Development and evaluation of genome-probing microarrays for monitoring lactic acid bacteria

Development of a selective medium for the enumeration of lactic acid bacteria and bifidobacteria in food products

This study was conducted to develop a selective medium for enumerating LAB and Bifidobacteria in food samples. Thirteen media were evaluated to determine their suitability for selectively enumerating LAB (17 bacilli and 7 cocci) and Bifidobacteria (12 strains) under aerobic and anaerobic conditions. When BL, BCP, and mMRS were supplemented with propionic acid (5 ml/l) and adjusted to pH 5, the growth of all indicator microorganisms was inhibited; however, these media also inhibited the growth of certain LAB and Bifidobacterial strains. Using propionic acid, the pH levels of BL, BCP, and mMRS were adjusted to pH 5.2, 6.0, and 6.0, respectively. These media inhibited the growth of all indicator microorganisms, whereas they did not inhibit any of the LAB and Bifidobacteria strains under anaerobic conditions. Overall, BLP (pH 5.8) lacking blood showed significantly higher bacterial counts compared with other media in food products. Further analyses indicated that BLP (pH 5.8) was the most suitable medium for enumerating LAB and Bifidobacteria in food.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-022-01202-z.

Molecular tools for the analysis of the microbiota involved in malolactic fermentation: from microbial diversity to selection of lactic acid bacteria of enological interest

Winemaking is a complex process involving two successive fermentations: alcoholic fermentation, by yeasts, and malolactic fermentation (MLF), by lactic acid bacteria (LAB). During MLF, LAB can contribute positively to wine flavor through decarboxylation of malic acid with acidity reduction and other numerous enzymatic reactions. However, some microorganisms can have a negative impact on the quality of the wine through processes such as biogenic amine production. For these reasons, monitoring the bacterial community profiles during MLF can predict and control the quality of the final product. In addition, the selection of LAB from a wine-producing area is necessary for the formulation of native malolactic starter cultures well adapted to local winemaking practices and able to enhance the regional wine typicality. In this sense, molecular biology techniques are fundamental tools to decipher the native microbiome involved in MLF and to select bacterial strains with potential to function as starter cultures, given their enological and technological characteristics. In this context, this work reviews the different molecular tools (both culture-dependent and -independent) that can be applied to the study of MLF, either in bacterial isolates or in the microbial community of wine, and of its dynamics during the process.

Distribution and characterization of prophages in Lactobacillus plantarum derived from kimchi

Prophage distribution and phage characteristics based on the genome of Lactobacillus plantarum derived from kimchi were investigated. Prophage genomes retrieved from a database were analyzed in silico with prophage inducibility. Twenty-one kimchi-derived L. plantarum had at least one intact prophage, including a putative cryptic state on the chromosome. They were all confirmed to belong to the Siphoviridae family. Intact prophages can be classified into three different groups: PM411-like, Sha1-like, and unclassified phage groups. Some prophage regions were encoded with superinfection exclusion proteins and orphan methylases, suggesting that the phages co-evolved with their hosts. Interestingly, prophage inducibility showed that only DNA damage could induce prophages and that pH stresses by organic acids could not. Therefore, the prophage of L. plantarum did not affect the host unless DNA was damaged, and it would hardly affect the viability of the host through phage induction during kimchi fermentation. Our results might provide insights into the distribution and non-inducibility of prophages, existence of phage-immunity genes, and role of plant-derived L. plantarum prophages in host survival during late acidic kimchi fermentation.

Effect of Fungi on Metabolite Changes in Kimchi During Fermentation

The purpose of this study is to investigate the effect of fungi on kimchi metabolites during fermentation. A gas chromatography-mass spectrometry (GC-MS) based metabolite profiling approach in combination with principal component analysis (PCA) is performed to differentiate metabolites produced by fungi or bacteria. To avoid bacterial growth, kimchi is treated with 100 μg/mL of ampicillin every three days from 30 to 50 days of fermentation. The relative content of the major fungi at 50 days of fermentation, between the control group and the ampicillin treatment group, was not significantly different. The administration of ampicillin changed the metabolites in kimchi by affecting the growth of kimchi bacteria. Based on the pattern of change of each metabolite, the changed metabolites are grouped into four categories: (1) metabolites produced or consumed by fungi, (2) metabolites involving both fungi and bacteria, (3) metabolites produced or consumed by bacteria, and (4) metabolites of undetermined origin. Alanine, thymine, galacturonic acid, and malonic acid can be regarded as the metabolites produced by fungi between 30 and 50 days of fermentation. In contrast, malic acid, oxaloacetic acid, galactitol, glucose, and mannitol are presumed to be the metabolites mainly consumed by fungi. This study is meaningful as the first study conducted by inhibiting growth of bacteria to identify the metabolites contributed by fungi or bacteria in the kimchi fermentation process. These results could be used to make customized kimchi that controls the production of desired metabolites by selectively controlling the formation of microbial communities in the kimchi industry.

Design of Primers for Evaluation of Lactic Acid Bacteria Populations in Complex Biological Samples

Lactic acid bacteria (LAB) are important for human health. However, the relative abundance of LAB in complex samples, such as fecal samples, is low and their presence and diversity (at the species level) is understudied. Therefore, we designed LAB-specific primer pairs based on 16S rRNA gene consensus sequences from 443 species of LAB from seven genera. The LAB strains selected were genetically similar and known to play a role in human health. Prior to primer design, we obtained consistent sequences for the primer-binding sites by comparing the 16S rRNA gene sequences, manually identifying single-stranded primers and modifying these primers using degenerate bases. We assembled primer pairs with product sizes of >400 bp. Optimal LAB-specific primers were screened using three methods: PCR amplification, agarose gel electrophoresis and single-molecule real-time (SMRT) sequencing analysis. During the SMRT analysis procedure, we focused on sequence reads and diversity at the species level of target LAB in three fecal samples, using the universal bacterium primer 27f/1492r as a reference control. We created a phylogenetic tree to confirm the ability of the best candidate primer pair to differentiate amongst species. The results revealed that LAB-specific primer L5, with a product size of 750 bp, could generate 3222, 2552, and 3405 sequence reads from fecal Samples 1, 2, and 3. This represented 14, 13 and 10% of all target LAB sequence reads, respectively, compared with 2, 0.8, and 0.8% using the 27f/1492r primer. In addition, L5 detected LAB that were in low abundance and could not be detected using the 27f/1492r primer. The phylogenetic tree based on the alignments between the forward and reverse primer of L5 showed that species within the seven target LAB genera could be distinguished from each other, confirming L5 is a powerful tool for inferring phylogenetic relationships amongst LAB species. In conclusion, L5 is a LAB-specific primer that can be used for high-throughput sequencing and identification of taxa to the species level, especially in complex samples with relatively low LAB content. This enables further research on LAB population diversity in complex ecosystem, and on relationships between LAB and their hosts.

