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

Baek, Chaeyun; Shin, Su Kyoung; Yi, Hana

doi:10.1099/ijsem.0.003401

Cited by 14 publications

(19 citation statements)

References 8 publications

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“…1). This conclusion is shared by the authors of the initial description of Limnobaculum, who noted that it shares the highest 16S rRNA gene sequence identity with the Budviciaceae genus, Pragia [3,12]. The genus 'Nissabacter' is currently described by the List of Prokaryotic names with Standing in Nomenclature as a member of Enterobacteriaceae [11], but in our phylogeny grouped within Yersiniaceae with strong support (Fig.…”

Section: Discussionsupporting

confidence: 72%

“…The Limnobaculum type strain was identified as Budvicia while the Enterobacillus type strain was identified as Pectobacterium although in both cases, support was low (Table S3). The RDP classifier database training set 16 was created in early 2016, prior to the creation of Enterobacterales , as well as prior to the description of multiple genera including Limnobaculum ; therefore, the weakly supported taxonomic assignment for these two strains is not unexpected [3, 12].…”

Section: Discussionmentioning

confidence: 99%

“…Adeolu and colleagues [3] officially established Enterobacterales from the unofficially-named order ‘ Enterobacteriales ’ and also divided Enterobacteriaceae into seven separate families: Budviciaceae , Enterobacteriaceae , Erwiniaceae , Hafniaceae , Morganellaceae , Pectobacteriaceae and Yersiniaceae [3]. New genera, such as Limnobaculum , continue to be added [12] while new genomes for several genera are now available in public databases, including Biostraticola , Enterobacillus , Gibbsiella , Pseudocitrobacter , Rosenbergiella and Samsonia [3]. Here, we sought to validate the current taxonomic assignments of members of the Enterobacterales through phylogenetic analysis of 64 genera using 32 core genes, and propose that eight should undergo taxonomic revision.…”

Section: Introductionmentioning

confidence: 99%

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Phylogenetic analysis supporting the taxonomic revision of eight genera within the bacterial order Enterobacterales

Soutar

Stavrinides

2020

International Journal of Systematic and Evolutionary Microbiology

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The diverse members of the Enterobacterales are agriculturally and medically relevant species that have continued to undergo taxonomic revision. To assess the current taxonomy of 64 genera of the Enterobacterales , we carried out a phylogenetic analysis using 32 single-copy core proteins. The resulting phylogeny was robust, and shows that eight genera – Biostraticola , Enterobacillus , Gibbsiella , Limnobaculum , Izhakiella , ‘Nissabacter’, Rosenbergiella and Samsonia – are currently assigned to incorrect families. Taxonomic reassignment of these genera was also supported by average amino acid identity comparisons. We propose taxonomic revision of these genera to reflect their phylogenetic position within the Enterobacterales .

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Section: Discussionsupporting

confidence: 72%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Phylogenetic analysis supporting the taxonomic revision of eight genera within the bacterial order Enterobacterales

Soutar

Stavrinides

2020

International Journal of Systematic and Evolutionary Microbiology

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“…The data were all from this study except for Limnobaculum parvum HYN0051 T [8]. +, Positive; -, negative; w, weakly positive; nd, no data available 3 %) and C 14 : 0 (10.6 %), with CF-917 exhibiting a very small variation (less than 1.5 %) in all fatty acids (Table 3).…”

mentioning

confidence: 95%

“…All data were obtained from this study except for Limnobaculum parvum HYN0051 T [8]. Major components are shown in bold text (>10 %); tr, trace level (<1 %); nd, no data available.…”

mentioning

confidence: 99%

Jinshanibacter, a new genus of Budviciaceae: identification of Jinshanibacter zhutongyuii sp. nov. and Jinshanibacter xujianqingii sp. nov. isolated from cloacal content of snow finch (Montifringilla taczanowskii)

