Lactobacillus allii sp. nov. isolated from scallion kimchi

“…The viral metagenomic sequences have been deposited in the European Bioinformatics Institute (EMBL-EBI) database 35 and are available under accession number PRJEB23957. Details on ODFM database contents are provided in Supplementary Table S1 1 , 7 , 9 – 14 , 16 – 34 , 36 – 108 .…”

Section: Resultsmentioning

confidence: 99%

ODFM, an omics data resource from microorganisms associated with fermented foods

Whon¹,

Ahn

Yang

et al. 2021

Sci Data

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ODFM is a data management system that integrates comprehensive omics information for microorganisms associated with various fermented foods, additive ingredients, and seasonings (e.g. kimchi, Korean fermented vegetables, fermented seafood, solar salt, soybean paste, vinegar, beer, cheese, sake, and yogurt). The ODFM archives genome, metagenome, metataxonome, and (meta)transcriptome sequences of fermented food-associated bacteria, archaea, eukaryotic microorganisms, and viruses; 131 bacterial, 38 archaeal, and 28 eukaryotic genomes are now available to users. The ODFM provides both the Basic Local Alignment Search Tool search-based local alignment function as well as average nucleotide identity-based genetic relatedness measurement, enabling gene diversity and taxonomic analyses of an input query against the database. Genome sequences and annotation results of microorganisms are directly downloadable, and the microbial strains registered in the archive library will be available from our culture collection of fermented food-associated microorganisms. The ODFM is a comprehensive database that covers the genomes of an entire microbiome within a specific food ecosystem, providing basic information to evaluate microbial isolates as candidate fermentation starters for fermented food production.

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“…Moreover, it contains a gene coding for the inner membrane protein YbiR, which is unique to this strain, and may derive from plasmid pL21533-3 ( Pediococcus damnosus ) or plasmid pLb464–8 ( L. brevis BSO). Plasmid 2 of L. hilgardii FLUB is most similar to plasmid pWIKIM01 of L. allii strain WiKim39, isolated from scallion kimchi [ 43 ]. Besides genes encoding mobile element proteins (9), replication initiation protein A (2), and an LtrC-like protein (3), the genes that deserve the most attention in this plasmid are those associated with the detoxification of arsenic-containing substances: arsenate reductase (EC 1.20.4.4), arsenical resistance operon repressor, arsenite/antimonite pump-driving ATPase ArsA (EC 3.6.3.16), arsenite/antimonite:H+ antiporter ArsB, and asenic metallochaperone ArsD.…”

Section: Resultsmentioning

confidence: 99%

Genome and Pangenome Analysis of Lactobacillus hilgardii FLUB—A New Strain Isolated from Mead

Gustaw

Koper

Polak-Berecka

et al. 2021

IJMS

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The production of mead holds great value for the Polish liquor industry, which is why the bacterium that spoils mead has become an object of concern and scientific interest. This article describes, for the first time, Lactobacillus hilgardii FLUB newly isolated from mead, as a mead spoilage bacteria. Whole genome sequencing of L. hilgardii FLUB revealed a 3 Mbp chromosome and five plasmids, which is the largest reported genome of this species. An extensive phylogenetic analysis and digital DNA-DNA hybridization confirmed the membership of the strain in the L. hilgardii species. The genome of L. hilgardii FLUB encodes 3043 genes, 2871 of which are protein coding sequences, 79 code for RNA, and 93 are pseudogenes. L. hilgardii FLUB possesses three clustered regularly interspaced short palindromic repeats (CRISPR), eight genomic islands (44,155 bp to 6345 bp), and three (two intact and one incomplete) prophage regions. For the first time, the characteristics of the genome of this species were described and a pangenomic analysis was performed. The concept of the pangenome was used not only to establish the genetic repertoire of this species, but primarily to highlight the unique characteristics of L. hilgardii FLUB. The core of the genome of L. hilgardii is centered around genes related to the storage and processing of genetic information, as well as to carbohydrate and amino acid metabolism. Strains with such a genetic constitution can effectively adapt to environmental changes. L. hilgardii FLUB is distinguished by an extensive cluster of metabolic genes, arsenic detoxification genes, and unique surface layer proteins. Variants of MRS broth with ethanol (10–20%), glucose (2–25%), and fructose (2–24%) were prepared to test the strain’s growth preferences using Bioscreen C and the PYTHON script. L. hilgardii FLUB was found to be more resistant than a reference strain to high concentrations of alcohol (18%) and sugars (25%). It exhibited greater preference for fructose than glucose, which suggests it has a fructophilic nature. Comparative genomic analysis supported by experimental research imitating the conditions of alcoholic beverages confirmed the niche specialization of L. hilgardii FLUB to the mead environment.

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Lactobacillus allii sp. nov. isolated from scallion kimchi

Cited by 17 publications

References 27 publications

A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae

A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae

ODFM, an omics data resource from microorganisms associated with fermented foods

Genome and Pangenome Analysis of Lactobacillus hilgardii FLUB—A New Strain Isolated from Mead

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