Proteus cibarius sp. nov., a swarming bacterium from Jeotgal, a traditional Korean fermented seafood, and emended description of the genus Proteus

A novel Proteus-like, Gram-stain-negative, facultatively anaerobic, rod-shaped bacterium, designated strain JS9T, was isolated from Korean fermented seafood, Jeotgal. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain JS9T belonged to the genus Proteus in the family Enterobacteriaceae. The highest 16S rRNA gene sequence similarity of strain JS9T was to Proteus vulgaris KCTC 2579T (98.98 %) and the genomic DNA G+C content is 39.0 mol%. DNA-DNA hybridization values were measured and strain JS9T showed <20.8 % genomic relatedness with closely-related members of the genus Proteus. The isolate showed bacterial motility and swarming activity similar to those of pathogenic Proteus mirabilis but distinct from those of other species of the genus Proteus. The isolate grows optimally at 30 °C, at pH 7, and in the presence of 2 % (w/v) NaCl. The main respiratory quinones are ubiquinone Q-8 and Q-10, and the major cellular fatty acids are C16 : 0, summed feature 3 and summed feature 8. The polar lipids comprise phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, an unidentified amino lipid, two unidentified amino-phospholipids, and three unidentified lipids. Based on phylogenetic, phenotypic, chemotaxonomic and genotypic analyses, strain JS9T represents a novel species of the genus Proteus, for which the name Proteus cibarius sp. nov. is proposed. The type strain is JS9T (=KACC 18404T=JCM 30699T). An emended description of the genus Proteus is also provided.

Simplicispira piscis sp. nov., isolated from the gut of a Korean rockfish, Sebastes schlegelii

A novel Gram-stain-negative, aerobic, motile and rod-shaped bacterium, designated strain RSG39T, was isolated from the gut of a Korean rockfish, Sebastes schlegelii. The 16S rRNA gene sequence analysis revealed that strain RSG39T belonged to the genus Simplicispira in the class Betaproteobacteria and its highest sequence similarity was shared with S. psychrophila (98.4 %). The isolate grew optimally at 20 °C, at pH 7 and with 0 % (w/v) NaCl. The main respiratory quinone of the isolate was ubiquinone Q-8. The major cellular fatty acids were C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The polar lipids of the isolate were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and six unidentified lipids. The DNA–DNA hybridization values showed < 7.4 % genomic relatedness with closely related strains. The genomic DNA G+C content was 65.2 mol %. Based on phylogenetic, phenotypic, chemotaxonomic and genotypic analyses, strain RSG39T represents a novel species of the genus Simplicispira, for which the name Simplocospira piscis sp. nov. is proposed. The type strain is RSG39T ( = KACC 17539T = JCM 19291T).

Molecular analysis of skin bacterial assemblages from codfish and pollock after dry-salted fish production

Dry-salted codfish and pollock are commercially important food products with a relatively long shelf life. To date, bacterial assemblages present in these products that are relevant for food safety have been monitored using only classical molecular and/or cultivation methods. The present study employed a rapid and accurate identification method involving PCR with denaturing gradient gel electrophoresis and pyrosequencing to characterize the bacterial assemblages in the skin of three closely related fishes: Gadus morhua, Gadus macrocephalus, and Theragra chalcogramma. This methodology can be crucial for timely identification of food spoilage, hazard analysis, and monitoring of critical control points during food production. Although all specimens were processed in the same factory, there were significant compositional differences in their skin bacterial communities. In general, the bacterial community was dominated by gram-negative species of the Gammaproteobacteria. Pyrosequencing yielded 90, 69, and 245 operational taxonomic units associated with G. morhua, G. macrocephalus, and T. chalcogramma, respectively. The most dominant operational taxonomic units were assigned in order to Pseudomonas sp., Serratia marcescens, Salinisphaera sp., and Psychrobacter pulmonis. Spoilage and pathogenic bacterial groups were detected in all the studied salted gadoid samples.

Corynebacterium atrinae sp. nov., isolated from the gastrointestinal tract of a pen shell, Atrina pectinata

A novel Gram-stain-positive, non-motile, facultatively anaerobic and rod-shaped bacterium, strain PSPT56T, was isolated from the gastrointestinal tract of a pen shell (Atrina pectinata). Optimal growth of strain PSPT56T was ascertained to occur at 30 °C, pH 8.0 and in the presence of 1–2 % (w/v) NaCl. The strain was catalase-positive and oxidase-negative. The major cellular fatty acids were C18 : 1ω9c, C16 : 0, C17 : 1ω8c and C17 : 0. Tuberculostearic acid was not present. The major cell-wall sugars were ribose, galactose, glucose and arabinose. Peptidoglycan amino acids were meso-diaminopimelic acid, alanine and glutamic acid. The predominant isoprenoid quinone was MK-8(H2). Strain PSPT56T contained phosphatidylglycerol, diphosphatidylglycerol, an unidentified phospholipid, two unidentified lipids and two unidentified amino-lipids. Mycolic acids were detected as constitutive components of the cell wall. A phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strain PSPT56T was most closely related to Corynebacterium testudinoris M935/96/4T and Corynebacterium felinum M714/95/5T with 98.69 % and 97.01 % similarity, respectively. DNA–DNA hybridization experiments indicated less than 29.9 % relatedness to the phylogenetically closest species. The G+C content of genomic DNA was 67.6 mol%. The phenotypic, phylogenetic and genotypic analyses indicated that strain PSPT56T represents a novel species within the genus Corynebacterium , for which the name Corynebacterium atrinae is proposed. The type strain is PSPT56T ( = KACC 17525T = JCM 19266T).

