Limnobaculum parvum gen. Nov., sp. nov., isolated from a freshwater lake

Chaeyun Baek; Su Kyoung Shin; Hana Yi

doi:10.1099/ijsem.0.003401

Limnobaculum parvum gen. Nov., sp. nov., isolated from a freshwater lake

Chaeyun Baek, Su Kyoung Shin, Hana Yi

School of Biosystem and Biomedical Science

Research output: Contribution to journal › Article › peer-review

6 Citations (Scopus)

Abstract

A Gram-stain-negative, rod-shaped, facultatively anaerobic bacterium, designated as strain HYN0051T, was isolated from lake water. 16S rRNA gene sequence analyses indicated that the isolate shares the highest sequence similarity with the genus Pragia (97.1%) of the family Enterobacteriaceae. Strain HYN0051^T did not form a rigid clade with the genus Pragia in any of the phylogenetic trees, demonstrating the novel generic status of the isolate. The genome of strain HYN0051^T (CP029185) is a single circular chromosome of 3.84 Mb. The major fatty acids detected were C14: 0, C16: 0, summed feature 2 (C_{12: 0} aldehyde and/or unknown 10.928), summed feature 3 (C_{16: 1}ω6c and/or C_{16: 1}ω7c) and summed feature 8 (C_{18: 1}ω 6c and/or C_{18: 1} ω 7c). The isoprenoid quinones were Q-8, MK-8 and DMK-8. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and one unidentified phospholipid. The genome size, G+C content and fatty acid profile were very similar to that of the genus Pragia, but the composition of isoprenoid quinones and polar lipids, and numerous phenotypic properties also supported the distinctiveness of the new isolate from the genus Pragia. Thus, based on phylogenetic and phenotypic data, a novel species of a new genus, Limnobaculum parvum gen. nov., sp. nov., is proposed. The type strain of Limnobaculum parvum is HYN0051^T (=KACC 19186T=NBRC 112742^T).

Original language	English
Pages (from-to)	1826-1830
Number of pages	5
Journal	International Journal of Systematic and Evolutionary Microbiology
Volume	69
Issue number	6
DOIs	https://doi.org/10.1099/ijsem.0.003401
Publication status	Published - 2019 Jun

Bibliographical note

Funding Information:
This study was supported by the research grant ‘Survey of Freshwater Organisms and Specimen Collection (Prokaryotes)’ from the Nakdonggang National Institute of Biological Resources of the Ministry of Environment in Korea, by the National Research Council of Science and Technology (NST) grant from the Korean government (MSIP) (No. CRC-16–01-KRICT) and by the Strategic Initiative for Microbiomes in Agriculture and Food, funded by the Ministry of Agriculture, Food and Rural Affairs (918010–4).

Funding Information:
This study was supported by the research grant ‘Survey of Freshwater Organisms and Specimen Collection (Prokaryotes)’ from the Nakdong-gang National Institute of Biological Resources of the Ministry of Environment in Korea, by the National Research Council of Science and Technology (NST) grant from the Korean government (MSIP) (No. CRC-16–01-KRICT) and by the Strategic Initiative for Microbiomes in Agriculture and Food, funded by the Ministry of Agriculture, Food and Rural Affairs (918010–4).

Publisher Copyright:
© 2019 IUMS.

Keywords

Lake water
Limnobaculum
Nakdong River

ASJC Scopus subject areas

Microbiology
Ecology, Evolution, Behavior and Systematics

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10.1099/ijsem.0.003401

Cite this

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title = "Limnobaculum parvum gen. Nov., sp. nov., isolated from a freshwater lake",

abstract = "A Gram-stain-negative, rod-shaped, facultatively anaerobic bacterium, designated as strain HYN0051T, was isolated from lake water. 16S rRNA gene sequence analyses indicated that the isolate shares the highest sequence similarity with the genus Pragia (97.1%) of the family Enterobacteriaceae. Strain HYN0051T did not form a rigid clade with the genus Pragia in any of the phylogenetic trees, demonstrating the novel generic status of the isolate. The genome of strain HYN0051T (CP029185) is a single circular chromosome of 3.84 Mb. The major fatty acids detected were C14: 0, C16: 0, summed feature 2 (C12: 0 aldehyde and/or unknown 10.928), summed feature 3 (C16: 1ω6c and/or C16: 1ω7c) and summed feature 8 (C18: 1ω 6c and/or C18: 1 ω 7c). The isoprenoid quinones were Q-8, MK-8 and DMK-8. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and one unidentified phospholipid. The genome size, G+C content and fatty acid profile were very similar to that of the genus Pragia, but the composition of isoprenoid quinones and polar lipids, and numerous phenotypic properties also supported the distinctiveness of the new isolate from the genus Pragia. Thus, based on phylogenetic and phenotypic data, a novel species of a new genus, Limnobaculum parvum gen. nov., sp. nov., is proposed. The type strain of Limnobaculum parvum is HYN0051T (=KACC 19186T=NBRC 112742T).",

