Leuconostoc miyukkimchii sp. nov., isolated from brown algae (Undaria pinnatifida) kimchi

Transfusion-transmitted bacterial infection risk due to the proliferation of psychrotrophic bacterial species in RBCs and their difficulty in detection

BACKGROUND

Reports of cases of bacterial infection due to transfusion of red blood cell (RBC) components (RBC-TTBI) are relatively rare. Hence, the possibility of undetectable bacterial contamination in RBCs, especially by psychrotrophic bacteria, must be clarified.

STUDY DESIGN AND METHODS

We assessed nine psychrotrophic bacterial species, including those implicated in bacteremia or RBC-TTBIs. They were cultured on plates from 4 to 37°C to determine their optimal growth temperatures. We also assessed the detection capabilities of the automated culture/alarm system BACT/ALERT VIRTUO (VIRTUO) using BPA (aerobic) and BPN (anaerobic) bottles. In addition, bacteria-inoculated RBCs were incubated at 4°C for 42 days, with samples assessed weekly for bacterial growth using plate culture, VIRTUO, visual inspection, and endotoxin production.

RESULTS

Two Psychrobacter species exhibited weak or no proliferation at temperatures ≥30°C in plate cultures. Three Pseudomonas species, one Psychrobacter species, and one psychrotrophic lactic acid bacteria proliferated in RBCs at 4°C, reaching 104-108 colony-forming units/mL (growth count) and 15-39,230 pg/mL (endotoxin production) by day 14. VIRTUO, operating at 36°C, failed to consistently yield reliable results for any of the tested bacterial species. Notably, visual changes in bag appearance were observed from day 21 in four species that proliferated in RBCs.

DISCUSSION

Each psychrotrophic bacteria demonstrated a specific temperature preference for optimal proliferation. Standard culture tests, typically conducted at 35-37°C, often fail to detect the growth of such bacteria, suggesting they may be overlooked in the cultural analysis of suspected RBC-TTBI cases.

Leuconostoc aquikimchii sp. nov., a Lactic Acid Bacterium Isolated from Cabbage Watery Kimchi

Two Gram-stain-positive, facultatively anaerobic, non-hemolytic, coccoid-shaped bacterial strains, designated MS01T and MS02, were isolated from cabbage watery kimchi in the Republic of Korea. Cellular growth occurred at 5-25 ℃ (optimum, 20 ℃), pH 5-8 (optimum, pH 7) and in the presence of 0-5% (w/v) NaCl (optimum, 1%). Results of 16S rRNA gene-based phylogenetic analyses showed that strains MS01T and MS02 shared identical sequences, clustered within the Leuconostoc clade in phylogenetic trees, and were most closely related to Leuconostoc inhae IH003T and Leuconostoc gasicomitatum LMG 18811T with sequence similarities of 98.74%. The complete whole-genome sequences of strains MS01T and MS02 measured 2.04-2.06 Mbp and harbored a 50.6 kb plasmid, with DNA G + C contents of 37.7% for both. Based on average nucleotide identities (ANI) and digital DNA-DNA hybridization (dDDH) values, both strains were confirmed to belong to the same species but showed ≤ 85.9% ANI and ≤ 29.9% dDDH values to other Leuconostoc species, indicating that they represent a novel species. Metabolic pathway reconstruction revealed that both strains perform heterolactic acid fermentation, producing lactate, acetate, and ethanol. Chemotaxonomic analyses, including cellular fatty acids, polar lipids, and peptidoglycan amino acid, confirmed the inclusion of both strains within the genus Leuconostoc. Based on the phylogenetic, genomic, and phenotypic characterization, strains MS01T and MS02 were considered to represent a novel species within the genus Leuconostoc, for which the name Leuconostoc aquikimchii sp. nov. is proposed with MS01T (= KACC 23748T = JCM 37028T) as the type strain.