Actibacter haliotis sp. nov., isolated from the gut of an abalone, Haliotis discus hannai, and emended description of the genus Actibacter

A novel strain, designated strain W113T, was isolated from the gut of an abalone, Haliotis discus hannai, which was collected from the northern coast of Jeju in Korea. The isolate was a Gram-staining-negative, facultatively anaerobic, non-motile, rod-shaped bacterium producing yellow-to-orange carotenoid-type pigments. 16S rRNA gene sequence analysis showed that the isolate belonged to the genus Actibacter in the family Flavobacteriaceae and it shared the highest sequence similarity with the type strain of Actibacter sediminis (98.8 % similarity). Optimal growth occurred at 25 °C, at pH 7 and with 2 % (w/v) NaCl. The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C15 : 1 G. Menaquinone-6 was the main respiratory quinone. The polar lipids of the isolate were phosphatidylethanolamine, three unidentified amino lipids, and three unidentified lipids. The genomic DNA G+C content was 42.6 mol% and DNA–DNA hybridization values indicated that the strain shared <18 % genomic relatedness with the most closely related species. The results of the phylogenetic, phenotypic and genotypic analyses indicated that strain W113T represents a novel species in the genus Actibacter , for which the name Actibacter haliotis sp. nov. is proposed. The type strain is W113T ( = KACC 17209T = JCM 18868T).

Acinetobacter apis sp. nov., isolated from the intestinal tract of a honey bee, Apis mellifera

A novel Gram-negative, obligate aerobic, non-motile, and both coccobacillus- and bacillus-shaped bacterium, designated strain HYN18(T), was isolated from the intestinal tract of a honey bee (Apis mellifera). The isolate was oxidase-negative and catalase-positive. Strain HYN18(T) showed optimum growth at 25°C, pH 6-7, and in the presence of 1% (w/v) NaCl in trypticase soy broth medium. The isolate was negative for hydrolyses of starch, casein, gelatin and urea, indole production from tryptone and hemolysis on sheep blood agar. A phylogenetic analysis based on the 16S rRNA gene and rpoB gene sequence showed that strain HYN18(T) was most closely related to Acinetobacter nectaris SAP 763.2(T) and A. boissieri SAP 284.1(T) with 98.3% and 98.1% similarity (16S rRNA gene), respectively, and 84.4% similarity with Acinetobacter nectaris SAP 763.2(T) (rpoB gene). The major cellular fatty acids were summed features 3 (comprising C16:1ω7c /C16:1ω6c ), C12:0 and C16:0. The main isoprenoid quinone was ubiquinone-9 (Q-9). The polar lipids of strain HYN18(T) were phosphatidylethanolamine, three unidentified lipids, an unidentified phospholipid and an unidentified glycolipid. The DNA G+C content was 40.6 mol%. DNA-DNA hybridization experiments indicated less than 33 ± 10% relatedness to the closest phylogenetic species, Acinetobacter nectaris SAP 763.2(T). Thus, the phenotypic, phylogenetic and genotypic analyses indicate that strain HYN18(T) is a novel species within the genus Acinetobacter, for which the name Acinetobacter apis is proposed. The type strain is HYN18(T) (=KACC 16906(T) =JCM 18575(T)).

Polaribacter atrinae sp. nov., isolated from the intestine of a comb pen shell, Atrina pectinata

A novel Gram-staining-negative, aerobic, non-motile, yellow-to-orange carotenoid-type-pigmented and rod-shaped bacterium, designated strain WP25T, was isolated from the intestine of a comb pen shell, Atrina pectinata, which was collected from the South Sea near Yeosu in Korea. The isolate grew optimally at 20 °C, at pH 7 and with 2 % (w/v) NaCl. 16S rRNA gene sequence analysis showed that strain WP25T belonged to the genus Polaribacter in the family Flavobacteriaceae and the highest sequence similarity was shared with the type strain of Polaribacter sejongensis (98.5 %). The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, C15 : 1ω6c and iso-C15 : 0 3-OH. The main respiratory quinone was menaquinone MK-6. The polar lipids of strain WP25T were phosphatidylethanolamine, two unidentified aminolipids, an unidentified phospholipid and four unidentified lipids. The genomic DNA G+C content was 31.2 mol%. DNA–DNA hybridization experiments indicated <12.6 % genomic relatedness with closely related strains. Based on phylogenetic, phenotypic and genotypic analyses, strain WP25T represents a novel species in the genus Polaribacter , for which the name Polaribacter atrinae sp. nov. is proposed, with the type strain WP25T ( = KACC 17473T = JCM 19202T).

Endozoicomonas atrinae sp. nov., isolated from the intestine of a comb pen shell Atrina pectinata

A novel bacterium, designated strain WP70(T), was isolated from the gut of a comb pen shell (Atrina pectinata) collected from the southern sea of Yeosu in Korea. The isolate was Gram-stain-negative, aerobic, non-motile and rod-shaped. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain WP70(T) belonged to the genus Endozoicomonas. The highest level of sequence similarity (98.4%) was shared with Endozoicomonas elysicola MKT110(T). Optimal growth occurred in 2% (w/v) NaCl at 30 °C and at pH 7. The major cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The main respiratory quinone was Q-9. The polar lipids comprised phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, three unidentified phospholipids, an unidentified aminolipid, an unidentified aminophospholipid and an unidentified lipid. The genomic DNA G+C content was 50.5 mol% and DNA-DNA hybridization values indicated <11% genomic relatedness to the closest species. Physiological, biochemical, chemotaxonomic and genotypic analyses indicated that strain WP70(T) represents a novel species of the genus Endozoicomonas, for which the name Endozoicomonas atrinae sp. nov. is proposed. The type strain is WP70(T) ( = KACC 17474(T)  = JCM 19190(T)).

