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Acinetobacter pullicarnis sp. nov. isolated from chicken meat

May 2020
Archives of Microbiology 202(4)

DOI:10.1007/s00203-019-01785-y

Authors:

Ju-Eun Lee

Chung-Ang University

Geun-Bae Kim

Chung-Ang University

A novel bacterial strain, named S23T, was isolated from chicken meat of local market in Korea. Cells were Gram-negative, milky-yellow colored, non-motile and coccobacillus. The strain was obligate aerobic and catalase-positive, oxidase-negative, optimum growth temperature and pH were 25 °C and pH 7.0, respectively. On the basis of 16S rRNA gene sequence analysis, strain S23T belongs to the genus Acinetobacter and is most closely related to Acinetobacter defluvii KCTC 52503 T (97.40%). The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) value between strain S23T and its closet phylogenetic neighbors was below 76% and 17%, respectively. The G + C content of genomic DNA of strain S23T was 41.53 mol%. The major respiratory quinone was Q-9. The major cellular fatty acids were summed feature 3 (comprising C16:1ω7c and/or C16:1ω6c), C18:1ω9c, and C16:0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanol-amine, and phosphatidylserine. The ANI and dDDH results and results of the genotypic analysis in combination with chemotaxonomic and physiological data demonstrated that strain S23T represented a novel species within the genus Acinetobacter, for which the name Acinetobacter pullicarnis sp. nov. is proposed. The strain type is S23T (= KACC 19921 T = JCM 33150 T).

Neighbour-joining (NJ) phylogenic tree of strain S23T and related type strains based on 16S rRNA gene sequences. Filled circles indicate that same branches between NJ and Maximum likelihood (ML) phylogenic tree. Numbers at nodes are bootstrap values based on 1000 resampling data sets; only values above 70% are shown. Moraxella lacunata ATCC 17967 T was used as an outgroup. Bar, 0.01 substitutions per nucleotide position

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Archives of Microbiology (2020) 202:727–732

https://doi.org/10.1007/s00203-019-01785-y

ORIGINAL PAPER

Acinetobacter pullicarnis sp. nov. isolated fromchicken meat

Rae‑HeeHan1· Ju‑EunLee1· Sung‑HeeYoon1· Geun‑BaeKim1

Received: 12 July 2019 / Revised: 21 October 2019 / Accepted: 25 November 2019 / Published online: 2 December 2019

Abstract

A novel bacterial strain, named S23T, was isolated from chicken meat of local market in Korea. Cells were Gram-negative,

milky-yellow colored, non-motile and coccobacillus. The strain was obligate aerobic and catalase-positive, oxidase-negative,

optimum growth temperature and pH were 25°C and pH 7.0, respectively. On the basis of 16S rRNA gene sequence analysis,

strain S23T belongs to the genus Acinetobacter and is most closely related to Acinetobacter deﬂuvii KCTC 52503T (97.40%).

The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) value between strain S23T and its

closet phylogenetic neighbors was below 76% and 17%, respectively. The G + C content of genomic DNA of strain S23T

was 41.53mol%. The major respiratory quinone was Q-9. The major cellular fatty acids were summed feature 3 (comprising

C16:1 ω7c and/or C16:1 ω6c), C18:1 ω9c, and C16:0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol,

phosphatidylethanol-amine, and phosphatidylserine. The ANI and dDDH results and results of the genotypic analysis in

combination with chemotaxonomic and physiological data demonstrated that strain S23T represented a novel species within

the genus Acinetobacter, for which the name Acinetobacter pullicarnis sp. nov. is proposed. The strain type is S23T (= KACC

19921T = JCM 33150T).

Keywords Acinetobacter strain S23T· Acinetobacter pullicarnis· Chicken meat

Abbreviations

ANI Average nucleotide identity

TEM Transmission electron microscopy

TSA Tryptic soy agar

MA MacConkey agar

DPG Diphosphatidylglycerol

PG Phosphatidylglycerol

PE Phosphatidylethanol-amine

PS Phosphatidylserine

APL Aminophospholipid

Introduction

The genus Acinetobacter was ﬁrst reported by Brisou and

Prévot (1954). Members of the genus Acinetobacter are

Gram-negative, obligate aerobic, catalase-positive, oxidase-

negative, and non-motile, except for twitching or swarm-

ing movement (Hu etal. 2017). The genus Acinetobacter

belongs to the family Moraxellaceae in the class Gammapro-

teobacteria. Acinetobacter species are widely distributed

and can be isolated from food items, including ﬁsh, meat,

cheese, milk, and vegetable samples. Furthermore, some

Acinetobacter species can be recovered from various envi-

ronmental sources such as activated sludge, sewage, dump

sites, raw wastewater, and hydrocarbon-contaminated areas

(Doughari etal. 2011). At the time of writing, 61 species of

the genus have been established including synonyms (https

://www.bacte rio.net/acine tobac ter.html), with Acinetobacter

calcoaceticus as the type species of the genus. In addition,

there are ﬁfteen Acinetobacter species with tentative des-

ignations (www.szu.cz/aneme c/Class iﬁca tion.pdf). In this

study, we report on the characterization of a novel species

of genus Acinetobacter, Acinetobacter pullicarnis sp. nov.,

designated as S23T, isolated from chicken meat of local mar-

ket, Republic of Korea, using polyphasic approach. On the

Communicated by Erko Stackebrandt.