Leuconostoc koreense sp. nov., isolated from kimchi, a fermented vegetable

The novel strain CBA3628T was isolated from kimchi, a Korean fermented vegetable. CBA3628T is a cocci-shaped, Gram-stain-positive, catalase- and oxidase-negative and facultatively anaerobic bacterium. The results of phylogenetic analysis based on 16S rRNA gene sequencing indicated that CBA3628T represented a member of the genus Leuconostoc of the family Leuconostocaceae. CBA3628T has a circular chromosomal genome and three plasmids of 1 864 558 bp (37% DNA G+C content), containing 1,887 genes, 1,762 predicted protein-coding genes, 4 complete rRNA loci and 70 tRNA genes. The cells were non-haemolytic, non-motile and non-spore forming. The optimal growth of CBA3628T occurred at 30 °C, pH 6.0 and with 0-2% (w/v) NaCl. The major polar lipids of CBA3628T were diphosphatidylglycerol and phosphatidylglycerol. The major fatty acids (>10%) of CBA3628T were C16  :  0, C20  :  0 and C19 : 0 cyclo ω8c. CBA3628T contained A3α-type peptidoglycans. CBA3628T was most closely related to Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293T, L. mesenteroides subsp. dextranicum DSM 20484T and L. suionicum DSM 20241T with 99.52% 16S rRNA gene sequence similarity. However, the average nucleotide identities of 91.9%, 91.7% and 91.1% and the digital DNA-DNA hybridisation values of 45.6%, 45.4% and 45.4% indicated that the novel isolate represented a distinct species. Phylogenetic analyses of both the 16S rRNA gene and genome sequences revealed that CBA3628T formed a distinct phylogenetic lineage within the genus Leuconostoc and was most closely related to Leuconostoc litchii MB7T. The ANI and dDDH values between CBA3628T and L. litchii MB7T were 84.9 and 22.8%, respectively. Functional genes belonging to COG categories E, J and K were enriched in the genome of CBA3628T (>7.9%). On the basis of its physiological, chemotaxonomic, phylogenetic and genomic properties, strain CBA3628T represents a novel species from the genus Leuconostoc, for which we propose the name Leuconostoc koreense sp. nov., with the type strain CBA3628T (= KACC 23049T = DSM 116836T).

The Role and Mechanism of Probiotics Supplementation in Blood Glucose Regulation: A Review

With economic growth and improved living standards, the incidence of metabolic diseases such as diabetes mellitus caused by over-nutrition has risen sharply worldwide. Elevated blood glucose and complications in patients seriously affect the quality of life and increase the economic burden. There are limitations and side effects of current hypoglycemic drugs, while probiotics, which are safe, economical, and effective, have good application prospects in disease prevention and remodeling of intestinal microecological health and are gradually becoming a research hotspot for diabetes prevention and treatment, capable of lowering blood glucose and alleviating complications, among other things. Probiotic supplementation is a microbiologically based approach to the treatment of type 2 diabetes mellitus (T2DM), which can achieve anti-diabetic efficacy through the regulation of different tissues and metabolic pathways. In this study, we summarize recent findings that probiotic intake can achieve blood glucose regulation by modulating intestinal flora, decreasing chronic low-grade inflammation, modulating glucagon-like peptide-1 (GLP-1), decreasing oxidative stress, ameliorating insulin resistance, and increasing short-chain fatty acids (SCFAs) content. Moreover, the mechanism, application, development prospect, and challenges of probiotics regulating blood glucose were discussed to provide theoretical references and a guiding basis for the development of probiotic preparations and related functional foods regulating blood glucose.

Influence of Isolation Temperature on Isolating Diverse Lactic Acid Bacteria from Kimchi and Cultural Characteristics of Psychrotrophs

Kimchi is a traditional Korean fermented vegetable that is stored and fermented at low temperatures. However, kimchi lactic acid bacteria (LAB) are typically isolated under mesophilic conditions, which may be inappropriate for isolating the diverse LAB. Therefore, this study investigated the suitable conditions for isolating various LAB from kimchi. Here, LAB were isolated from four kimchi samples using MRS, PES, and LBS media and varying isolation temperatures (30, 20, 10, and 5°C). Then, MRS was selected as the suitable medium for LAB isolation. A comparison of culture-dependent and culture-independent approaches indicated that 5°C was not a suitable isolation temperature. Thus, the number and diversity of LAB were determined at 30, 20, and 10°C using 12 additional kimchi samples to elucidate the effect of isolation temperature. With the exception of two samples, most samples did not substantially differ in LAB number. However, Leuconostoc gelidum, Leuconostoc gasicomitatum, Leuconostoc inhae, Dellaglioa algida, Companilactobacillus kimchiensis, Leuconostoc miyukkimchii, Leuconostoc holzapfelii, and Leuconostoc carnosum were isolated only at 10 and 20°C. The growth curves of these isolates, except Leu. holzapfelii and Leu. carnosum, showed poor growth at 30°C. This confirmed their psychrotrophic characteristics. In Weissella koreensis, which was isolated at all isolation temperatures, there was a difference in the fatty acid composition of membranes between strains that could grow well at 30°C and those that could not. These findings can contribute to the isolation of more diverse psychrotrophic strains that were not well isolated under mesophilic temperatures.