Actinomyces haliotis sp. nov., a bacterium isolated from the gut of an abalone, Haliotis discus hannai

A novel, Gram-staining-positive, facultatively anaerobic, non-motile and coccus-shaped bacterium, strain WL80T, was isolated from the gut of an abalone, Haliotis discus hannai, collected from the northern coast of Jeju in Korea. Optimal growth occurred at 30 °C, pH 7–8 and with 1 % (w/v) NaCl. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that strain WL80T fell within the cluster of the genus Actinomyces , with highest sequence similarity to the type strains of Actinomyces radicidentis (98.8 % similarity) and Actinomyces urogenitalis (97.0 % similarity). The major cellular fatty acids were C18 : 1ω9c and C16 : 0. Menaquinone-10 (H4) was the major respiratory quinone. The genomic DNA G+C content of the isolate was 70.4 mol%. DNA–DNA hybridization values with closely related strains indicated less than 7.6 % genomic relatedness. The results of physiological, biochemical, chemotaxonomic and genotypic analyses indicated that strain WL80T represents a novel species of the genus Actinomyces , for which the name Actinomyces haliotis sp. nov. is proposed. The type strain is WL80T ( = KACC 17211T = JCM 18848T).

Shimia haliotis sp. nov., a bacterium isolated from the gut of an abalone, Haliotis discus hannai

A novel Gram-stain-negative, motile, rod-shaped bacterium, designated strain WM35T, was isolated from the intestinal tract of an abalone, Haliotis discus hannai, which was collected from the northern coast of Jeju in Korea. The cells of the isolate grew optimally at 30 °C, pH 7, and with 3 % (w/v) NaCl. Based on 16S rRNA gene sequence similarity comparisons, strain WM35T was grouped in the genus Shimia and was closely related to the type strains of Shimia isoporae (98.7 % similarity) and Shimia marina (97.8 % similarity). The major cellular fatty acids were summed feature 8 and C16 : 0 2-OH. Ubiquinone Q-10 was the predominant respiratory quinone. The polar lipids of strain WM35T comprised phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminolipid and an unidentified lipid. The DNA G+C content of the isolate was 53.8 mol%. DNA–DNA hybridization values indicated <16 % genomic relatedness with members of the genus Shimia . The physiological, chemical and genotypic analyses indicated that strain WM35T represents a novel species of the genus Shimia , for which the name Shimia haliotis sp. nov. is proposed. The type strain is WM35T ( = KACC 17212T = JCM 18870T).

Cloacibacterium haliotis sp. nov., isolated from the gut of an abalone, Haliotis discus hannai

A novel Gram-stain-negative, aerobic, non-motile, yellow-pigmented and rod-shaped bacterium, designated strain WB5(T), was isolated from the intestinal tract of an abalone, Haliotis discus hannai, collected from the northern coast of Jeju in Korea. The isolate grew optimally at 30 °C, at pH 7 and in the presence of 0.5 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain WB5(T) was clustered in the genus Cloacibacterium and shared the highest sequence similarity with C. normanense (98.2 % similarity). The predominant fatty acids were iso-C15 : 0 and iso-C17 : 0 3-OH. Menaquinone-6 was the major respiratory quinone. The genomic DNA G+C content was 29.6 mol%. The DNA-DNA hybridization values indicated <22 % genomic relatedness with other members of the genus Cloacibacterium. The results of physiological, biochemical, chemotaxonomic and genotypic analyses showed that strain WB5(T) represents a novel species of the genus Cloacibacterium, for which the name Cloacibacterium haliotis sp. nov. is proposed. The type strain is WB5(T) ( = KACC 17210(T) = JCM 18869(T)).

Pseudoruegeria haliotis sp. nov., isolated from the gut of the abalone Haliotis discus hannai

A novel Gram-negative, aerobic, non-motile and rod-shaped bacterium, designated strain WM67(T), was isolated from the gut of an abalone (Haliotis discus hannai) collected from the northern coast of Jeju Island in Korea. Phylogenetic analyses based on the 16S rRNA gene sequence indicated that strain WM67(T) clustered in the genus Pseudoruegeria, and the highest sequence similarity was shared with Pseudoruegeria lutimaris (98.0 % similarity to the type strain). Optimal growth of the isolate occurred at 30 °C, pH 7-8 and with 1 % (w/v) NaCl. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. Ubiquinone Q-10 was the major respiratory quinone. The polar lipids of strain WM67(T) comprised phosphatidylserine, phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, an unidentified glycolipid and three unidentified lipids. The genomic DNA G+C content was 66.5 mol%. DNA-DNA hybridization indicated <17 % genomic relatedness to other members of the genus Pseudoruegeria. The physiological, biochemical, chemotaxonomic and genotypic analyses indicated that strain WM67(T) represents a novel species of Pseudoruegeria, for which the name Pseudoruegeria haliotis sp. nov. is proposed. The type strain is WM67(T) ( = KACC 17214(T) = JCM 18872(T)).

Weissella diestrammenae sp. nov., isolated from the gut of a camel cricket (Diestrammena coreana)

A novel, Gram-stain-positive, non-motile, facultatively anaerobic, rod- or coccoid-shaped bacterium, designated strain ORY33T, was isolated from the gut of a camel cricket (Diestrammena coreana). The 16S rRNA gene sequence analysis showed that strain ORY33T belonged to the genus Weissella , with highest sequence similarity to Weissella koreensis S-5623T (97.7 %). The strain grew optimally at 30 °C and pH 7 in the presence of 0 % (w/v) NaCl. Catalase and oxidase activities were negative. The genomic DNA G+C content of strain ORY33T was 45.1 mol%. DNA–DNA hybridization values between strain ORY33T and closely related members of the genus Weissella were less than 27 %. The major fatty acids of strain ORY33T were C18 : 1ω9c, C16 : 0 and C14 : 0. Based on these phenotypic, phylogenetic and genotypic analyses, strain ORY33T represents a novel species belonging to the genus Weissella , for which the name Weissella diestrammenae sp. nov. is proposed. The type strain is ORY33T ( = KACC 16890T = JCM 18559T).

