Lactobacillus mudanjiangensis sp. nov., Lactobacillus songhuajiangensis sp. nov. and Lactobacillus nenjiangensis sp. nov., isolated from Chinese traditional pickle and sourdough

Gu, Chun Tao; Li, Chun Yan; Yang, Li Jie; Huo, Gui Cheng

doi:10.1099/ijs.0.054296-0

“…284 mudanjiangensis showed a slightly larger number of GHs than L. plantarum (Data not 285 shown), indicating that this species is capable of transforming and metabolizing a broad 286 spectrum of carbohydrate sources. This observation was confirmed by the fact that the 287 type strain was found to be capable of producing organic acids from at least 21 different 288 carbon sources [10]. Furthermore, here, a putative cellulose-degrading enzyme, 289 annotated as endoglucanase E1, was found in all four L. mudanjiangensis strains, which 290 was not found in any other LGC genome so far.…”

supporting

confidence: 57%

“…AMBF197, AMBF209 and AMBF249, which were isolated from three different 256 spontaneous carrot juice fermentations [11]. Since previous phylogenetic analysis of this 257 species, using the 16S rRNA, pheS, and rpoA genes, showed a close genetic relatedness 258 with the members of the L. plantarum group [10], it was decided to study these 259 genomes in relation to the closely related members of the L. plantarum group with a 260 comparative genomics approach. A maximum likelihood phylogenetic tree confirmed 261 that L. mudanjiangensis was closely related to all other L. plantarum group members.…”

mentioning

confidence: 99%

Comparative genome analysis ofLactobacillus mudanjiangensis, an understudied member of theLactobacillus plantarumgroup

Wuyts

¹

,

Allonsius

²

,

Wittouck

³

et al. 2019

Preprint

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The genus Lactobacillus is known to be extremely diverse and consists of different phylogenetic groups that show a diversity roughly equal to the expected diversity of a typical bacterial genus. One of the most prominent phylogenetic groups within this genus is the Lactobacillus plantarum group which contains the understudied Lactobacillus mudanjiangensis species. Before this study, only one L. mudanjiangensis strain, DSM 28402 T , was described but without whole-genome analysis. In this study, three strains classified as L. mudanjiangensis, were isolated from three different carrot juice fermentations and their whole-genome sequence was determined, together with the genome sequence of the type strain. The genomes of all four strains were compared with publicly available L. plantarum group genome sequences. This analysis showed that L. mudanjiangensis harbored the second largest genome size and gene count of the whole L. plantarum group. In addition, all members of this species showed the presence of a gene coding for a putative cellulose-degrading enzyme. Finally, three of the four L. mudanjiangensis strains studied showed the presence of pili on scanning electron microscopy (SEM) images, which were linked to conjugative gene regions, coded on plasmids in at least two of the strains studied. Author summaryLactobacillus mudanjiangensis is an understudied species within the Lactobacillus plantarum group. Since its first description, no other studies have reported its isolation. Here, we present the first four genome sequences of this species, which include the genome sequence of the type strain and three new L. mudanjiangensis strains isolated from fermented carrot juice. The genomes of all four strains were compared with publicly available L. plantarum group genome sequences. We found that this species February 5, 2019 1/20 harbored the second largest genome size and gene count of the whole L. plantarum group. Furthermore, we present the first scanning electron microscopy (SEM) images of L. mudanjiangensis, which showed the formation of pili in three strains that we linked to genes related to conjugation. Finally, we found the presence of a unique putative cellulose-degrading enzyme, opening the door for different industrial applications of these Lactobacillus strains. Introduction 1The genus Lactobacillus is known to be extremely diverse [1]. Furthermore, it has been 2 shown that different phylogenetic groups within this genus display a diversity roughly 3 equal to the expected diversity of a typical bacterial genus [2][3][4][5][6]. Each of these 4 phylogenetic groups can be recognized as an entity with unique properties and a distinct 5 natural history, ecology, function and physiology [5]. Therefore, the study of these 6 phylogenetic groups separately, as if they would be one genus, can be an interesting 7 approach that might reveal new, previously overlooked, phylogenetic relationships and 8 functional properties. 9 One of the more abundantly studied species within the genus Lactobacillus, is 10 Lactobacillus...

