Yoonia algicola sp. nov., Yoonia rhodophyticola sp. nov. and Yoonia phaeophyticola sp. nov., isolated from marine algae.

Three Gram-stain-negative, strictly aerobic, non-motile, oxidase- and catalase-positive, short-rod-shaped bacteria, designated as strains G8-12T, SS1-5T and BS5-3T, were isolated from marine algae in South Korea. Strain G8-12T exhibited optimal growth at 20-25 °C, pH 8.0 and 2.0-2.5% (w/v) NaCl, while strains SS1-5T and BS5-3T grew optimally at 25 °C, pH 7.0 and 1.5% NaCl. All strains contained ubiquinone-10 as the sole respiratory quinone, with phosphatidylglycerol and phosphatidylcholine as major polar lipids, and C18 : 1 ω7c and C16 : 0 as major fatty acids (>5 %); C18 : 1 ω7c 11-methyl and C18 : 1 2-OH were additionally identified as major fatty acids in strain SS1-5T. The genomic DNA G+C contents were 57.0, 58.3 and 56.4% for strains G8-12T, SS1-5T and BS5-3T, respectively. Strains G8-12T, SS1-5T and BS5-3T exhibited less than 74.8% average nucleotide identity (ANI) and 19.7% digital DNA-DNA hybridization (dDDH) values with each other, indicating that they represent different species. Phylogenetic analyses based on both 16S rRNA gene and genome sequences revealed that strains G8-12T, SS1-5T and BS5-3T form distinct phylogenetic lineages within the genus Yoonia. Relative to other closely related Yoonia species, these strains exhibited ANI and dDDH values below 83.5 and 26.9%, respectively, suggesting that they constitute novel species within the genus Yoonia. Based on their phenotypic, chemotaxonomic and phylogenetic characteristics, strains G8-12T, SS1-5T and BS5-3T represent three novel species of the genus Yoonia, for which the names Yoonia algicola sp. nov. (G8-12T=KACC 22753T=JCM 35790T), Yoonia rhodophyticola sp. nov. (SS1-5T=KACC 22649T=JCM 35753T) and Yoonia phaeophyticola sp. nov. (BS5-3T=KACC 22648T=JCM 35751T) are proposed, respectively.

Polaribacter ponticola sp. nov., isolated from seawater, reclassification of Polaribacter undariae as a later heterotypic synonym of Polaribacter sejongensis, and emended description of Polaribacter sejongensis Kim et al. 2013.

A Gram-stain-negative, yellow-pigmented, and strictly aerobic bacterium, designated as strain MSW5T, was isolated from seawater of the Yellow Sea in South Korea. The cells were non-motile rods exhibiting oxidase- and catalase-positive activities. Growth was observed at 15-25 °C (optimum, 25 °C) and pH 5.0-9.0 (optimum, pH 7.0-8.0) and in the presence of 1.0-5.0% (w/v) NaCl (optimum, 2.0%). Menaquinone-6 was the sole respiratory quinone, and iso-C15 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), iso-C15 : 0 3-OH, and C15 : 1 ω6c were the major cellular fatty acids. Major polar lipids included phosphatidylethanolamine, two unidentified aminolipids, and three unidentified lipids. Phylogenetic analyses based on 16S rRNA gene sequences and 92 concatenated core protein sequences revealed that strain MSW5T formed a distinct lineage within the genus Polaribacter. The genome of strain MSW5T was 3582 kb in size with a 29.1 mol% G+C content. Strain MSW5T exhibited the highest similarity to Polaribacter atrinae WP25T, with a 97.9% 16S rRNA gene sequence similarity. However, the average nucleotide identity and digital DNA-DNA hybridization values were 79.4 and 23.3%, respectively, indicating that strain MSW5T represents a novel species. Based on its phenotypic, chemotaxonomic, and phylogenetic characteristics, strain MSW5T is proposed to represent a novel species, with the name Polaribacter ponticola sp. nov. The type strain is MSW5T (=KACC 22340T=NBRC 116025T). In addition, whole genome sequence comparisons and phenotypic features suggested that Polaribacter sejongensis and Polaribacter undariae belong to the same species, with P. undariae proposed as a later heterotypic synonym of P. sejongensis. An emended description of Polaribacter sejongensis is also proposed.

Fermentative metabolic features of doenjang-meju as revealed by genome-centered metatranscriptomics.