Consumer Trend of Using Ready-to-Use Salted Napa Cabbage at Home: Current Consumer Behaviors, Beliefs, and Opinions about the Main Ingredient of Kimchi

ABSTRACT

Salted napa cabbage is the most important ingredient of kimchi. Currently, people have started to prepare ready-to-use salted napa cabbage at home. This study focused on this trend by investigating consumers' beliefs, opinions, and actual use of the products by conducting a telephone survey (895 female consumers) and face-to-face interviews (n = 514) in 2016 and a telephone survey (n = 200) in 2021. Most respondents (93 and 91% in 2016 and 2021, respectively) answered that convenience was the main reason for using salted napa cabbage. Regarding consumption behavior, 22 and 16% of the respondents in each year used salted napa cabbage after storing it for more than 24 h. In particular, 85 and 91% of consumers stored the product at room temperature, and 60 and 58% used it without washing, which could affect the quality of the food, as microorganisms could multiply during the storage. Inappropriate handling increased by age group, especially in 2021 (P < 0.05). In the query on satisfaction after using the products, 85 and 80% of respondents were satisfied because the product was convenient (54%) and hygienic (17%). Conversely, the respondents who were not satisfied with the products did not like the degree of salting and unhygienic status of the products. The majority (93 and 80%) of consumers preferred buying salted napa cabbage again because of its convenience. Although consumers thought that hygiene and quality were important factors, many respondents (83 and 72%) were not aware of foodborne illnesses associated with kimchi. Nevertheless, consumers intended to pay more for safe, salted napa cabbage (72 and 76%). The results of this study provide useful and credible data for understanding the factors affecting consumers' consumption and general beliefs and opinions on the use of salted napa cabbage, especially for food safety management.

HIGHLIGHTS

Exploring Antibiotic Resistance Diversity in Leuconostoc spp. by a Genome-Based Approach: Focus on the lsaA Gene

Leuconostoc spp. are environmental microorganisms commonly associated with fermented foods. Absence of antibiotic resistance (AR) in bacteria is a critical issue for global food safety. Herein, we updated the occurrence of AR genes in the Leuconostoc genus through in silico analyses of the genomes of 17 type strains. A total of 131 putative AR traits associated with the main clinically relevant antibiotics were detected. We found, for the first time, the lsaA gene in L. fallax ATCC 700006^T and L. pseudomesenteroides NCDO 768^T. Their amino acid sequences displayed high similarities (59.07% and 52.21%) with LsaA of Enterococcusfaecalis V583, involved in clindamycin (CLI) and quinupristin-dalfopristin (QUD) resistance. This trait has different distribution patterns in Leuconostoc nontype strains-i.e., L. pseudomesenteroides, L. lactis and L. falkenbergense isolates from fermented vegetables, cheeses, and starters. To better explore the role of lsaA, MIC for CLI and QUD were assessed in ATCC 700006^T and NCDO 768^T; both strains were resistant towards CLI, potentially linking lsaA to their resistant phenotype. Contrarily, NCDO 768^T was sensitive towards QUD; however, expression of lsaA increased in presence of this antibiotic, indicating an active involvement of this trait and thus suggesting a revision of the QUD thresholds for this species.

Companilactobacillus pabuli sp. nov., a lactic acid bacterium isolated from animal feed

