Kimchi, a traditional food in the Korean culture, is made from vegetables by fermentation. In this study, metagenomic approaches were used to monitor changes in bacterial populations, metabolic potential, and overall genetic features of the microbial community during the 29-day fermentation process. Metagenomic DNA was extracted from kimchi samples obtained periodically and was sequenced using a 454 GS FLX Titanium system, which yielded a total of 701,556 reads, with an average read length of 438 bp. Phylogenetic analysis based on 16S rRNA genes from the metagenome indicated that the kimchi microbiome was dominated by members of three genera: Leuconostoc, Lactobacillus, and Weissella. Assignment of metagenomic sequences to SEED categories of the Metagenome Rapid Annotation using Subsystem Technology (MG-RAST) server revealed a genetic profile characteristic of heterotrophic lactic acid fermentation of carbohydrates, which was supported by the detection of mannitol, lactate, acetate, and ethanol as fermentation products. When the metagenomic reads were mapped onto the database of completed genomes, the Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293 and Lactobacillus sakei subsp. sakei 23K genomes were highly represented. These same two genera were confirmed to be important in kimchi fermentation when the majority of kimchi metagenomic sequences showed very high identity to Leuconostoc mesenteroides and Lactobacillus genes. Besides microbial genome sequences, a surprisingly large number of phage DNA sequences were identified from the cellular fractions, possibly indicating that a high proportion of cells were infected by bacteriophages during fermentation. Overall, these results provide insights into the kimchi microbial community and also shed light on fermentation processes carried out broadly by complex microbial communities.

A Gram-reaction-negative, strictly aerobic, non-motile bacterium, designated strain G4T, was isolated from a sandy beach of Taean in South Korea. Cells were ovoid rods and were catalase- and oxidase-positive. Growth of strain G4T was determined at 15–35 °C (optimum 25–30 °C) and pH 6–8 (optimum pH 6.5–7.5). Strain G4T contained Q-10 as the predominant isoprenoid quinone and C18 : 1ω7c (59.0 %), C18 : 1 ω7c 11-methyl (11.3 %) and C12 : 1 3-OH (9.8 %) as the major fatty acids. The major cellular polar lipids were identified as phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, an unidentified amino lipid, an unidentified phospholipid and an unidentified lipid. The DNA G+C content was 62.4 mol%. Phylogenetic and comparative analysis based on 16S rRNA gene sequences indicated that strain G4T fell within the family Rhodobacteraceae of Alphaproteobacteria and was most closely related to members of the genera Marinovum, Leisingera and Phaeobacter with 95.5–96.4 % sequence similarities. On the basis of phenotypic, chemotaxonomic and molecular properties, strain G4T represents a novel species of a novel genus within the family Rhodobacteraceae, for which the name Litorimicrobium taeanense gen. nov., sp. nov. is proposed. The type strain is G4T ( = KACC 13706T  = DSM 22007T).

Aestuariibaculum suncheonense gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from a tidal flat and emended descriptions of the genera Gaetbulibacter and Tamlana T was observed at 5-40 6C (optimum, 25-30 6C), at pH 6.0-8.5 (optimum, pH 7.0) and in the presence of 1-8 % (w/v) NaCl (optimum, 1-2 %). The major cellular fatty acids were iso-C 15 : 0 , summed feature 3 (comprising C 16 : 1 v7c and/or C 16 : 1 v6c and/or iso-C 15 : 0 2-OH), iso-C 17 : 0 3-OH, iso-C 15 : 1 G and anteiso-C 15 : 0. The polar lipid content consisted of phosphatidylethanolamine and unidentified amino lipids and lipids. The G+C content of the genomic DNA was 46.4 mol% and the only respiratory quinone detected was menaquinone-6 (MK-6). Phylogenetic inference based on 16S rRNA gene sequences showed that strain SC17T formed a distinct phyletic lineage within the family Flavobacteriaceae and was most closely related to members of the genera Gaetbulibacter and Tamlana with 95.0-95.8 % sequence similarity. On the basis of phenotypic and molecular features, strain SC17 T represents a novel genus of the family Flavobacteriaceae, for which the name Aestuariibaculum suncheonense gen. nov., sp. nov. is proposed. The type strain is SC17 T (5KACC 16186 T 5JCM 17789 T ). Emended descriptions of the genera Gaetbulibacter and Tamlana are also proposed.The families Flavobacteriaceae, Bacteroidaceae, Cryomorphaceae, Cytophagaceae, Chitinophagaceae and Sphingobacteriaceae consist of very diverse taxa and they are affiliated with the different classes of the phylum Bacteroidetes: the class Flavobacteriia (families Flavobacteriaceae and Cryomorphaceae), the class Bacteroidia (family Bacteroidaceae), the class Cytophagia (family Cytophagaceae) and the class Sphingobacteriia (families Chitinophagaceae and Sphingobacteriaceae) (Ludwig et al., 2010). The family Flavobacteriaceae contains Gram-stain-negative, rod-shaped, chemoheterotrophic bacteria that are non-motile or motile by gliding and contain menaquinone-6 (MK-6) as the major isoprenoid quinone (Bernardet et al., 2002;Bowman & Nichols, 2005;Bernardet & Nakagawa, 2006;Bernardet, 2011). Currently, the family Flavobacteriaceae consists of more than 90 genera with validly published names. Sea tidal flats are broad, plain marshes with low-gradients, or muddy coast areas that experience exposure and flooding by seawater between low and high tides. The west and south-west coast of the Korean peninsula largely consists of sea tidal flats, called getbol, that contain a wealth of valuable biological resources such as micro-organisms and marine animals. Recently, numerous microbial species have been isolated from sea tidal flats. Therefore, efforts have been made in our laboratory to isolate and characterize marine bacteria from sea tidal flats (Jin et al., 2011a, b;Jung et al., 2011;Lee et al., 2011;Park et al., 2011).In the course of this study, a novel yellow-pigmented, Gramstaining-negative, rod-shaped bacterium was isolated. Here, we describe its taxonomic characterization and pro...