Fermentative features of doenjang-meju, a traditional Korean soybean brick, were investigated over 45 days via genome-centered metatranscriptomics. The pH value rapidly decreased within 10 days and successively increased after 20 days, along with an initial bacterial growth, including lactic acid bacteria, and subsequent fungal growth, suggesting their association. Polysaccharides and lipids underwent degradation, and amino acids, free sugars, and organic acids increased during the early stage. Metagenome analysis identified Aspergillus, Bacillus, Enterococcus, Staphylococcus, and Leuconostoc as major microbes, which were isolated and genome-sequenced. Metatranscriptomic analysis revealed the major roles of Bacillus and Enterococcus during the early period, shifting to Aspergillus dominance after 10 days. Metabolic pathway reconstruction and transcriptional analysis reveal that Aspergillus primarily decomposed polysaccharides to free sugars; Aspergillus and Bacillus metabolized lipids, free sugars, and organic acids generated by Enterococcus; and Aspergillus and Bacillus were instrumental in amino acid metabolism: their contributions varied by compounds and pathways.

Chitinophaga pollutisoli sp. nov., isolated from contaminated sediment.

A Gram-stain-negative, yellow-pigmented, and facultatively aerobic bacterium, designated strain GPA1T, was isolated from plastic waste landfill soil in the Republic of Korea. The cells were non-motile short rods exhibiting oxidase-negative and catalase-positive activities. Growth was observed at 15-40 °C (optimum, 30 °C), at pH 6.0-9.0 (optimum, pH 7.0-8.0) and in the presence of 0-2.5 % (w/v) NaCl (optimum, 0 %). Menaquinone-7 was the sole respiratory quinone, and iso-C15 : 0, C16 : 1 ω5c, and iso-C17 : 0 3-OH were the major cellular fatty acids (>10 % of the total fatty acids). Phosphatidylethanolamine was identified as a major polar lipid. Phylogenetic analyses based on 16S rRNA gene sequences and 120 concatenated marker protein sequences revealed that strain GPA1T formed a distinct lineage within the genus Chitinophaga. The genome of strain GPA1T was 6078 kb in size with 53.8 mol% G+C content. Strain GPA1T exhibited the highest similarity to Chitinophaga rhizosphaerae T16R-86T, with a 98.6 % 16S rRNA gene sequence similarity, but their average nucleotide identity and digital DNA-DNA hybridization values were 82.5 and 25.9 %, respectively. Based on its phenotypic, chemotaxonomic, and phylogenetic characteristics, strain GPA1T represents a novel species of the genus Chitinophaga, for which the name Chitinophaga pollutisoli sp. nov. is proposed. The type strain is GPA1T (=KACC 23415T=JCM 36644T).

Shewanella phaeophyticola sp. nov. and Vibrio algarum sp. nov., isolated from marine brown algae.

Two Gram-stain-negative, rod-shaped bacteria, designated as strains KJ10-1T and KJ40-1T, were isolated from marine brown algae. Both strains were catalase-positive, oxidase-positive, and facultative aerobic. Strain KJ10-1T exhibited optimal growth at 25 °C, pH 7.0, and 3 % NaCl, whereas strain KJ40-1T showed optimal growth at 25 °C, pH 7.0, and 2 % NaCl. The respiratory quinones of strain KJ10-1T were ubiquinone-8, ubiquinone-7, menaquinone-7, and methylated menaquinone-7, while the respiratory quinone of strain KJ40-1T was only ubiquinone-8. As major fatty acids, strain KJ10-1T contained C16 : 0, C17 : 1 ω8c, iso-C15 : 0, and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and strain KJ40-1T contained C16 : 0 and summed features 3 and 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The major polar lipids in strain KJ10-1T were phosphatidylethanolamine, phosphatidylglycerol, and an unidentified aminolipid, whereas those in strain KJ40-1T were phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. The DNA G+C contents of strains KJ10-1T and KJ40-1T were 42.1 and 40.8 mol%, respectively. Based on 16S rRNA gene sequences, strains KJ10-1T and KJ40-1T exhibited the closest relatedness to Shewanella saliphila MMS16-UL250T (98.6 %) and Vibrio rumoiensis S-1T (95.4 %), respectively. Phylogenetic analyses, based on both 16S rRNA and 92 housekeeping genes, showed that the strains formed distinct phylogenic lineages within the genera Shewanella and Vibrio. Digital DNA-DNA hybridization and orthologous average nucleotide identity values between strain KJ10-1T and other Shewanella species, as well as between strain KJ40-1T and other Vibrio species, were below the thresholds commonly accepted for prokaryotic species delineation. Based on the phenotypic, chemotaxonomic, and phylogenetic data, strains KJ10-1T and KJ40-1T represent novel species of the genera Shewanella and Vibrio, respectively, for which the names Shewanella phaeophyticola sp. nov. and Vibrio algarum sp. nov. are proposed, respectively. The type strains of S. phaeophyticola and V. algarum are KJ10-1T (=KACC 22589T=JCM 35409T) and KJ40-1T (=KACC 22588T=JCM 35410T), respectively.