A Gram-positive, facultative anaerobic, catalase-negative, non-motile, non-spore-forming and rod-shaped lactic acid bacterium strain, denoted as NFFJ11^T and isolated from total mixed fermentation feed in the Republic of Korea, was characterized through polyphasic approaches, including sequence analyses of the 16S rRNA gene and housekeeping genes (rpoA and pheS), determination of average nucleotide identity and in silico DNA-DNA hybridization, fatty acid methyl ester analysis, and phenotypic characterization. Phylogenetic analyses based on 16S rRNA, rpoA and pheS gene sequences revealed that strain NFFJ11^T belonged to the genus Companilactobacillus. The 16S rRNA gene sequence of strain NFFJ11^T exhibited high similarity to Companilactobacillus formosensis S215^T (99.66 %), Companilactobacillus farciminis Rv4 na^T (99.53 %), Companilactobacillus crustorum LMG 23699^T (99.19 %), Companilactobacillus futsaii YM 0097^T (99.06 %), Companilactobacillus zhachilii HBUAS52074^T (98.86 %) and Companilactobacillus heilongiiangensis S4-3^T (98.66 %). However, average nucleotide identity and in silico DNA-DNA hybridization values for these type strains were in the range of 79.90-92.93 % and 23.80-49.30 %, respectively, which offer evidence that strain NFFJ11^T belongs to a novel species of the genus Companilactobacillus. The cell-wall peptidoglycan type was A4α (l-Lys-d-Asp) and the G+C content of the genomic DNA was 35.7 mol%. The main fatty acids of strain NFFJ11^T were C_18 : 1  ω9c (43.3 %), C_16 : 0 (20.1 %) and summed feature 7 (18.3 %; comprising any combination of C_19 : 1  ω7c, C_19 : 1  ω6c and C_19 : 0 cyclo ω10c). Through polyphasic taxonomic analysis, it was observed that strain NFFJ11^T represents a novel species belonging to the genus Companilactobacillus, for which the name Companilactobacillus pabuli sp. nov. is proposed. The type strain is NFFJ11^T (= KACC 21771^T= JCM 34088^T).

Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory

This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.

Unraveling microbial fermentation features in kimchi: from classical to meta-omics approaches

Kimchi is a traditional Korean fermented food prepared via spontaneous fermentation by various microorganisms originating from vegetables such as kimchi cabbage, radishes, and garlic. Recent advances in meta-omics approaches that integrate metataxonomics, metagenomics, metatranscriptomics, and metabolomics have contributed to explaining and understanding food fermentation processes. Kimchi microbial communities are composed of majorly lactic acid bacteria such as Leuconostoc, Lactobacillus, and Weissella and fewer eukaryotic microorganisms and kimchi fermentation are accomplished by complex microbial metabolisms to produce diverse metabolites such as lactate, acetate, CO₂, ethanol, mannitol, amino acids, formate, malate, diacetyl, acetoin, and 2, 3-butanediol, which determine taste, quality, health benefit, and safety of fermented kimchi products. Therefore, in the future, kimchi researches should be systematically performed using the meta-omics approaches to understand complex microbial metabolisms during kimchi fermentation. KEY POINTS: • Spontaneous fermentation by raw material microbes gives kimchi its unique flavor. • The kimchi microbiome is altered by environmental factors and raw materials. • Through the multi-omics approaches, it is possible to accurately analyze the diversity and metabolic characteristics of kimchi microbiome and discover potential functionalities.

Complete genome sequence of Leuconostoc suionicum DSM 20241T provides insights into its functional and metabolic features

The genome of Leuconostoc suionicum DSM 20241^T (=ATCC 9135^T = LMG 8159^T = NCIMB 6992^T) was completely sequenced and its fermentative metabolic pathways were reconstructed to investigate the fermentative properties and metabolites of strain DSM 20241^T during fermentation. The genome of L. suionicum DSM 20241^T consists of a circular chromosome (2026.8 Kb) and a circular plasmid (21.9 Kb) with 37.58% G + C content, encoding 997 proteins, 12 rRNAs, and 72 tRNAs. Analysis of the metabolic pathways of L. suionicum DSM 20241^T revealed that strain DSM 20241^T performs heterolactic acid fermentation and can metabolize diverse organic compounds including glucose, fructose, galactose, cellobiose, mannose, sucrose, trehalose, arbutin, salcin, xylose, arabinose and ribose.

A proposal of Leuconostoc mesenteroides subsp. jonggajibkimchii subsp. nov. and reclassification of Leuconostoc mesenteroides subsp. suionicum (Gu et al., 2012) as Leuconostoc suionicum sp. nov. based on complete genome sequences