keywords = "Lake water, Limnobaculum, Nakdong River",

author = "Chaeyun Baek and Shin, {Su Kyoung} and Hana Yi",

note = "Funding Information: This study was supported by the research grant {\textquoteleft}Survey of Freshwater Organisms and Specimen Collection (Prokaryotes){\textquoteright} from the Nakdonggang National Institute of Biological Resources of the Ministry of Environment in Korea, by the National Research Council of Science and Technology (NST) grant from the Korean government (MSIP) (No. CRC-16–01-KRICT) and by the Strategic Initiative for Microbiomes in Agriculture and Food, funded by the Ministry of Agriculture, Food and Rural Affairs (918010–4). Funding Information: This study was supported by the research grant {\textquoteleft}Survey of Freshwater Organisms and Specimen Collection (Prokaryotes){\textquoteright} from the Nakdong-gang National Institute of Biological Resources of the Ministry of Environment in Korea, by the National Research Council of Science and Technology (NST) grant from the Korean government (MSIP) (No. CRC-16–01-KRICT) and by the Strategic Initiative for Microbiomes in Agriculture and Food, funded by the Ministry of Agriculture, Food and Rural Affairs (918010–4). Publisher Copyright: {\textcopyright} 2019 IUMS.",

year = "2019",

month = jun,

doi = "10.1099/ijsem.0.003401",

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volume = "69",

pages = "1826--1830",

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T1 - Limnobaculum parvum gen. Nov., sp. nov., isolated from a freshwater lake

AU - Baek, Chaeyun

AU - Shin, Su Kyoung

AU - Yi, Hana

N1 - Funding Information: This study was supported by the research grant ‘Survey of Freshwater Organisms and Specimen Collection (Prokaryotes)’ from the Nakdonggang National Institute of Biological Resources of the Ministry of Environment in Korea, by the National Research Council of Science and Technology (NST) grant from the Korean government (MSIP) (No. CRC-16–01-KRICT) and by the Strategic Initiative for Microbiomes in Agriculture and Food, funded by the Ministry of Agriculture, Food and Rural Affairs (918010–4). Funding Information: This study was supported by the research grant ‘Survey of Freshwater Organisms and Specimen Collection (Prokaryotes)’ from the Nakdong-gang National Institute of Biological Resources of the Ministry of Environment in Korea, by the National Research Council of Science and Technology (NST) grant from the Korean government (MSIP) (No. CRC-16–01-KRICT) and by the Strategic Initiative for Microbiomes in Agriculture and Food, funded by the Ministry of Agriculture, Food and Rural Affairs (918010–4). Publisher Copyright: © 2019 IUMS.

PY - 2019/6

Y1 - 2019/6

N2 - A Gram-stain-negative, rod-shaped, facultatively anaerobic bacterium, designated as strain HYN0051T, was isolated from lake water. 16S rRNA gene sequence analyses indicated that the isolate shares the highest sequence similarity with the genus Pragia (97.1%) of the family Enterobacteriaceae. Strain HYN0051T did not form a rigid clade with the genus Pragia in any of the phylogenetic trees, demonstrating the novel generic status of the isolate. The genome of strain HYN0051T (CP029185) is a single circular chromosome of 3.84 Mb. The major fatty acids detected were C14: 0, C16: 0, summed feature 2 (C12: 0 aldehyde and/or unknown 10.928), summed feature 3 (C16: 1ω6c and/or C16: 1ω7c) and summed feature 8 (C18: 1ω 6c and/or C18: 1 ω 7c). The isoprenoid quinones were Q-8, MK-8 and DMK-8. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and one unidentified phospholipid. The genome size, G+C content and fatty acid profile were very similar to that of the genus Pragia, but the composition of isoprenoid quinones and polar lipids, and numerous phenotypic properties also supported the distinctiveness of the new isolate from the genus Pragia. Thus, based on phylogenetic and phenotypic data, a novel species of a new genus, Limnobaculum parvum gen. nov., sp. nov., is proposed. The type strain of Limnobaculum parvum is HYN0051T (=KACC 19186T=NBRC 112742T).

AB - A Gram-stain-negative, rod-shaped, facultatively anaerobic bacterium, designated as strain HYN0051T, was isolated from lake water. 16S rRNA gene sequence analyses indicated that the isolate shares the highest sequence similarity with the genus Pragia (97.1%) of the family Enterobacteriaceae. Strain HYN0051T did not form a rigid clade with the genus Pragia in any of the phylogenetic trees, demonstrating the novel generic status of the isolate. The genome of strain HYN0051T (CP029185) is a single circular chromosome of 3.84 Mb. The major fatty acids detected were C14: 0, C16: 0, summed feature 2 (C12: 0 aldehyde and/or unknown 10.928), summed feature 3 (C16: 1ω6c and/or C16: 1ω7c) and summed feature 8 (C18: 1ω 6c and/or C18: 1 ω 7c). The isoprenoid quinones were Q-8, MK-8 and DMK-8. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and one unidentified phospholipid. The genome size, G+C content and fatty acid profile were very similar to that of the genus Pragia, but the composition of isoprenoid quinones and polar lipids, and numerous phenotypic properties also supported the distinctiveness of the new isolate from the genus Pragia. Thus, based on phylogenetic and phenotypic data, a novel species of a new genus, Limnobaculum parvum gen. nov., sp. nov., is proposed. The type strain of Limnobaculum parvum is HYN0051T (=KACC 19186T=NBRC 112742T).

KW - Lake water

KW - Limnobaculum

KW - Nakdong River

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U2 - 10.1099/ijsem.0.003401

DO - 10.1099/ijsem.0.003401

M3 - Article

C2 - 30994436

AN - SCOPUS:85067089809

SN - 1466-5026

VL - 69

SP - 1826

EP - 1830

JO - International Journal of Systematic and Evolutionary Microbiology

JF - International Journal of Systematic and Evolutionary Microbiology

IS - 6

ER -

Limnobaculum parvum gen. Nov., sp. nov., isolated from a freshwater lake

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

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