Comparative pangenome analysis of Aspergillus flavus and Aspergillus oryzae reveals their phylogenetic, genomic, and metabolic homogeneity.

Aspergillus flavus and Aspergillus oryzae are closely related fungal species with contrasting roles in food safety and fermentation. To comprehensively investigate their phylogenetic, genomic, and metabolic characteristics, we conducted an extensive comparative pangenome analysis using complete, dereplicated genome sets for both species. Phylogenetic analyses, employing both the entirety of the identified single-copy orthologous genes and six housekeeping genes commonly used for fungal classification, did not reveal clear differentiation between A. flavus and A. oryzae genomes. Upon analyzing the aflatoxin biosynthesis gene clusters within the genomes, we observed that non-aflatoxin-producing strains were dispersed throughout the phylogenetic tree, encompassing both A. flavus and A. oryzae strains. This suggests that aflatoxin production is not a distinguishing trait between the two species. Furthermore, A. oryzae and A. flavus strains displayed remarkably similar genomic attributes, including genome sizes, gene contents, and G + C contents, as well as metabolic features and pathways. The profiles of CAZyme genes and secondary metabolite biosynthesis gene clusters within the genomes of both species further highlight their similarity. Collectively, these findings challenge the conventional differentiation of A. flavus and A. oryzae as distinct species and highlight their phylogenetic, genomic, and metabolic homogeneity, potentially indicating that they may indeed belong to the same species.

Enzymatic Activity and Amino Acids Production of Predominant Fungi from Traditional Meju during Soybean Fermentation.

To investigate the effect of the predominant fungal species from Korean traditional meju and doenjang on soybean fermentation, the enzymatic activity and amino acid production of twenty-two fungal strains were assessed through solid- and liquid-state soybean fermentation. Enzymatic activity analyses of solid-state fermented soybeans revealed different enzyme activities involving protease, leucine aminopeptidase (LAP), carboxypeptidase (CaP), glutaminase, γ-glutamyl transferase (GGT), and amylase, depending on the fungal species. These enzymatic activities significantly affected the amino acid profile throughout liquid-state fermentation. Strains belonging to Mucoromycota, including Lichtheimia, Mucor, Rhizomucor, and Rhizopus, produced smaller amounts of total amino acids and umami-producing amino acids, such as glutamic acid and aspartic acid, than strains belonging to Aspergillus subgenus circumdati. The genera Penicillium and Scopulariopsis produced large amounts of total amino acids and glutamic acid, suggesting that these genera play an essential role in producing umami and kokumi tastes in fermented soybean products. Strains belonging to Aspergillus subgenus circumdati, including A. oryzae, showed the highest amino acid content, including glutamic acid, suggesting the potential benefits of A. oryzae as a starter for soybean fermentation. This study showed the potential of traditional meju strains as starters for soybean fermentation. However, further analysis of processes such as the production of G-peptide for kokumi taste and volatile compounds for flavor and safety is needed.

Comparative pangenome analysis of Enterococcus faecium and Enterococcus lactis provides new insights into the adaptive evolution by horizontal gene acquisitions.

BACKGROUND: Enterococcus faecium and E. lactis are phylogenetically closely related lactic acid bacteria that are ubiquitous in nature and are known to be beneficial or pathogenic. Despite their considerable industrial and clinical importance, comprehensive studies on their evolutionary relationships and genomic, metabolic, and pathogenic traits are still lacking. Therefore, we conducted comparative pangenome analyses using all available dereplicated genomes of these species. RESULTS: E. faecium was divided into two subclades: subclade I, comprising strains derived from humans, animals, and food, and the more recent phylogenetic subclade II, consisting exclusively of human-derived strains. In contrast, E. lactis strains, isolated from diverse sources including foods, humans, animals, and the environment, did not display distinct clustering based on their isolation sources. Despite having similar metabolic features, noticeable genomic differences were observed between E. faecium subclades I and II, as well as E. lactis. Notably, E. faecium subclade II strains exhibited significantly larger genome sizes and higher gene counts compared to both E. faecium subclade I and E. lactis strains. Furthermore, they carried a higher abundance of antibiotic resistance, virulence, bacteriocin, and mobile element genes. Phylogenetic analysis of antibiotic resistance and virulence genes suggests that E. faecium subclade II strains likely acquired these genes through horizontal gene transfer, facilitating their effective adaptation in response to antibiotic use in humans. CONCLUSIONS: Our study offers valuable insights into the adaptive evolution of E. faecium strains, enabling their survival as pathogens in the human environment through horizontal gene acquisitions.