Wang

Yang

et al. 2021

International Journal of Systematic and Evolutionary Microbiology

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Four novel strains isolated from the cloacal contents of snow finches (Montifringilla taczanowskii) were characterized as aerobic, Gram-stain-negative, slightly motile, and rod-shaped. Analysis of the 16S rRNA gene sequence revealed that strain CF-458T had the highest similarities of 96.9 and 96.4 % with Limnobaculum parvum HYN0051T and Pragia fontium DSM 5563T, while strain CF-1111T shared the highest similarities of 96.4 and 96.1 % with Pantoea rodasii LMG 26273T and Pectobacterium punjabense SS95T. Phylogenomic analysis showed the four isolates were separated into group Ⅰ (CF-458T and CF-917) and group Ⅱ (CF-1111T and CF-509), and clustered independently in the vicinity of the genera Limnobaculum and Pragia . Summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c, 23.9 and 17.2 %, respectively), C16 : 0 (21.8 and 22.1 %, respectively) and C14 : 0 (10.6 and 17.7 %, respectively) were the common major fatty acids, and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c, 12.3 %) was also a major fatty acid for strain CF-458T while cyclo-C17 : 0 (13.1%) was for strain CF-1111T. Both had Q-8 as the sole quinone and contained phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol as the major polar lipids. The DNA G+C content of strains CF-458T and CF-1111T was 45.7 and 45.4 mol%, respectively. Based on taxonomic position in the phylogenomic tree and phenotypic properties, two novel species of a new genus within the family Budviciaceae are thus proposed, with the name Jinshanibacter gen. nov., zhutongyuii sp. nov. (type strain CF-458T=CGMCC 1.16483T=GDMCC 1.1586T=JCM 33489T) and Jinshanibacter xujianqingii sp. nov. (type strain CF-1111T=CGMCC 1.16786T=GDMCC 1.1587T=JCM 33490T), respectively.

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Limnobaculum

Baek¹,

Yi²

2021

Bergey's Manual of Systematics of Archaea and Bacteria

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Lim.no.ba'cu.lum. Gr. fem. n. limne lake; L. neut. n. baculum stick; N.L. neut. n. Limnobaculum a rod from the lake. Proteobacteria / Gammaproteobacteria / Enterobacterales / Budviciaceae / Limnobaculum The genus Limnobaculum belongs to the family Budviciaceae of the order Enterobacterales . Cells of the genus are facultatively anaerobic, Gram‐stain negative, and nonflagellated rods. They grow well at neutral pH and mesophilic condition without salts. The type strain of the type species was isolated from lake water. The closest relative of this genus is the genus Pragia by sharing the highest sequence similarity (97.1%) and by forming a robust monophyletic clade in the 16S rRNA gene and genome trees. The only strain in the genus possesses a single circular chromosome of 3.84 Mb. The major fatty acids are C 14:0 , C 16:0 , C 12:0 aldehyde and/or unknown 10.928, C 16:1 ω6 c and/or C 16:1 ω7 c , and C 18:1 ω6 c and/or C 18:1 ω7 c . The predominant polar lipids are phosphatidylglycerol (PG), phosphatidylethanolamine (PE), and one unidentified phospholipid (PL). The major respiratory quinone is ubiquinone 8 (Q‐8), and the minor ones are menaquinone 8 (MK‐8) and demethylmenaquinone‐8 (DMK‐8). DNA G + C content (mol%) : 46.0 (genome). Type species : Limnobaculum parvum Baek et al. 2019 VP .

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

Cited by 14 publications

References 8 publications

Phylogenetic analysis supporting the taxonomic revision of eight genera within the bacterial order Enterobacterales

Phylogenetic analysis supporting the taxonomic revision of eight genera within the bacterial order Enterobacterales

Jinshanibacter, a new genus of Budviciaceae: identification of Jinshanibacter zhutongyuii sp. nov. and Jinshanibacter xujianqingii sp. nov. isolated from cloacal content of snow finch (Montifringilla taczanowskii)

Limnobaculum

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