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CORRECTION article

Front. Microbiol., 08 December 2020 | https://doi.org/10.3389/fmicb.2020.615117

Corrigendum: Precise Species Identification and Taxonomy Update for the Genus Kluyvera With Reporting Kluyvera sichuanensis sp. nov.

Lina Liu1,2, Yu Feng1,3, Li Wei4, Fu Qiao4 and Zhiyong Zong1,2,3,4*
  • 1Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
  • 2Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China
  • 3Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
  • 4Department of Infection Control, West China Hospital, Sichuan University, Chengdu, China

A Corrigendum on
Precise Species Identification and Taxonomy Update for the Genus Kluyvera With Reporting Kluyvera sichuanensis sp. nov.

by Liu, L., Feng, Y., Wei, L., Qiao, F., and Zong, Z. (2020). Front. Microbiol. 11:579306. doi: 10.3389/fmicb.2020.579306

In the original article, there was an error in the Results and Description sections, which provided an incorrect accession number for the type strain deposited into the Guangdong Microbiology Culture Center (GDMCC).

A correction has been made to the “Results” section, which included an incorrect accession number for the deposited type strain. The subsection “Strain identification” should read as follows:

Strain Identification

Strain 090646T was recovered from the residual water of a handwashing sink at an ICU in Chengdu, China, on April 2019 as part of an infection control surveillance program on sinks. The strain was preliminarily identified as Kluyvera ascorbata by MALDI-TOF. A nearly complete sequence (1,411 bp) of the 16S rRNA gene of strain 090646T has the highest identity with that of Kluyvera ascorbata ATCC 33433T (99.22%) and is also highly similar with those of K. intermedia NCTC 12125T (98.88%), K. cryocrescens NBRC 102467T (98.58%), K. georgiana ATCC 51603T (98.30%), Klebsiella aerogenes KCTC 2190T (98.23%), Raoultella terrigena ATCC 33257T (98.09%), Citrobacter braakii ATCC 51113T (97.95%), and Lelliottia amnigena NBRC 105700T (97.94%). In a maximum-likelihood phylogenetic tree (Figure 1) based on the 16S rRNA gene sequence alignment, strain 090646T was allocated within the Kluyvera clade. However, strain 090646T forms a relatively long branch separating from other Kluyvera species (Figure 1) and it is well known that analysis on 16S rRNA gene sequence is insufficient for accurate bacterial species assignation (Mulet et al., 2020). We therefore performed whole genome sequencing by HiSeq X 10 (Illumina; San Diego, CA, United States) for strain 090646T. A total of 1.42 gigabyte bases were generated, which were then assembled into 117 contigs (N50, 144,979 bp). The draft genome of strain 090646T is 5,476,810 bp with a 54.51 mol% G + C content, which has been deposited at DDBJ/EMBL/GenBank under the accession JABBJF000000000.

A total of 684 core genes (Supplementary Dataset S2 in the Supplementary file) were identified in genome sequences of type strains of all Enterobacteriaceae species (Supplementary Table S1). In the maximum-likelihood phylogenomic tree based on core genes (Figure 2), strain 090646T was also allocated within the Kluyvera clade. The POCP values between strain 090646T and type strains of all Kluyvera species ranged from 90.81 to 93.18% (Table 1), suggesting that strain 090646T indeed belonged to the genus Kluyvera. The ANI values between strain 090646T and type strains of all Kluyvera species ranged from 84.15 to 90.10% (Table 1), lower than the ≥95–95% cutoff for defining species (Richter and Rossello-Mora, 2009). Consistently, isDDH values between strain 090646T and type strains of all Kluyvera species ranged from 28.2 to 42.3% (Table 1), which are well below the ≥70.0% cutoff to define species (Richter and Rossello-Mora, 2009; Meier-Kolthoff et al., 2013). Both ANI and isDDH analyses clearly suggest that strain 090646T represents a novel species of the genus Kluyvera. We proposed the species name as Kluyvera sichuanensis (si.chuan.en'sis. N.L. adj. sichuanensis, referring to Sichuan Province, China, where the type strain was recovered) after phenotypic characterization (see below). The type strain 090646T has been deposited into Guangdong Microbial Culture Collection Center as GDMCC 1.1872T and into the Korean Collection for Type Cultures as KCTC82166T.