Devosia rhodophyticola sp. nov. and Devosia algicola sp. nov., isolated from a marine red alga.

Two Gram-stain-negative, obligately aerobic, motile rod bacteria, designated as G2-5T and G20-9T, exhibiting catalase- and oxidase-positive activities, were isolated from the phycosphere of a Chondrus species, a marine red alga. Strain G2-5T exhibited optimal growth at 30 °C and pH 5.0-6.0 and in the presence of 0.5-1.0% NaCl. In contrast, strain G20-9T demonstrated optimal growth at 25 °C and pH 6.0 and in the presence of 0.5-1.5% NaCl. Both strains contained ubiquinone-10, summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C18 : 0 and 11-methyl-C18 : 1 ω7c, and diphosphatidylglycerol and phosphatidylglycerol as the major respiratory isoprenoid quinone, cellular fatty acids and polar lipids, respectively. The genomic DNA G+C contents were 57.2 mol% for strain G2-5T and 57.5 mol% for strain G20-9T. Strains G2-5T and G20-9T exhibited 98.2 % 16S rRNA gene sequence similarity, along with 82.3 % average nucleotide identity (ANI) and 25.0 % digital DNA-DNA hybridization (dDDH) values, indicating that they represent different species. Phylogenetic analyses based on both 16S rRNA gene and genome sequences revealed that strains G2-5T and G20-9T formed distinct phylogenic lineages within the genus Devosia. Strains G2-5T and G20-9T were most closely related to Devosia limi DSM 17137T and Devosia beringensis S02T with 97.7 and 96.9 % 16S rRNA gene sequence similarities, respectively. The ANI and dDDH values between strains G2-5T and G20-9T and other Devosia species were lower than 73.9 and 19.2 %, respectively, suggesting that they constitute novel species within the genus Devosia. Based on their distinct phenotypic, chemotaxonomic, and molecular characteristics, strains G2-5T and G20-9T represent two novel species of the genus Devosia, for which the names Devosia rhodophyticola sp. nov. (G2-5T=KACC 22601T=JCM 35404T) and Devosia algicola sp. nov. (G20-9T=KACC 22650T=JCM 35405T) are proposed, respectively.

Psychroserpens ponticola sp. nov. and Marinomonas maritima sp. nov., isolated from seawater.

Two Gram-stain-negative, catalase- and oxidase-positive, aerobic non-motile and motile rod bacteria, strains MSW6T and RSW2T, were isolated from surface seawater. Strain MSW6T optimally grew at 20 °C, pH 7.0 and 3 % NaCl, while strain RSW2T optimally grew at 25 °C, pH 7.0-8.0 and 2 % NaCl. Strain MSW6T possessed menaquinone-6 as the major respiratory quinone, and its major fatty acids were iso-C15 : 1 G, iso-C15 : 0 and iso-C15 : 0 3-OH. The major polar lipid identified in strain MSW6T was phosphatidylethanolamine (PE). On the other hand, strain RSW2T had ubiquinone-8 as the predominant respiratory quinone, and its major fatty acids consisted of summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C16 : 0. The major polar lipids identified in strain RSW2T were PE and phosphatidylglycerol. As the sole respiratory quinone, strain MSW6T possessed menaquinone-6, while strain RSW2T had ubiquinone-8. The DNA G+C contents of strains MSW6T and RSW2T were 31.9 and 43.4 mol%, respectively. Phylogenetic analyses based on 16S rRNA and core gene sequences showed that strain MSW6T formed a phylogenic lineage with Psychroserpens mesophilus KOPRI 13649T, while strain RSW2T formed a phylogenic lineage with Marinomonas primoryensis KMM 3633T. Strain MSW6T shared 97.9 % 16S rRNA gene sequence similarity and 80.7 % average nucleotide identity (ANI) ith P. mesophilus KOPRI 13649T, and strain RSW2T shared 99.1 % 16S rRNA gene sequence similarity and 93.1 % ANI with M. primoryensis KMM 3633T. Based on the results of phenotypic, chemotaxonomic and phylogenetic analyses, strains MSW6T and RSW2T represent novel species of the genera Psychroserpens and Marinomonas, respectively, for which the names Psychroserpens ponticola sp. nov. and Marinomonas maritima sp. nov. are proposed, respectively. The type strain of P. ponticola is MSW6T (=KACC 22338T=JCM 35022T) and the type strain of M. maritima is RSW2T (=KACC 22716T=JCM 35550T).

