyvera species, the type strains and their nucleotide accession numbers are listed alongside the names of species. The tree was inferred using the maximum likelihood method under GTRGAMMA model with a 1,000-bootstrap test and branches with support over 75% are indicated by different colors. Bar, value indicates the nucleotide substitution per site.