The type strains of four subspecies of Leuconostocmesenteroides, L. mesenteroidessubsp. mesenteroides, L. mesenteroidessubsp. cremoris, L. mesenteroidessubsp. dextranicum and L. mesenteroidessubsp. suionicum, and strain DRC1506T, used as a starter culture for commercial kimchi production in Korea, were phylogenetically analyzed on the basis of their complete genome sequences. Although the type strains of the four L. mesenteroides subspecies and strain DRC1506T shared very high 16S rRNA gene sequence similarities (>99.72 %), the results of analysis of average nucleotide identity (ANI), in silico DNA-DNA hybridization (DDH) and core-genome-based relatedness indicated that they could form five different phylogenetic lineages. The type strains of L. mesenteroidessubsp. mesenteroides, L. mesenteroidessubsp. cremoris and L. mesenteroidessubsp. dextranicum and DRC1506T shared higher ANI and in silico DDH values than the thresholds (95-96 % and 70 %, respectively) generally accepted for different species delineation, whereas the type strain of L. mesenteroidessubsp. suionicum (DSM 20241T) shared lower ANI (<94.1 %) and in silico DDH values (<57.0 %) with the other four L. mesenteroides lineage strains, indicating that DSM 20241T couldn be reclassified as representing a different species. Here, we report that DRC1506T represents a novel subspecies within the species Leuconostoc mesenteroides, for which the name Leuconostoc mesenteroidessubsp. jonggajibkimchii subsp. nov. is proposed. The type strain is DRC1506T (=KCCM 43249T=JCM 31787T). In addition, L. mesenteroidessubsp. suionicum is also reclassified as Leuconostoc suionicum. sp. nov. (type strain DSM 20241T=ATCC 9135T=LMG 8159T=NCIMB 6992T).

New horizons in the extraction of bioactive compounds using deep eutectic solvents: A review

With the rapid development of ionic liquid analogues, termed 'deep eutectic solvents' (DESs), and their application in a wide range of chemical and biochemical processes in the past decade, the extraction of bioactive compounds has attracted significant interest. Recently, numerous studies have explored the extraction of bioactive compounds using DESs from diverse groups of natural sources, including animal and plant sources. This review summarizes the-state-of-the-art effort dedicated to the application of DESs in the extraction of bioactive compounds. The aim of this review also was to introduce conventional and recently-developed extraction techniques, with emphasis on the use of DESs as potential extractants for various bioactive compounds, such as phenolic acid, flavonoids, tanshinone, keratin, tocols, terpenoids, carrageenans, xanthones, isoflavones, α-mangostin, genistin, apigenin, and others. In the near future, DESs are expected to be used extensively for the extraction of bioactive compounds from various sources.

Mycobacterium paraintracellulare sp. nov., for the genotype INT-1 of Mycobacterium intracellulare

Three mycobacterial strains, isolated from independent Korean patients with pulmonary infections, belonging to the Mycobacterium intracellulare genotype 1 (INT-1) were characterized using a polyphasic approach. The sequences of the 16S rRNA gene and internal transcribed spacer 1 (ITS1) of the INT-1 strains were identical to those of Mycobacterium intracellulare ATCC 13950T. However, multilocus sequence typing (MLST) analysis targeting five housekeeping genes (hsp65, rpoB, argG, gnd and pgm) revealed the phylogenetic separation of these strains from M. intracellulare ATCC 13950T. DNA-DNA hybridization values of >70 % confirmed that the three isolates belong to the same species, while the values of <70 % between one of them and the type strains of M. intracellulare and Mycobacterium chimaera confirmed their belonging to a distinct species. In addition, phenotypic characteristics such as positive growth on MacConkey agar and in acidic broth culture, unique matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS profiles of lipids, and unique mycolic acids profiles further supported the taxonomic status of these strains as representatives of a novel species of the Mycobacterium avium complex named Mycobacterium paraintracellulare. The type strain is MOTT64T (=KCTC 29084T=JCM 30622T).

Antibiotic Susceptibility Profiles of Dairy Leuconostoc, Analysis of the Genetic Basis of Atypical Resistances and Transfer of Genes In Vitro and in a Food Matrix