Hoeflea algicola sp. nov. and Hoeflea ulvae sp. nov., isolated from phycosphere of marine algae.

Two Gram-negative, moderately halophilic, and motile rod bacteria, strains G2-23T and J2-29T, showing catalase- and oxidase-positive activities were isolated from species of the marine algae Chondrus and Ulva, respectively. Both strains optimally grew at 30 °C, pH 7.0 and 2% (w/v) NaCl. Both strains contained ubiquinone-10 as the sole isoprenoid quinone. Strain G2-23T contained summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C16 : 0 and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c/ω6c) as major cellular fatty acids, and phosphatidylethanolamine (PE), phosphatidyl-N-monomethylethanolamine (PME), phosphatidylglycerol (PG), diphosphatidylglycerol and an unidentified phospholipid (PL) as major polar lipids. Strain J2-29T contained summed feature 8, C18 : 1 ω7c 11-methyl and C16 : 0 as major cellular fatty acids and PE, PME, PG and PL as major polar lipids. The genomic DNA G+C contents of strains G2-23T and J2-29T were 59.5 and 62.2 mol%, respectively. Both strains shared 97.9 % 16S rRNA gene sequence similarity, 79.8 % average nucleotide identity (ANI) and 22.8 % digital DNA-DNA hybridization (dDDH) values, indicating that they represent different species. Phylogenetic and phylogenomic analyses by 16S rRNA gene and genome sequences, respectively, revealed that strains G2-23T and J2-29T formed different phylogenic lineages within the genus Hoeflea. ANI and dDDH values between strains G2-23T and J2-29T and other Hoeflea type strains were less than 79.0 and 22.1% and 80.5 and 23.3 %, respectively, suggesting that they represent novel species of the genus Hoeflea. In summary, based on their phenotypic, chemotaxonomic and molecular properties, strains G2-23T and J2-29T represent two different novel species of the genus Hoeflea, for which the names Hoeflea algicola sp. nov. (G2-23T=KACC 22714T=JCM 35548T) and Hoeflea ulvae sp. nov. (J2-29T=KACC 22715T=JCM 35549T), respectively, are proposed.

Alkalicoccobacillus porphyridii sp. nov., isolated from a marine red alga, reclassification of Shouchella plakortidis and Shouchella gibsonii as Alkalicoccobacillus plakortidis comb. nov. and Alkalicoccobacillus gibsonii comb. nov., and emended description of the genus Alkalicoccobacillus Joshi et al. 2022.

A Gram-stain-positive alkali-tolerant and strictly aerobic bacterium, designated strain P16T, was isolated from a marine red alga, Porphyridium cruentum, in the Yellow Sea, Republic of Korea. Cells were motile rods with peritrichous flagella and exhibited catalase and oxidase activities. The optimal growth of strain P16T was observed to occur at 30 °C and pH 8.0 and in the presence of 2.0 % (w/v) NaCl. Menaquinone-7 was identified as the sole respiratory quinone. Strain P16T contained anteiso-C15 : 0, iso-C15 : 0, iso-C14 : 0 and iso-C16 : 0, and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as major cellular fatty acids and polar lipids, respectively. The G+C content of strain P16T was 40.8 mol%. Strain P16T was most closely related to Shouchella plakortidis P203T, Shouchella gibsonii DSM 8722T and Alkalicoccobacillus murimartini LMG 21005T with 98.1, 98.1 and 98.0 % 16S rRNA gene sequence similarities, respectively. Phylogenetic analyses based on 16S rRNA gene and genome sequences revealed that strain P16T, S, plakortidis, S. gibsonii and A. murimartini formed a single phylogenetic lineage cluster, and genomic relatedness analyses showed that they are different species. Based on phylogenetic, phenotypic, chemotaxonomic and molecular features, strain P16T represents a novel species of the genus Alkalicoccobacillus, for which the name Alkalicoccobacillus porphyridii sp. nov. is proposed. The type strain is P16T (=KACC 19520T=JCM 32931T). In addition, S. plakortidis and S. gibsonii are reclassified as Alkalicoccobacillus plakortidis comb. nov. (type strain P203T=DSM 19153T=NCIMB 14288T) and Alkalicoccobacillus gibsonii comb. nov. (type strain PN-109T=ATCC 700164T=DSM 8722T=KCCM 41407T), respectively.