Lactobacillus kimchiensis sp. nov., isolated from a fermented food

A novel bacterium was isolated from a traditional fermented food, kimchi. The morphology, physiology, biochemical properties and 16S rRNA gene sequence of strain L133T were studied. Strain L133T was Gram-reaction-positive, catalase-negative and homofermentative, with rod-shaped cells that formed cream colonies. Cells grew in the presence of 0–5 % (w/v) NaCl (optimum, 1–2 %), at pH 5.0–9.0 (optimum, pH 7.0–8.0) and at 15–37 °C (optimum, 25 °C). Comparative 16S rRNA gene and pheS sequence analysis of strain L133T indicated that the strain belonged to the genus Lactobacillus . The major fatty acids were identified as C18 : 1ω9c, C16 : 0 and C18 : 0, and the cell wall contained peptidoglycan of the l-Lys–d-Asp type. DNA–DNA relatedness values between strain L133T and related species were below 11±0.4 %. The DNA G+C content of strain L133T was 35.7 mol%. Analysis of 16S rRNA gene sequences, as well as physiological and biochemical tests, identified genotypic and phenotypic differences between strain L133T and other species of the genus Lactobacillus . Based on these analyses, strain L133T is proposed to be a novel species of the genus Lactobacillus , named Lactobacillus kimchiensis. The type strain is L133T ( = KACC 15533T = JCM 17702T = DSM 24716T).

RubisCO gene clusters found in a metagenome microarray from acid mine drainage

The enzyme responsible for carbon dioxide fixation in the Calvin cycle, ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), is always detected as a phylogenetic marker to analyze the distribution and activity of autotrophic bacteria. However, such an approach provides no indication as to the significance of genomic content and organization. Horizontal transfers of RubisCO genes occurring in eubacteria and plastids may seriously affect the credibility of this approach. Here, we presented a new method to analyze the diversity and genomic content of RubisCO genes in acid mine drainage (AMD). A metagenome microarray containing 7,776 large-insertion fosmids was constructed to quickly screen genome fragments containing RubisCO form I large-subunit genes (cbbL). Forty-six cbbL-containing fosmids were detected, and six fosmids were fully sequenced. To evaluate the reliability of the metagenome microarray and understand the microbial community in AMD, the diversities of cbbL and the 16S rRNA gene were analyzed. Fosmid sequences revealed that the form I RubisCO gene cluster could be subdivided into form IA and IB RubisCO gene clusters in AMD, because of significant divergences in molecular phylogenetics and conservative genomic organization. Interestingly, the form I RubisCO gene cluster coexisted with the form II RubisCO gene cluster in one fosmid genomic fragment. Phylogenetic analyses revealed that horizontal transfers of RubisCO genes may occur widely in AMD, which makes the evolutionary history of RubisCO difficult to reconcile with organismal phylogeny.

Nucleic acid-based approaches to investigate microbial-related cheese quality defects

The microbial profile of cheese is a primary determinant of cheese quality. Microorganisms can contribute to aroma and taste defects, form biogenic amines, cause gas and secondary fermentation defects, and can contribute to cheese pinking and mineral deposition issues. These defects may be as a result of seasonality and the variability in the composition of the milk supplied, variations in cheese processing parameters, as well as the nature and number of the non-starter microorganisms which come from the milk or other environmental sources. Such defects can be responsible for production and product recall costs and thus represent a significant economic burden for the dairy industry worldwide. Traditional non-molecular approaches are often considered biased and have inherently slow turnaround times. Molecular techniques can provide early and rapid detection of defects that result from the presence of specific spoilage microbes and, ultimately, assist in enhancing cheese quality and reducing costs. Here we review the DNA-based methods that are available to detect/quantify spoilage bacteria, and relevant metabolic pathways in cheeses and, in the process, highlight how these strategies can be employed to improve cheese quality and reduce the associated economic burden on cheese processors.

Gibbsiella papilionis sp. nov., isolated from the intestinal tract of the butterfly Mycalesis gotama, and emended description of the genus Gibbsiella

A novel Gram-negative, non-motile, facultative anaerobic and rod-shaped bacterium, designated strain LEN33(T), was isolated from the intestinal tract of a butterfly (Mycalesis gotama). Strain LEN33(T) grew optimally at 37 °C in the presence of 1 % (w/v) NaCl and at pH 9. The novel strain was oxidase-negative and catalase-positive. The major cellular fatty acids were C14 : 0, C16 : 0 and cyclo-C17 : 0. Strain LEN33(T) contained two unidentified lipids, three unidentified amino-phospholipids, phosphatidylethanolamine (PE) and phosphatidylglycerol (PG). The major isoprenoid quinone was ubiquinone-8 (Q-8). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain LEN33(T) was most closely related to Gibbsiella quercinecans FRB 97(T) and Gibbsiella dentisursi NUM 1720(T), with 98.7 % similarities. DNA-DNA hybridization experiments indicated less than 40.7 ± 2 % relatedness to the closest phylogenetic species, G. quercinecans FRB 97(T). The G+C content of genomic DNA was 58.7 mol%. Phenotypic, phylogenetic and genotypic analysis indicated that strain LEN33(T) represents a novel species within the genus Gibbsiella, for which the name Gibbsiella papilionis is proposed. The type strain is referred to as LEN33(T) ( = KACC 16707(T) = JCM 18389(T)). An emended description of the genus Gibbsiella is also proposed.

Ruegeria conchae sp. nov., isolated from the ark clam Scapharca broughtonii

A slightly halophilic, Gram-negative, strictly aerobic, non-motile rod, designated TW15T, was isolated from an ark clam in South Korea. Growth occurred at 10–37 °C, with 1–5 % (w/v) NaCl and at pH 7.0–10.0. Optimal growth occurred at 25–30 °C, with 2 % (w/v) NaCl and at pH 8.0. Strain TW15T exhibited both oxidase and catalase activities. The major fatty acids of strain TW15T were summed feature 8 (consisting of C18 : 1ω7c and/or C18 : 1ω6c) and 11-methyl C18 : 1ω7c. The predominant isoprenoid quinone was ubiquinone-10 (Q-10). The polar lipids of strain TW15T comprised phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified phospholipid, an unidentified aminolipid and five unidentified lipids. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain TW15T was most closely related to Ruegeria lacuscaerulensis DSM 11314T (98.0 % 16S rRNA gene sequence similarity). DNA–DNA relatedness with closely related strains was <52±3 %. The DNA G+C content was 55.7 mol%. On the basis of phenotypic, genotypic and phylogenetic data, strain TW15T represents a novel species of the genus Ruegeria , for which the name Ruegeria conchae sp. nov. is proposed. The type strain is TW15T ( = KACC 15115T  = JCM 17315T).