In spite of a global concern on the transfer of antibiotic resistances (AR) via the food chain, limited information exists on this issue in species of Leuconostoc and Weissella, adjunct cultures used as aroma producers in fermented foods. In this work, the minimum inhibitory concentration was determined for 16 antibiotics in 34 strains of dairy origin, belonging to Leuconostoc mesenteroides (18), Leuconostoc citreum (11), Leuconostoc lactis (2), Weissella hellenica (2), and Leuconostoc carnosum (1). Atypical resistances were found for kanamycin (17 strains), tetracycline and chloramphenicol (two strains each), and erythromycin, clindamycin, virginiamycin, ciprofloxacin, and rifampicin (one strain each). Surprisingly, L. mesenteroides subsp. mesenteroides LbE16, showed resistance to four antibiotics, kanamycin, streptomycin, tetracycline and virginiamycin. PCR analysis identified tet(S) as responsible for tetracycline resistance in LbE16, but no gene was detected in a second tetracycline-resistant strain, L. mesenteroides subsp. cremoris LbT16. In Leuconostoc mesenteroides subsp. dextranicum LbE15, erythromycin and clindamycin resistant, an erm(B) gene was amplified. Hybridization experiments proved erm(B) and tet(S) to be associated to a plasmid of ≈35 kbp and to the chromosome of LbE15 and LbE16, respectively. The complete genome sequence of LbE15 and LbE16 was used to get further insights on the makeup and genetic organization of AR genes. Genome analysis confirmed the presence and location of erm(B) and tet(S), but genes providing tetracycline resistance in LbT16 were again not identified. In the genome of the multi-resistant strain LbE16, genes that might be involved in aminoglycoside (aadE, aphA-3, sat4) and virginiamycin [vat(E)] resistance were further found. The erm(B) gene but not tet(S) was transferred from Leuconostoc to Enterococcus faecalis both under laboratory conditions and in cheese. This study contributes to the characterization of AR in the Leuconostoc-Weissella group, provides evidence of the genetic basis of atypical resistances, and demonstrates the inter-species transfer of erythromycin resistance.

Leuconostoc rapi sp. nov., isolated from sous-vide-cooked rutabaga

A Gram-stain-positive, ovoid, lactic acid bacterium, strain LMG 27676T, was isolated from a spoiled sous-vide-cooked rutabaga. 16S rRNA gene sequence analysis indicated that the novel strain belongs to the genus Leuconostoc, with Leuconostoc kimchii and Leuconostoc miyukkimchii as the nearest neighbours (99.1 and 98.8% 16S rRNA gene sequence similarity towards the type strain, respectively). Phylogenetic analysis of the 16S rRNA gene, multilocus sequence analysis of the pheS, rpoA and atpA genes, and biochemical and genotypic characteristics allowed differentiation of strain LMG 27676T from all established species of the genus Leuconostoc. Strain LMG 27676T ( = R-50029T = MHB 277T = DSM 27776T) therefore represents the type strain of a novel species, for which the name Leuconostoc rapi sp. nov. is proposed.

A novel multi-locus sequence typing (MLST) protocol for Leuconostoc lactis isolates from traditional dairy products in China and Mongolia

BACKGROUND

Economically, Leuconostoc lactis is one of the most important species in the genus Leuconostoc. It plays an important role in the food industry including the production of dextrans and bacteriocins. Currently, traditional molecular typing approaches for characterisation of this species at the isolate level are either unavailable or are not sufficiently reliable for practical use. Multilocus sequence typing (MLST) is a robust and reliable method for characterising bacterial and fungal species at the molecular level. In this study, a novel MLST protocol was developed for 50 L. lactis isolates from Mongolia and China.

RESULTS

Sequences from eight targeted genes (groEL, carB, recA, pheS, murC, pyrG, rpoB and uvrC) were obtained. Sequence analysis indicated 20 different sequence types (STs), with 13 of them being represented by a single isolate. Phylogenetic analysis based on the sequences of eight MLST loci indicated that the isolates belonged to two major groups, A (34 isolates) and B (16 isolates). Linkage disequilibrium analyses indicated that recombination occurred at a low frequency in L. lactis, indicating a clonal population structure. Split-decomposition analysis indicated that intraspecies recombination played a role in generating genotypic diversity amongst isolates.

CONCLUSIONS

Our results indicated that MLST is a valuable tool for typing L. lactis isolates that can be used for further monitoring of evolutionary changes and population genetics.

Flavihumibacter solisilvae sp. nov., isolated from forest soil

A Gram-stain-positive, strictly aerobic, yellow colony-forming bacterium, designated strain 3-3(T), was isolated from forest soil of Bac Kan Province in Vietnam. Cells were non-motile rods without gliding motility, showing oxidase- and catalase-positive reactions. Growth was observed at 20-37 °C (optimum, 28 °C) and pH 5.5-9.5 (optimum, pH 7.5). The major cellular fatty acids were iso-C(15 : 0), iso-C(15 : 1) G and summed feature 3 (comprising C(16 : 1)ω6c and/or C(16 : 1)ω7c). Strain 3-3(T) contained phosphatidylethanoamine, three unidentified aminolipids and three unidentified lipids. The G+C content of the genomic DNA was 49.5 mol% and the only isoprenoid quinone detected was menaquinone 7 (MK-7). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 3-3(T) formed a tight phylogenetic lineage with Flavihumibacter petaseus T41(T) with a bootstrap value of 100%. Strain 3-3(T) was related most closely to F. petaseus T41(T) with 97.3% 16S rRNA gene sequence similarity and the level of DNA-DNA relatedness between the two was 9.4±1.2%. Based on phenotypic, chemotaxonomic and molecular features, strain 3-3(T) represents a novel species of the genus Flavihumibacter, for which the name Flavihumibacter solisilvae sp. nov. is proposed. The type strain is 3-3(T) ( = KACC 17917(T) = JCM 19891(T)).