Description and Genomic Characteristics of Weissella fermenti sp. nov., Isolated from Kimchi.

A Gram-positive, non-motile, and non-spore-forming lactic acid bacterium, designated as BK2T, was isolated from kimchi, a Korean traditional fermented vegetable food, and the taxonomic characteristics of strain BK2T, along with strain LMG 11983, were analyzed. Both strains optimally grew at 30°C, pH 7.0, and 1.0% NaCl. Cells of both strains were heterofermentative and facultatively anaerobic rods, demonstrating negative reactions for catalase and oxidase. Major fatty acids (>10%) identified in both strains were C18:1 ω9c, C16:0, and summed feature 7 (comprising C19:1 ω6c and/or C19:1 ω7c). The genomic DNA G+C contents of both strains were 44.7 mol%. The 16S rRNA gene sequence similarity (99.9%), average nucleotide identity (ANI; 99.9%), and digital DNA-DNA hybridization (dDDH; 99.7%) value between strains BK2T and LMG 11983 indicated that they are different strains of the same species. Strain BK2T was most closely related to Weissella confusa JCM 1093T and Weissella cibaria LMG 17699T, with 100% and 99.4% 16S rRNA gene sequence similarities, respectively. However, based on the ANI and dDDH values (92.3% and 48.1% with W. confusa, and 78.4% and 23.5% with W. cibaria), it was evident that strain BK2T represents a distinct species separate from W. confusa and W. cibaria. Based on phylogenetic, phenotypic, and chemotaxonomic features, strains BK2T and LMG 11983 represent a novel species of the genus Weissella, for which the name Weissella fermenti sp. nov. is proposed. The type of strain is BK2T (=KACC 22833T=JCM 35750T).

Tahibacter soli sp. nov., isolated from soil and Tahibacter amnicola sp. nov., isolated from freshwater.

Two Gram-stain-negative, facultative aerobic, catalase- and oxidase-positive, and non-motile rod bacteria, strains BLT and W38T, that were isolated from soil and freshwater, respectively, were taxonomically characterized. Both strains optimally grew at 30 °C and pH 7.0 in Reasoner's 2A medium and contained ubiquinone-8 as the sole respiratory quinone. As major fatty acids (>10 %), strain BLT contained iso-C15 : 0 and summed features 3 and 9 (comprising iso-C15 : 0 2-OH and/or C16 : 1 ω7c/ω6c and iso-C17 : 1 ω9c and/or C16 : 0 10-methyl, respectively), whereas strain W38T contained iso-C15 : 0, iso-C16 : 0 and summed feature 9. Diphosphatidylglycerol and phosphatidylmonomethylethanolamine as major polar lipids and phosphatidylethanolamine and phosphatidylglycerol as minor polar lipids were detected in both strains. The DNA G+C contents of strains BLT and W38T were 68.3 and 65.3 %, respectively. Phylogenetic analyses based on 16S rRNA gene and genome sequences revealed that strains BLT and W38T formed a tight phylogenetic lineage with Tahibacter species, and they shared 98.8 % 16S rRNA gene sequence similarity and 75.5 % average nucleotide identity (ANI) and 16.6 % digital DNA-DNA hybridization (dDDH) values, indicating that they are different species. Strains BLT and W38T were most closely related to Tahibacter caeni BUT-6T and Tahibacter aquaticus PYM5-11T with 97.7 and 98.0 % 16S rRNA gene sequence similarities, respectively. ANI and dDDH values between strain BLT and T. caeni BUT-6T and between strain W38T and T. aquaticus DSM 21667T were 78.5 and 21.6% and 75.3 and 21.0 %, respectively. Based on their phenotypic, chemotaxonomic and genomic properties, strains BLT and W38T represent two different novel species of the genus Tahibacter, for which the names Tahibacter soli sp. nov. and Tahibacter amnicola sp. nov. are proposed. The type strains of T. soli and T. amnicola are BLT (=KACC 22831T=JCM 35402T) and W38T (=KACC 22832T=JCM 35749T), respectively.

Dyadobacter pollutisoli sp. nov., isolated from plastic waste landfill soil.