Kistimonas scapharcae sp. nov., isolated from a dead ark clam (Scapharca broughtonii), and emended description of the genus Kistimonas

A Gram-negative, motile, facultatively anaerobic rod, designated A36T, was isolated from a dead ark clam found on the south coast of Korea. The isolate was catalase- and oxidase-negative. 16S rRNA gene sequence analysis indicated that strain A36T was most closely related to Kistimonas asteriae KMD 001T, with which it shared 98.2 % 16S rRNA gene sequence similarity. Strain A36T grew optimally at 30–37 °C, with 1 % (w/v) NaCl and at pH 8.0. The major respiratory quinone was ubiquinone-9 (Q-9). The major polar lipids were phosphatidylserine, phosphoethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The major fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 2-OH) and C16 : 0. The genomic DNA G+C content was 47.3 mol%. DNA–DNA relatedness between the isolate and K. asteriae JCM 15607T was <25±3 %. Strain A36T represents a novel species of the genus Kistimonas , for which the name Kistimonas scapharcae sp. nov. is proposed. The type strain is A36T ( = KACC 16204T  = JCM 17805T). An emended description of the genus Kistimonas is also provided.

Effects of red pepper powder on microbial communities and metabolites during kimchi fermentation

To investigate the effects of red pepper powder on kimchi fermentation, Baechu (Chinese cabbage) and Mu (radish) kimchi, with and without red pepper powder, were prepared and their characteristics, including pH, colony-forming units (CFU), microbial communities, and metabolites, were periodically monitored for 40days. Measurements of pH and CFU showed that the lag phases of kimchi fermentation were clearly extended by the addition of red pepper powder. Microbial community analysis using a barcoded pyrosequencing analysis showed that the bacterial diversities in kimchi with red pepper powder decreased more slowly than kimchi without red pepper powder as kimchi fermentation progressed. The kimchi microbial communities were represented mainly by the genera Leuconostoc and Lactobacillus in all kimchi, and the abundance of Weissella was negligible in kimchi without red pepper powder. However, interestingly, kimchi with red pepper powder contained much higher proportions of Weissella than kimchi without red pepper powder, while the proportions of Leuconostoc and Lactobacillus were evidently lower in kimchi with red pepper powder compared to kimchi without red pepper powder. Metabolite analysis using a (1)H NMR technique also showed that the fermentation of kimchi with red pepper powder progressed a little more slowly than that of kimchi without red pepper powder. Principle component analysis using microbial communities and metabolites supported the finding that the addition of red pepper powder into kimchi resulted in the slowing of the kimchi fermentation process, especially during the early fermentation period and influenced the microbial succession and metabolite production during the kimchi fermentation processes.

Neptunomonas concharum sp. nov., isolated from a dead ark clam, and emended description of the genus Neptunomonas

A novel Gram-staining-negative, facultatively anaerobic, motile and rod-shaped bacterium, designated strain LHW37T, was isolated from a dead ark clam collected on the south coast of Korea. The novel strain grew optimally at 37 °C, at pH 7.0–8.0 and with 2 % (w/v) NaCl. The predominant cellular fatty acids were C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The major isoprenoid quinone was ubiquinone-8 (Q-8) and the predominant polar lipids were phosphatidylethanolamine and phosphatidylglycerol. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel strain was most closely related to Neptunomonas japonica JAMM 0745T (97.1 % sequence similarity). The genomic DNA G+C content of strain LHW37T was 48.2 mol%. The DNA–DNA relatedness values recorded in hybridization experiments between the novel strain and its closest known relative were ≤18 %. Based on the phenotypic, genotypic and phylogenetic data, strain LHW37T represents a novel species belonging to the genus Neptunomonas for which the name Neptunomonas concharum sp. nov. is proposed. The type strain is LHW37T ( = KACC 15543T  = JCM 17730T). An emended description of the genus Neptunomonas is also provided.

Tropicimonas sediminicola sp. nov., isolated from marine sediment

A novel Gram-negative, obligately aerobic, non-motile, rod-shaped bacterium, strain M97T, was isolated from marine sediment of a cage-cultured ark clam farm on the south coast of Korea. Strain M97T was positive for oxidase and catalase. Optimal growth occurred at 37 °C, with 1–2 % (w/v) NaCl and at pH 7–8. The main cellular fatty acids were C16 : 0, C18 : 1ω7c, C12 : 0 3-OH and cyclo-C19 : 0ω8c. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, an unknown aminolipid and three unknown lipids. The predominant respiratory quinone was ubiquinone-10 (Q-10). Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain M97T belongs to the genus Tropicimonas , with highest sequence similarity to Tropicimonas aquimaris DPG-21T (99.0 %). The DNA G+C content of strain M97T was 68.5 mol%. Mean DNA–DNA relatedness between strain M97T and T. aquimaris DPG-21T was 46±10 %. Based on phylogenetic, phenotypic and genotypic analyses, strain M97T is considered to represent a novel species of the genus Tropicimonas , for which the name Tropicimonas sediminicola sp. nov. is proposed. The type strain is M97T ( = KACC 15544T = JCM 17731T).

Development of bacteria identification array to detect lactobacilli in Thai fermented sausage

To improve the quality and safety of food products, there is a need in the food industry for a reliable method for simultaneously monitoring multiple bacterial strains. Microarray technology is a high-throughput screening approach that can provide an alternative for bacteria detection. A total of 164 bacteria-specific probes were designed from 16S rRNA gene sequences to target 12 bacteria species, including lactic acid bacteria and selected food pathogens. After fabrication onto aminosilane-coated slides, hybridization conditions of the array were optimized for high specificity and signal intensities. The array was applied to detect 12 bacteria individually and was specific to all (Lactobacillus plantarum group, L. fermentum, L. brevis, L. delbrueckii, L. casei, L. sakei, Escherichia coli, Staphylococcus aureus, Micrococcus luteus and Listeria monocytogenes) except L. animalis. Multiplex detection using mixed bacteria populations was evaluated and accurate detection was obtained. The feasibility of using the array to detect the target bacteria in food was evaluated with Thai fermented sausages (Nham). Meat samples were collected on days 2, 3 and 7 after natural fermentation, L. plantarum-inoculated fermentation and L. brevis-inoculated fermentation before applying to the array. The naturally-fermented Nham contained L. sakei, L. delbrueckii, L. plantarum and L. fermentum. The L. plantarum-inoculated Nham showed a similar lactic acid bacteria population but the positive signal level for L. plantarum was higher than with natural fermentation. The L. brevis-inoculated Nham contained L. brevis, L. plantarum, L. delbrueckii and L. fermentum. The array was used to monitor bacteria population dynamics during the fermentation process. The naturally-fermented and L. brevis-inoculated samples showed lower positive signal levels of L. plantarum on day 2, but signals gradually increased on days 3 and 7 of the fermentation. In contrast, the L. plantarum-started fermentation showed a higher positive signal level on day 2 than the natural and L. brevis-inoculated samples, and the positive signal level remained high on days 3 and 7. The bacteria identification array was proven to be useful as an alternative method to detect and monitor target bacteria populations during food fermentation.