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“…L. hokkaidonensis is classified as an obligate heterofermentative LAB in the L. vaccinostercus group [ 2 ], which includes five species ( L. vaccinostercus [ 3 ], L. suebicus [ 4 ], L. oligofermentans [ 5 ], L. nenjiangensis [ 6 ], and L. hokkaidonensis ) that form a clade distinct from the well-known heterofermentative clades, which include L. reuteri , L. brevis , and L. buchneri . They share common phenotypic features such as the presence of meso -diaminopimelic acid in their peptidoglycan cell walls and faster assimilation of pentoses compared with hexoses, but little is known about their genetic background or genomic information.…”

Section: Introductionmentioning

confidence: 99%

Complete genome sequence and analysis of Lactobacillus hokkaidonensis LOOC260T, a psychrotrophic lactic acid bacterium isolated from silage

Tanizawa

¹

,

Tohno

²

,

Kaminuma

³

et al. 2015

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BackgroundLactobacillus hokkaidonensis is an obligate heterofermentative lactic acid bacterium, which is isolated from Timothy grass silage in Hokkaido, a subarctic region of Japan. This bacterium is expected to be useful as a silage starter culture in cold regions because of its remarkable psychrotolerance; it can grow at temperatures as low as 4°C. To elucidate its genetic background, particularly in relation to the source of psychrotolerance, we constructed the complete genome sequence of L. hokkaidonensis LOOC260T using PacBio single-molecule real-time sequencing technology.ResultsThe genome of LOOC260T comprises one circular chromosome (2.28 Mbp) and two circular plasmids: pLOOC260-1 (81.6 kbp) and pLOOC260-2 (41.0 kbp). We identified diverse mobile genetic elements, such as prophages, integrated and conjugative elements, and conjugative plasmids, which may reflect adaptation to plant-associated niches. Comparative genome analysis also detected unique genomic features, such as genes involved in pentose assimilation and NADPH generation.ConclusionsThis is the first complete genome in the L. vaccinostercus group, which is poorly characterized, so the genomic information obtained in this study provides insight into the genetics and evolution of this group. We also found several factors that may contribute to the ability of L. hokkaidonensis to grow at cold temperatures. The results of this study will facilitate further investigation for the cold-tolerance mechanism of L. hokkaidonensis.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1435-2) contains supplementary material, which is available to authorized users.

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“…plantarum and L. plantarum subsp. argentoratensis had been shown in previous studies [6][7][8][9][10].…”

Section: Proposal Of Lactobacillus Kosoimentioning

confidence: 51%

Proposal of Lactobacillus kosoi Chiou et al. 2018 as a later heterotypic synonym of Lactobacillus micheneri McFrederick et al. 2018, elevation of Lactobacillus plantarum subsp. argentoratensis to the species level as Lactobacillus argentoratensis sp. nov., and Lactobacillus zhaodongensis sp. nov., isolated from traditional Chinese pickle and the intestinal tract of a honey bee (Apis mellifera)