A Gram-stain-negative, yellow-pigmented and facultatively aerobic bacterium, designated strain U1T, was isolated from plastic dumped soil sampled in the Republic of Korea. Cell of strain U1T were non-motile rods showing catalase-negative and oxidase-positive activities. Strain U1T was shown to grow at 10-37 °C (optimum, 25-30 °C) and pH 6.0-9.0 (optimum, pH 8.0), and in the presence of 0-0.5 % (w/v) NaCl (optimum, 0 %). Strain U1T contained iso-C15 : 0, C16 : 0, C16 : 1 ω5c and summed feature 3 (comprising C16 : 1 ω6c and/or C16 : 1 ω7c) as the major cellular fatty acids (>5 %) and menaquinone-7 as the sole respiratory quinone. Phosphatidylethanolamine, two unidentified aminolipids and three unidentified lipids were identified as the major polar lipids. The DNA G+C content of strain U1T calculated from the whole-genome sequence was 45.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain U1T formed a distinct phylogenetic lineage within the genus Dyadobacter. Strain U1T has the highest 16S rRNA sequence similarity to Dyadobacter bucti QTA69T (97.9 %). Average nucleotide identity and digital DNA-DNA hybridization values between strain U1T and D. bucti QTA69T were 74.6 % and 18.9 %, respectively. Based on phenotypic, chemotaxonomic and molecular features, strain U1T represents a novel species of the genus Dyadobacter, for which the name Dyadobacter pollutisoli sp. nov. is proposed. The type strain is U1T (= KACC 22210T=JCM 34491T).

Neobacillus terrae sp. nov., isolated from mountain soil.

A Gram-stain-positive, spore-forming and facultative aerobic bacterium, designated C11T, was isolated from mountain soil collected in the Republic of Korea. The cells were motile rods with peritrichous flagella, and positive for catalase and oxidase activities. Strain C11T grew at 15-45 °C (optimum, 30-37 °C) and pH 6.0-8.0 (optimum, pH 6.0) and in the presence of 0-1 % (w/v) NaCl (optimum, 0.5 %). Strain C11T contained menaquinone-7 as the sole isoprenoid quinone and iso-C15 : 0, iso-C16 : 0 and anteiso-C15 : 0 as the major fatty acids. Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were the major polar lipids. The G+C content of the genomic DNA was 38.8 mol%. Strain C11T was most closely related to Neobacillus drentensis IDA1967T and Mesobacillus foraminis CV53T, with 98.0 and 97.7 %, 71.7 and 69.9 %, and 20.1 and 20.3 % 16S rRNA gene sequence similarity, average nucleotide identity, and digital DNA-DNA hybridization values, respectively. Phylogenetic analyses based on 16S rRNA gene and genome sequences showed that strain C11T was included in a phyletic lineage with members of the genus Neobacillus but was distinct from members of the genus Mesobacillus. Phenotypic, chemotaxonomic and molecular properties suggested that strain C11T represents a novel species of the genus Neobacillus, for which the name Neobacillus terrae sp. nov. is proposed. The type strain is C11T (=KACC 21661T=JCM 33943T).

Chitinophaga horti sp. nov., Isolated from Garden Soil.

A strictly aerobic Gram-negative bacterium, designated R8T, isolated from garden soil in South Korea was subjected to a taxonomic study. The cells were non-spore-forming, oxidase-positive and catalase-negative, and non-motile rods (without flagella). Growth was observed between 10 °C and 40 °C (optimum, 30 °C) and between pH 6.0 and 9.0 (optimum, pH 7.0) and in the presence of 0%-1.5% (w/v) NaCl (optimum, 0%). The G + C content of the genomic DNA was 49.9% and the major isoprenoid quinone was found to be menaquinone-7. The major fatty acids of strain R8T were iso-C15:0, C16:1 ω5c, and summed feature 3 (comprising iso-C15:0 2-OH and/or C16:1 ω7c/ω6c). Phosphatidylethanolamine was identified as a major polar lipid. Comparative 16S rRNA gene sequence analysis showed that strain R8T had the highest 16S rRNA gene sequence similarity of 98.3% with Chitinophaga sedimenti TFL-3 T. Phylogenetic analyses using 16S rRNA gene sequences and concatenated 92 marker protein sequences revealed that strain R8T formed a robust phylogenetic lineage with C. sedimenti within the genus Chitinophaga. Average nucleotide identity and digital DNA-DNA hybridization values of strain R8T to Chitinophaga species were less than 77.9% and 21.1%, respectively. The phenotypic, phylogenetic, and chemotaxonomic properties support that strain R8T represents a novel species of the genus Chitinophaga, for which the name Chitinophaga horti sp. nov. is proposed. The type strain is R8T (= KACC 19895 T = JCM 33215 T).