Novel Podoviridae family bacteriophage infecting Weissella cibaria isolated from Kimchi

The first complete genome sequence of a phage infecting Weissella cibaria (Weissella kimchii) is presented. The bacteriophage YS61 was isolated from kimchi, a Korean fermented vegetable dish. Bacteriophages are recognized as a serious problem in industrial fermentations; however, YS61 differed from many virulent phages associated with food fermentations since it was difficult to propagate and was very susceptible to resistance development. Sequence analysis revealed that YS61 resembles Podoviridae of the subfamily Picovirinae. Within the subfamily Picovirinae, the 29-like phages have been extensively studied, and their terminal protein-primed DNA replication is well characterized. Our data strongly suggest that YS61 also replicates by a protein-primed mechanism. Weissella phage YS61 is, however, markedly different from members of the Picovirinae with respect to genome size and morphology. Picovirinae are characterized by small (approximately 20-kb) genomes which contrasts with the 33,594-bp genome of YS61. Based on electron microscopy analysis, YS61 was classified as a member of the Podoviridae of morphotype C2, similar to the 29-like phages, but its capsid dimensions are significantly larger than those reported for these phages. The novelty of YS61 was also emphasized by the low number of open reading frames (ORFs) showing significant similarity to database sequences. We propose that the bacteriophage YS61 should represent a new subfamily within the family Podoviridae.

Molecular techniques in the biotechnological fight against halogenated compounds in anoxic environments

Microbial treatment of environmental contamination by anthropogenic halogenated organic compounds has become popular in recent decades, especially in the subsurface environments. Molecular techniques such as polymerase chain reaction-based fingerprinting methods have been extensively used to closely monitor the presence and activities of dehalogenating microbes, which also lead to the discovery of new dehalogenating bacteria and novel functional genes. Nowadays, traditional molecular techniques are being further developed and optimized for higher sensitivity, specificity, and accuracy to better fit the contexts of dehalogenation. On the other hand, newly developed high throughput techniques, such as microarray and next-generation sequencing, provide unsurpassed detection ability, which has enabled large-scale comparative genomic and whole-genome transcriptomic analysis. The aim of this review is to summarize applications of various molecular tools in the field of microbially mediated dehalogenation of various halogenated organic compounds. It is expected that traditional molecular techniques and nucleic-acid-based biomarkers will still be favoured in the foreseeable future because of relative low costs and high flexibility. Collective analyses of metagenomic sequencing data are still in need of information from individual dehalogenating strains and functional reductive dehalogenase genes in order to draw reliable conclusions.

Paenibacillus oceanisediminis sp. nov. isolated from marine sediment

A Gram-stain-negative, non-motile, aerobic, endospore forming and rod-shaped bacterium, designated strain L10(T), was isolated from marine sediment collected from the South Korean coast. The organism grew optimally under conditions of 30 °C, 1 % (w/v) NaCl and pH 6.0. It was oxidase-negative and catalase-positive. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain L10(T) was associated with the genus Paenibacillus and most closely related to Paenibacillus barcinonensis BP-23(T) (98.2 % similarity). The major fatty acids of strain L10(T) were iso-C(14 : 0), anteiso-C(15 : 0) and iso-C(16 : 0). The cell-wall peptidoglycan was the A1γ type, and the predominant isoprenoid quinone was menaquinone-7. Strain L10(T) contained two unidentified lipids, an unidentified amino-phospholipid, phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. The G+C content of the genomic DNA was 44 mol% and the DNA-DNA hybridization values with closely related strains were below 14±2 %. Based on phenotypic, genotypic, and phylogenetic data, strain L10(T) should be classified as a novel species within the genus Paenibacillus. The name Paenibacillus oceanisediminis sp. nov. is proposed. The type strain is L10(T) ( = KACC 16203(T) = JCM 17814(T)).

Effects of Leuconostoc mesenteroides starter cultures on microbial communities and metabolites during kimchi fermentation

Kimchi fermentation usually relies upon the growth of naturally-occurring various heterofermentative lactic acid bacteria (LAB). This sometimes makes it difficult to produce kimchi with uniform quality. The use of Leuconostoc mesenteroides as a starter has been considered to produce commercial fermented kimchi with uniform and good quality in Korea. In this study, a combination of a barcoded pyrosequencing strategy and a (1)H NMR technique was used to investigate the effects of Leu. mesenteroides strain B1 as a starter culture for kimchi fermentation. Baechu (Chinese cabbage) and Chonggak (radish) kimchi with and without Leu. mesenteroides inoculation were prepared, respectively and their characteristics that included pH, cell number, bacterial community, and metabolites were monitored periodically for 40 days. Barcoded pyrosequencing analysis showed that the numbers of bacterial operational taxonomic units (OTU) in starter kimchi decreased more quickly than that in non-starter kimchi. Members of the genera Leuconostoc, Lactobacillus, and Weissella were dominant LAB regardless of the kimchi type or starter inoculation. Among the three genera, Leuconostoc was the most abundant, followed by Lactobacillus and Weissella. The use of Leu. mesenteroides as a starter increased the Leuconostoc proportions and decreased the Lactobacillus proportions in both type of kimchi during kimchi fermentation. However, interestingly, the use of the kimchi starter more highly maintained the Weissella proportions of starter kimchi compared to that in the non-starter kimchi until fermentation was complete. Metabolite analysis using the (1)H NMR technique showed that both Baechu and Chonggak kimchi with the starter culture began to consume free sugars earlier and produced a little greater amounts of lactic and acetic acids and mannitol. Metabolite analysis demonstrated that kimchi fermentation using Leu. mesenteroides as a starter was completed earlier with more production of kimchi metabolites compared to that not using a starter, which coincided with the decreases in pH and the increases in bacterial cell number. The PCA strategy using all kimchi components including carbohydrates, amino acids, organic acids, and others also showed that starter kimchi fermented faster with more organic acid and mannitol production. In conclusion, the combination of the barcoded pyrosequencing strategy and the (1)H NMR technique was used to effectively monitor microbial succession and metabolite production and allowed for a greater understanding of the relationships between the microbial community and metabolite production in kimchi fermentation.