A correction has been made to the section “Descriptions”, which included an incorrect accession number for the deposited type strain. The subsection “Description of Kluyvera sichuanensis sp. nov.” should read as follows:

Description of Kluyvera sichuanensis sp. nov.

Kluyvera sichuanensis (si.chuan.en'sis. N.L. fem. adj. sichuanensis, referring to Sichuan Province, China, where the type strain was recovered). The species status is determined using ANI, isDDH (Table 1 and Supplementary Dataset S1), core gene-based phylogenomic analysis (Figure 2) and phenotypic assays (see below).

Cells are Gram-stain-negative, facultatively anaerobic, motile, non-spore-forming and short-rod shaped (0.5–0.8 μm wide and 1.0–2.0 μm long, Supplementary Figure S1). Colonies growing on the nutrient agar after 12 h are round, smooth, convex, white. Growth occurs between 8 and 42°C, in the 0 to 5% NaCl (w/v), and at pH 5.0 to 9.0. Nitrate reduction, citrate utilization, and activities of lysine decarboxylase and ornithine decarboxylase are positive. It is able to assimilate esculin, amygdalin, arbulin, D-cellobiose, D-fructose, D-glucose, D-galactose, D-lactose, D-maltose, D-melibiose, D-sorbitol, D-trehalose, D-xylose, 5-keto-gluconate, L-arabinose, L-rhamnose, mannitol, malonate, methyl-α-D-glucopyranoside, N-acetylglucosamine, potassium gluconate, ribose, and salicin. It is negative for acetoin production (Voges–Proskauer), catalase, DNase, H2S production, indole production, oxidase and phenylalanine deaminase, and activities of arginine dihydrolase, β-galactosidase (ONPG), gelatinase, tryptophan deaminase and urease. It does not utilize adonitol, D-mannose, D-saccharose, dulcitol, erythritol, glycerol, inositol, raffinose and sucrose. The major cellular fatty acids are C16:0 (31.28%), C17:0 cyclo (17.56%) and summed in feature 8 (C18:1ω7c) (15.74%).

The type strain is 090646T (also called SCKS090646T), recovered from a hospital sink in Chengdu, Sichuan province, China. Strain 090646T has been deposited into Guangdong Microbiology Culture Center as GDMCC 1.1872T and into Korean Collection for Type Cultures as KCTC 82166T. The draft genome of the type strain is 5,476,810 bp with a 54.51 mol% G + C content (DDBJ/EMBL/GenBank accession no. JABBJF000000000).

The authors apologize for the error and state that this correction does not change the scientific conclusions of the article in any way. The original article has been updated.

References

Meier-Kolthoff, J. P., Auch, A. F., Klenk, H. P., and Goker, M. (2013). Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14:60. doi: 10.1186/1471-2105-14-60

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Richter, M., and Rossello-Mora, R. (2009). Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. U.S.A. 106, 19126–19131. doi: 10.1073/pnas.0906412106

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Keywords: Kluyvera sichuanensis, Kluyvera, genome sequences, sinks, taxonomy

Citation: Liu L, Feng Y, Wei L, Qiao F and Zong Z (2020) Corrigendum: Precise Species Identification and Taxonomy Update for the Genus Kluyvera With Reporting Kluyvera sichuanensis sp. nov.. Front. Microbiol. 11:615117. doi: 10.3389/fmicb.2020.615117

Received: 08 October 2020; Accepted: 19 November 2020;
Published: 08 December 2020.

Edited and reviewed by: Martin G. Klotz, Washington State University, United States

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.

*Correspondence: Zhiyong Zong, zongzhiy@scu.edu.cn

These authors have contributed equally to this work