Ramlibacter solisilvae sp. nov., isolated from forest soil, and emended description of the genus Ramlibacter

A Gram-staining-negative, strictly aerobic, white-colony-forming bacterium, designated strain 5-10T, was isolated from forest soil of Bac Kan Province in Vietnam. Cells were non-motile rods or coccoids, showing oxidase- and catalase-positive reactions. Growth was observed at 10–37 °C (optimum, 30 °C), at pH 5.0–9.0 (optimum, pH 7.0) and in the presence of 0–1.0 % (w/v) NaCl (optimum, 0–0.5 %). The major cellular fatty acids were summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0, C10 : 0 3-OH and summed feature 8 (comprising C18 : 1ω6c and/or C18 : 1ω7c). The G+C content of the genomic DNA was 69.9 mol% and the only respiratory quinone detected was ubiquinone 8 (Q-8). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 5-10T formed a tight phyletic lineage with members of the genus Ramlibacter . Strain 5-10T was most closely related to Ramlibacter tataouinensis TTB310T (97.3 %), but the DNA–DNA relatedness level between the two strains was 38.2±1.8 %. Based on phenotypic, chemotaxonomic and molecular features, strain 5-10T was shown to represent a novel species of the genus Ramlibacter , for which the name Ramlibacter solisilvae sp. nov. is proposed. The type strain is 5-10T ( = KACC 17567T = JCM 19319T). An emended description of the genus Ramlibacter is also proposed.

Reclassification of Leuconostoc gasicomitatum as Leuconostoc gelidum subsp. gasicomitatum comb. nov., description of Leuconostoc gelidum subsp. aenigmaticum subsp. nov., designation of Leuconostoc gelidum subsp. gelidum subsp. nov. and emended description of Leuconostoc gelidum

In the present study we investigated the taxonomic status of 20 lactic acid bacteria (LAB) originating from packaged meat. On the basis of 16S rRNA gene sequence similarity, these strains were shown to belong to the genus Leuconostoc with Leuconostoc gelidum, Leuconostoc inhae and Leuconostoc gasicomitatum as the closest phylogenetic relatives. The novel strains shared more than 70 % DNA-DNA relatedness with type and reference strains of both L. gelidum and L. gasicomitatum. The DNA-DNA relatedness values between L. gelidum type and reference strains and L. gasicomitatum type and reference strains were also above 70 %, showing that all these strains belonged to the same species. Sequence analyses of concatenated atpA, pheS, and rpoA genes demonstrated that the novel strains as well as type and reference strains of L. gelidum and L. gasicomitatum are phylogenetically closely related, but form three clearly separated subgroups. Numerical analysis of HindIII ribopatterns and phenotypic tests supported this subdivision. Based on the data presented in this study, we propose to reclassify Leuconostoc gasicomitatum as Leuconostoc gelidum subsp. gasicomitatum comb. nov. (type strain, LMG 18811(T) = DSM 15947(T)). The novel strains isolated in the present study represent a novel subspecies, for which the name Leuconostoc gelidum subsp. aenigmaticum subsp. nov. is proposed, with POUF4d(T) ( = LMG 27840(T) = DSM 19375(T)) as the type strain. The proposal of these two novel subspecies automatically creates the subspecies Leuconostoc gelidum subsp. gelidum subsp. nov. (type strain, NCFB 2775(T) = DSM 5578(T)). An emended description of Leuconostoc gelidum is also provided.