Electronic supplementary material The online version of this

article (https ://doi.org/10.1007/s0020 3-019-01785 -y) contains

supplementary material, which is available to authorized users.

* Geun-Bae Kim

kimgeun@cau.ac.kr

1 Department ofAnimal Science andTechnology, Chung-Ang

University, Anseong17546, RepublicofKorea

Content courtesy of Springer Nature, terms of use apply. Rights reserved.

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Apr 2023

While searching for the bacteria which are responsible for degradation of pesticide in soybean field soil, a novel bacterial strain, designated 5-5T , was isolated. The cells of the strain were Gramstaining-positive, aerobic and non-motile rods. Growth occurred at 10-42°C (optimum, 30°C), pH 5.5- 9.0 (optimum, pH 7.0-7.5), and 0-2% (w/v) NaCl (optimum, 1%). The predominant fatty acids were C15:0 anteiso, C17:0 anteiso, and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c). The predominant menaquinone was MK-9 (H2). Diphosphatidylglycerol, glycolipids, phosphatidylinositol, and phosphatidylglycerol were the major polar lipids. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain 5-5T is a member of the genus Sinomonas and its closest relative is Sinomonas humi MUSC 117T , sharing a genetic similarity of 98.4%. The draft genome of strain 5-5T was 4,727,205 bp long with an N50 contig of 4,464,284 bp. Genomic DNA G+C content of strain 5-5T was68.0 mol%. The average nucleotide identity (ANI) values between strain 5-5T and its closest strains S. humi MUSC 117T and S. susongensis A31T were 87.0, and 84.3 % respectively. In silico DNA-DNA hybridization values between strain 5-5T and its closest strains S. humi MUSC 117T and S. susongensis A31T were 32.5% and 27.9% respectively. Based on the ANI and in silico DNA-DNA hybridization analyses, the 5- 5T strain was considered as novel species belonging to the genus Sinomonas. On the basis of the results from phenotypic, genotypic and chemotaxonomic analyses, strain 5-5T represents a novel speciesof the genus Sinomonas, for which the name Sinomonas terrae sp. nov. is proposed. The type strain is 5-5T (=KCTC 49650T =NBRC 115790T ).

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Mar 2020
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Mar 2019

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May 2021

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Acinetobacter

Chapter

Full-text available

May 2022

Alexandr Nemec

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Jan 2018

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Full-text available

Feb 2017
INT J SYST EVOL MICR

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Acinetobacter larvae sp. nov., isolated from the larval gut of Omphisa fuscidentalis

Article

Full-text available

Nov 2016
INT J SYST EVOL MICR

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MIDI technical note 101. Identification of bacteria by gas chromatography of cellular fatty acids. MIDI, Newark

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DNA-DNA hybridization values and their relationship to whole-genome sequence similarities

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DNA–DNA hybridization (DDH) values have been used by bacterial taxonomists since the 1960s to determine relatedness between strains and are still the most important criterion in the delineation of bacterial species. Since the extent of hybridization between a pair of strains is ultimately governed by their respective genomic sequences, we examined the quantitative relationship between DDH values and genome sequence-derived parameters, such as the average nucleotide identity (ANI) of common genes and the percentage of conserved DNA. A total of 124 DDH values were determined for 28 strains for which genome sequences were available. The strains belong to six important and diverse groups of bacteria for which the intra-group 16S rRNA gene sequence identity was greater than 94 %. The results revealed a close relationship between DDH values and ANI and between DNA–DNA hybridization and the percentage of conserved DNA for each pair of strains. The recommended cutoff point of 70 % DDH for species delineation corresponded to 95 % ANI and 69 % conserved DNA. When the analysis was restricted to the protein-coding portion of the genome, 70 % DDH corresponded to 85 % conserved genes for a pair of strains. These results reveal extensive gene diversity within the current concept of 'species'. Examination of reciprocal values indicated that the level of experimental error associated with the DDH method is too high to reveal the subtle differences in genome size among the strains sampled. It is concluded that ANI can accurately replace DDH values for strains for which genome sequences are available.

CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP

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EVOLUTION

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The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data. In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.

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A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.

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