Two moderately halophilic, facultatively aerobic, motile bacteria with flagella, designated strains 10-C-3(T) and 30-C-3, were isolated from jeotgal, a traditional Korean fermented seafood. Cells of the strains were observed to be ovoid-rods showing catalase- and oxidase-positive reactions and production of creamy-pink pigments. Growth of strain 10-C-3(T) was observed at 15-35 °C (optimum, 25-30 °C), at pH 5.5-9.0 (optimum, pH 7.0-7.5), and in the presence of 3-15 % (w/v) salts (optimum: 5-10 %). The two strains were found to contain C(18:1) ω7c, C(16:0), summed feature 3 (as defined by the MIDI system, comprising C(16:1) ω7c and/or C(16:1) ω6c), and C(12:0) 3-OH as the major cellular fatty acids. The G+C contents of the genomic DNA of strains 10-C-3(T) and 30-C-3 were determined to be 63.2 and 63.1 mol%, respectively and the respiratory quinone detected was ubiquinone 9 (Q-9) only. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strains 10-C-3(T)and 30-C-3 formed a distinct phyletic lineage within the genus Halomonas and are most closely related to Halomonas fontilapidosi 5CR(T) with 95.2 % of 16S rRNA sequence similarity. Strains 10-C-3(T)and 30-C-3 shared 99.2 % of 16S rRNA gene sequence similarity and their DNA-DNA relatedness value was 96.6 ± 0.9 %. On the basis of phenotypic, chemotaxonomic and molecular features, strains 10-C-3(T)and 30-C-3 represent a novel species of the genus Halomonas, for which the name Halomonas cibimaris sp. nov. is proposed. The type strain is 10-C-3(T) (= KACC 14932(T) = JCM 16914(T)).

A Gram-staining-positive, non-motile and non-spore-forming lactic acid bacterium, designated strain M2 T , was isolated from fermented brown algae (Undaria pinnatifida) kimchi in South Korea. Cells of the isolate were facultatively anaerobic ovoids and showed catalase-and oxidasenegative reactions. Growth of strain M2 T was observed at 4-35 6C and at pH 5.0-9.0. The G+C content of the genomic DNA was 42.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain M2 T belonged to the genus Leuconostoc and was most closely related to Leuconostoc inhae IH003 T , Leuconostoc kimchii IH25 T , Leuconostoc gasicomitatum LMG 18811 T , Leuconostoc gelidum DSM 5578 T , Leuconostoc palmae TMW2.694 T and Leuconostoc holzapfelii BFE 7000 T with 98.9 %, 98.8 %, 98.8 %, 98.7 %, 98.5 % and 98.2 % sequence similarity, respectively. DNA-DNA hybridization values between strain M2 T and Leuconostoc inhae KACC 12281 T , Leuconostoc kimchii IH25 T , Leuconostoc gelidum KACC 12256 T , Leuconostoc gasicomitatum KACC 13854 T , Leuconostoc palmae DSM 21144 T and Leuconostoc holzapfelii DSM 21478 T were 13.8±3.2 %, 14.3±3.4 %, 9.9±1.0 %, 13.2±0.8 %, 22.4±4.9 % and 16.2±4.6 %, respectively, which allowed differentiation of strain M2 T from the closely related species of the genus Leuconostoc. On the basis of phenotypic and molecular properties, strain M2 T represents a novel species in the genus Leuconostoc, for which the name Leuconostoc miyukkimchii sp. nov. is proposed. The type strain is M2 T (5KACC 15353 T 5JCM 17445 T ).Kimchi is a traditional food, emblematic of Korean culture, that is fermented from vegetables such as Chinese cabbage and radish. In recent years, kimchi's health-promoting characteristics have been recognized continually and kimchi is known as one of the world's five healthiest foods (Song, 2004). Fermentated vegetables in kimchi are usually processed with various seasoning ingredients such as red pepper powder, garlic, ginger and salts at low temperatures and lactic acid bacteria such as those of the genera Leuconostoc, Lactobacillus, Streptococcus, Pediococcus and Lactococcus play an important role in kimchi fermentation and resulting taste (Cheigh et al., 1994;Mheen & Kwon, 1984;So & Kim, 1995;Lee et al., 1997; Jung et al., 2011). Generally, different kinds of kimchi are classified based on the main raw materials (vegetables) and there are many kinds of kimchi in several regional provinces of Korea. Many lactic acid bacteria have been isolated from Korean kimchi (Kim et al., , 2003Yoon et al., 2000;Choi et al., 2002;Lee et al., 2002). The genus Leuconostoc encompasses a phylogenetically coherent group of lactic acid bacteria that are Gram-positive, facultatively anaerobic, asporogenous, catalase-negative, spherical organisms containing genomic DNA with relatively low G+C content (36-45 mol%) (Chambel et al., 2006; De Bruyne et al., 2007;Ehrmann et al., 2009). In the course of a study on kimchi microbiota, a novel bacterium belonging to the genus Leuconostoc was isolated from brown algae ki...