Draft genome sequence of Lactobacillus zeae KCTC 3804

We announce the draft genome sequence of the type strain Lactobacillus zeae KCTC 3804 (3,110,326 bp, with a G+C content of 47.8%), which is one of the most prevalent lactic acid bacteria present during the processing of raw cow's milk. The genome consists of 113 large contigs (>100 bp). All of the contigs were assembled by Newbler Assembler 2.3 (454 Life Science).

Leucobacter celer sp. nov., isolated from Korean fermented seafood

A novel, Gram-reaction-positive, aerobic, rod-shaped, non-motile bacterial strain, designated NAL101T, was isolated from gajami-sikhae, a traditional Korean fermented seafood made of flatfish. Growth occurred at 4–45 °C, at pH 5–10 and in 0–12 % (w/v) NaCl. Optimum growth occurred at 30–37 °C, at pH 8 and in 0–1 % (w/v) NaCl. The cell-wall amino acids were 2,4-diaminobutyric acid, alanine, glycine, threonine and glutamic acid and the major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The predominant menaquinone was MK-11. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unknown glycolipid. The 16S rRNA gene sequence of strain NAL101T showed 97.7 % similarity to that of Leucobacter chironomi MM2LBT, its closest relative. The DNA G+C content was 68.8 mol% and DNA–DNA hybridization values with closely related strains were <22 %. Phylogenetic analyses based on 16S rRNA gene sequences as well as differences in its physiological and biochemical characteristics indicated that strain NAL101T represents a novel species of the genus Leucobacter in the family Microbacteriaceae, for which the name Leucobacter celer sp. nov. is proposed. The type strain is NAL101T ( = KACC 14220T  = JCM 16465T).

Dietzia alimentaria sp. nov., isolated from a traditional Korean food

An actinobacterial strain, designated 72T, was isolated from a traditional salt-fermented seafood in Korea. Colonies were coral red and cells were Gram-reaction-positive, non-motile rods. Strain 72T grew with 0–10 % (w/v) NaCl, at pH 7–10 and at 15–37 °C. Optimum growth conditions were 2 % NaCl, pH 7.0 and 30 °C. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain 72T belonged to the genus Dietzia. The major cellular fatty acids (>5 %) were C16 : 0, summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c), 10-methyl C18 : 0, C17 : 0, C19 : 0 and C18 : 1ω9c. 16S rRNA gene sequence analysis and DNA–DNA hybridization, coupled with physiological and biochemical tests, revealed genotypic and phenotypic differences between strain 72T and other members of the genus Dietzia. Based on these data, strain 72T represents a novel species, for which the name Dietzia alimentaria sp. nov. is proposed. The type strain is 72T ( = JCM 16360T  = KACC 21126T).

Oceanisphaera sediminis sp. nov., isolated from marine sediment

Two strains, designated TW92(T) and TW93, were isolated from marine sediment collected from the south coast of Korea. Cells of both strains were Gram-staining-negative, coccus-shaped, aerobic, motile and catalase- and oxidase-positive. Strain TW92(T) grew optimally in the presence of 2 % (w/v) NaCl (range 1-5%) while strain TW93 grew optimally in the presence of 1% (w/v) NaCl (range 0-12%), and both strains had an optimal growth temperature of 30 °C (range 4-37 °C). Strains TW92(T) and TW93 had the same optimum pH (pH 7), but differed in their ability to grow at pH 10. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strains TW92(T) and TW93 were most closely related to Oceanisphaera donghaensis BL1(T), with 98.8% and 98.7% similarity, respectively. Pairwise similarity between the 16S rRNA gene sequences of strains TW92(T) and TW93 was 99.9%. The major fatty acids of both strains were summed features 3 (comprising C(16:1)ω7c/iso-C(15) 2-OH), C(16:0) and C(18:1)ω7c. Both strains possessed the ubiquinone Q-8 as the predominant respiratory quinone and phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol as the polar lipids. The genomic DNA G+C contents of strains TW92(T) and TW93 were 58.5 and 59.6 mol%, respectively. Genomic relatedness values based on DNA-DNA hybridization of strains TW92(T) and TW93 with related species were below 47% and 31%, respectively. DNA-DNA hybridization values between strains TW92(T) and TW93 were above 85%. On the basis of a taxonomic study using polyphasic analysis, it is proposed that the two isolates represent a novel species, Oceanisphaera sediminis sp. nov., with strain TW92(T) (=KACC 15117(T)=JCM 17329(T)) as the type strain and strain TW93 (=KACC 15118=JCM 17330) as an additional strain.

Draft genome sequence of Lactobacillus mali KCTC 3596

We announce the draft genome sequence of the type strain Lactobacillus mali KCTC 3596 (2,652,969 bp, with a G+C content of 36.0%), which is one of the most prevalent lactic acid bacteria present during the manufacturing process of apple juice. The genome consists of 122 large contigs (>100 bp). All of the contigs were assembled by Newbler Assembler 2.3 (454 Life Science).

Genome sequence of Leuconostoc pseudomesenteroides KCTC 3652

We announce the genome sequence of one of the most prevalent lactic acid bacteria present during the manufacturing process of cane juice, the type strain Leuconostoc pseudomesenteroides KCTC 3652 (3,244,985 bp, with a G+C content of 38.3%), which consists of 1,160 large contigs (>100 bp in size). All of the contigs were assembled by the Newbler Assembler 2.3 software program (454 Life Sciences).