Li

¹

,

Liu

²

,

Fu

³

et al. 2020

International Journal of Systematic and Evolutionary Microbiology

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Lactobacillus kosoi Chiou et al. 2018 and Lactobacillus micheneri McFrederick et al. 2018 are closely related, and they share 100 % 16S rRNA gene sequence similarity, 99.6 % pheS gene sequence similarity, 100 % rpoA gene sequence similarity, 97.3 % average nucleotide identity (ANI) value and 76.6 % in silico DNA–DNA hybridization (isDDH) value, indicating that they represent the same species. Fatty acid methyl esters (FAME) analysis and phenotypic characterization also indicated that L. kosoi and L. micheneri are very similar. We propose L. kosoi Chiou et al. 2018 as a later heterotypic synonym of L. micheneri McFrederick et al. 2018. The taxonomic position of Lactobacillus plantarum subsp. argentoratensis in the L. plantarum group was re-examined using a polyphasic approach, including sequence analyses of 16S rRNA, pheS, rpoA and recA genes, average nucleotide identity analysis, in silico DNA–DNA hybridization, fatty acid methyl ester analysis and phenotypic characterization. Results of 16S rRNA gene sequence analysis indicated that L. plantarum subsp. argentoratensis was closely related to L. plantarum subsp. plantarum , L. pentosus and L. paraplantarum in the L. plantarum group, sharing 99.6–99.7 % 16S rRNA gene sequence similarities. Results of pheS, rpoA and recA gene sequence analyses indicated that L. plantarum subsp. argentoratensis was most closely related to L. plantarum subsp. plantarum , having 91.8 % pheS gene sequence similarity, 98.9 % rpoA gene sequence similarity and 93.1 % recA gene sequence similarity. L. plantarum subsp. argentoratensis DSM 16365T shared 95.6 % ANI value and 62.9 % isDDH value with L. plantarum subsp. plantarum ATCC 14917T. The low isDDH value confirmed that L. plantarum subsp. argentoratensis and L. plantarum subsp. plantarum represent two different species, rather than two different subspecies in the L. plantarum group. On the basis of the data from polyphasic characterization obtained in the present study and in previous studies, L. plantarum subsp. argentoratensis is elevated to the species level and represents a novel species of the genus Lactobacillus , for which the name Lactobacillus argentoratensis sp. nov. is proposed and the type strain is DKO 22T (=CIP 108320T=DSM 16365T=JCM 16169T). Two novel Gram-stain-positive bacterial strains, designated 1206-1T and F027-1-2, were isolated from traditional pickle in Heilongjiang Province, PR China, and from the intestinal tract of a honey bee (Apis mellifera) in Hubei Province, PR China, respectively. The two bacteria were characterized by a polyphasic approach, including 16S rRNA gene sequence analysis, pheS gene sequence analysis, rpoA gene sequence analysis, fatty acid methyl ester analysis, average nucleotide identity analysis, in silico DNA–DNA hybridization analysis and an analysis of phenotypic features. The results of 16S rRNA gene sequence analysis indicated that strains 1206-1T and F027-1-2 were distantly related to Lactobacillus sharpeae , Lactobacillus hulanensis , Lactobacillus songhuajiangensis , Lactobacillus pantheris , Lactobacillus thailandensis , Lactobacillus camelliae , Lactobacillus jixianensis , Lactobacillus nasuensis , Lactobacillus baoqingensis , Lactobacillus manihotivorans and Lactobacillus porcinae . Strain 1206-1T exhibited 94.2–96.4 % 16S rRNA gene sequence similarities, 69.5–83.3 % pheS gene sequence similarities and 73.1–90.3 % rpoA gene sequence similarities to type strains of phylogenetically related species. ANI and isDDH values between strain 1206-1T and the type strains of phylogenetically related species were 52.7–73.7 % and 21.1–30.1 %, respectively. On the basis of the data obtained in the present study, a novel species, Lactobacillus zhaodongensis sp. nov. is proposed and the type strain is 1206-1T (=CCM 8981T=CCTCC AB 2019200T=LMG 31620T).

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Lactobacillus mudanjiangensis sp. nov., Lactobacillus songhuajiangensis sp. nov. and Lactobacillus nenjiangensis sp. nov., isolated from Chinese traditional pickle and sourdough

Cited by 45 publications

References 32 publications

Comparative genome analysis ofLactobacillus mudanjiangensis, an understudied member of theLactobacillus plantarumgroup

Comparative genome analysis ofLactobacillus mudanjiangensis, an understudied member of theLactobacillus plantarumgroup

Complete genome sequence and analysis of Lactobacillus hokkaidonensis LOOC260T, a psychrotrophic lactic acid bacterium isolated from silage

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