Fermentative features of Bacillus velezensis and Leuconostoc mesenteroides in doenjang-meju, a Korean traditional fermented soybean brick.

To investigate the fermentative characteristics of Bacillus and lactic acid bacteria, the key microbes known to be involved in doenjang-meju (a Korean traditional fermented soybean brick) fermentation, we prepared and analyzed two sets of doenjang-meju inoculated with either Aspergillus oryzae and Bacillus velezensis (BDM) or A. oryzae and Leuconostoc mesenteroides (LDM). A large decrease in pH was observed during the early fermentation period in LDM, whereas the pH remained relatively constant in BDM. Although observed in higher levels in BDM during the early fermentation period, free sugar and amino acid contents and Aspergillus abundance were higher in LDM thereafter, which aligned with α-amylase and protease activity profiles in LDM and BDM, suggesting their association with Aspergillus. Higher levels of isoflavone aglycones and glycerol along with greater ß-glucosidase and lipase activities in LDM and BDM, respectively, were suggestive of the characteristics of Leuconostoc and Bacillus, respectively. More diverse and higher amounts of volatile compounds were observed in BDM than in LDM. The α-amylase, lipase, protease, ß-glucosidase, and antimicrobial activities of A. oryzae, B. velezensis, and L. mesenteroides were examined through genomic analyses and in vitro assays, which well supported the results of their fermentative characteristics in LDM and BDM.

Dynamics and correlation of microbial communities and metabolic compounds in doenjang-meju, a Korean traditional soybean brick.

To investigate the general fermentation characteristics of doenjang-meju (a Korean traditional soybean brick), they were periodically collected from eight different manufacturers during all fermentation stages, and their microbial communities and metabolic compounds (metabolites and volatile compounds) were analyzed. Bacillus and/or lactic acid bacteria (LAB, mainly Enterococcus) and Aspergillus were abundant during fermentation. Fructose and glucose; glycerol; acetate and lactate; and cadaverine, putrescine, tyramine, and histamine were identified as the major sugars, carbon compound, organic acids, and biogenic amines, respectively. Tetramethylpyrazine, butyric acid, butyl butyrate, butanol, acetic acid, 2-methylbutyrate, acetoin, 2,3-butandiol, and nonadecane were the major volatile compounds. However, the profiles of microbial communities, metabolites, and volatile compounds during fermentation varied significanlty among samples. Principal component analysis revealed that doenjang-meju had two differentiated fermentation features, Bacillus-dominated fermentation and LAB (mainly Enterococcus)-dominated fermentation, each having different metabolite and volatile compound profiles. Particularly, fewer volatile compounds were detected in LAB-dominated doenjang-meju samples. Correlation analysis showed a strong negative correlation between Bacillus and LAB, and bacteria and fungi were less correlated with each other. Enterococcus, LAB, and Bacillus were positively correlated with lactate, flavonoid aglycones, and putrescine, respectively, suggesting that they might be mainly responsible for producing the compounds during fermentation. This study provides insights into the general fermentation characteristics of doenjang-meju.

Genomic features, aroma profiles, and probiotic potential of the Debaryomyces hansenii species complex strains isolated from Korean soybean fermented food.

Fermented soybean products are gaining attention in the food industry owing to their nutritive value and health benefits. In this study, we performed genomic analysis and physiological characterization of two Debaryomyces spp. yeast isolates obtained from a Korean traditional fermented soy sauce "ganjang". Both Debaryomyces hansenii ganjang isolates KD2 and C11 showed halotolerance to concentrations of up to 15% NaCl and improved growth in the presence of salt. Ploidy and whole-genome sequencing analyses indicated that the KD2 genome is haploid, whereas the C11 genome is heterozygous diploid with two distinctive subgenomes. Interestingly, phylogenetic analysis using intron sequences indicated that the C11 strain was generated via hybridization between D. hansenii and D. tyrocola ancestor strains. The D. hansenii KD2 and D. hansenii-hybrid C11 produced various volatile flavor compounds associated with butter, caramel, cheese, and fruits, and showed high bioconversion activity from ferulic acid to 4-vinylguaiacol, a characteristic flavor compound of soybean products. Both KD2 and C11 exhibited viability in the presence of bile salts and at low pH and showed immunomodulatory activity to induce high levels of the anti-inflammatory cytokine IL-10. The safety of the yeast isolates was confirmed by analyzing virulence and acute oral toxicity. Together, the D. hansenii ganjang isolates possess physiological properties beneficial for improving the flavor and nutritional value of fermented products.