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

Three Gram-stain-positive bacterial strains, 11050T, 7-19T and 11102T, were isolated from traditional pickle and sourdough in Heilongjiang Province, China. These bacteria were characterized by a polyphasic approach, including 16S rRNA gene sequence analysis, pheS gene sequence analysis, rpoA gene sequence analysis, dnaK gene sequence analysis, fatty acid methyl ester (FAME) analysis, determination of DNA G+C content, DNA–DNA hybridization and an analysis of phenotypic features. Strain 11050T belonged to the Lactobacillus plantarum species group and shared 98.0–98.4 % 16S rRNA gene sequence similarities and 84.7–88.9 % dnaK gene sequence similarities with type strains of Lactobacillus plantarum subsp. plantarum , Lactobacillus plantarum subsp. argentoratensis , Lactobacillus pentosus , Lactobacillus paraplantarum , Lactobacillus fabifermentans and Lactobacillus xiangfangensis and had 75.9–80.7 % pheS gene sequence similarities and 90.7–92.5 % rpoA gene sequence similarities with Lactobacillus plantarum subsp. plantarum LMG 6907T, Lactobacillus plantarum subsp. argentoratensis LMG 9205, Lactobacillus pentosus LMG 10755T, Lactobacillus paraplantarum LMG 16673T, Lactobacillus fabifermentans LMG 24284T and Lactobacillus xiangfangensis 3.1.1T, respectively. Strain 7-19T was phylogenetically related to Lactobacillus thailandensis , Lactobacillus pantheris and Lactobacillus sharpeae , having 94.1–96.7 % 16S rRNA gene sequence similarities, 71.5–82.3 % pheS gene sequence similarities and 71.2–83.4 % rpoA gene sequence similarities with type strains of Lactobacillus thailandensis , Lactobacillus pantheris and Lactobacillus sharpeae , respectively. Strain 11102T was phylogenetically related to Lactobacillus oligofermentans , Lactobacillus suebicus , Lactobacillus vaccinostercus and Lactobacillus hokkaidonensis . Strain 11102T had 99.2 % 16S rRNA gene sequence similarity, 81.3 % pheS gene sequence similarity and 96.1 % rpoA gene sequence similarity with Lactobacillus oligofermentans LMG 22743T, respectively. Strain 11102T shared 96.0–96.8 % 16S rRNA gene sequence similarities, 73.3–81.0 % pheS gene sequence similarities and 74.6–76.9 % rpoA gene sequence similarities with type strains of Lactobacillus suebicus , Lactobacillus vaccinostercus and Lactobacillus hokkaidonensis , respectively. Based upon the data from polyphasic characterization obtained in the present study, three novel species, Lactobacillus mudanjiangensis sp. nov., Lactobacillus songhuajiangensis sp. nov. and Lactobacillus nenjiangensis sp. nov., are proposed and the type strains are 11050T ( = LMG 27194T = CCUG 62991T), 7-19T ( = LMG 27191T = NCIMB 14832T = CCUG 62990T) and 11102T ( = LMG 27192T = NCIMB 14833T), respectively.

Lactobacillus heilongjiangensis sp. nov., isolated from Chinese pickle

A Gram-stain-positive bacterial strain, S4-3T, was isolated from traditional pickle in Heilongjiang Province, China. The bacterium was characterized by a polyphasic approach, including 16S rRNA gene sequence analysis, pheS gene sequence analysis, rpoA gene sequence analysis, dnaK gene sequence analysis, fatty acid methyl ester (FAME) analysis, determination of DNA G+C content, DNA–DNA hybridization and an analysis of phenotypic features. Strain S4-3T showed 97.9–98.7 % 16S rRNA gene sequence similarities, 84.4–94.1 % pheS gene sequence similarities and 94.4–96.9 % rpoA gene sequence similarities to the type strains of Lactobacillus nantensis , Lactobacillus mindensis , Lactobacillus crustorum , Lactobacillus futsaii , Lactobacillus farciminis and Lactobacillus kimchiensis . dnaK gene sequence similarities between S4-3T and Lactobacillus nantensis LMG 23510T, Lactobacillus mindensis LMG 21932T, Lactobacillus crustorum LMG 23699T, Lactobacillus futsaii JCM 17355T and Lactobacillus farciminis LMG 9200T were 95.4, 91.5, 90.4, 91.7 and 93.1 %, respectively. Based upon the data obtained in the present study, a novel species, Lactobacillus heilongjiangensis sp. nov., is proposed and the type strain is S4-3T ( = LMG 26166T = NCIMB 14701T).

Complete genome sequence of Leuconostoc mesenteroides subsp. mesenteroides strain J18, isolated from kimchi

Leuconostoc mesenteroides subsp. mesenteroides is one of the most predominant lactic acid bacterial groups during kimchi fermentation. Here, we report the complete genome sequence of L. mesenteroides subsp. mesenteroides J18, which was isolated from kimchi. The genome of the strain consists of a 1,896,561-bp chromosome and five plasmids.