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1.
Article in English | MEDLINE | ID: mdl-38536087

ABSTRACT

A Gram-stain-positive, non-spore-forming, and obligate anaerobic bacteria designated strain CBA3647T was isolated from a horse faecal sample in Jeju, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CBA3647T formed a distinct phyletic lineage from closely related species within the genus Peptostreptococcus. Based on comparative analysis of 16S rRNA gene sequences, Peptostreptococcus anaerobius ATCC 27337T is most closely related to strain CBA3647T with a 16S rRNA gene similarity of 98.31 %, while similarity to other type strains is below 98.0 %. The genomic DNA G+C content of strain CBA3647T was 30.0 mol%. The digital DNA-DNA hybridization values between strain CBA3647T and the six Peptostreptococcus species were equal to or less than 24 %. Cells were non-motile and oval-shaped cocci with catalase-positive and oxidase-negative activities. Growth occurred at 20-40 °C (optimum, 35 °C), pH 6-8 (optimum, pH 7), and in the presence of 0-2 % (w/v) NaCl (optimum, 1 %). Strain CBA3647T contained C14 : 0 iso and C16 : 0 as major fatty acids. Phenotypic, chemotaxonomic, and molecular properties of strain CBA3647T suggest that it represents a novel species in the genus Peptostreptococcus, which has been named Peptostreptococcus equinus sp. nov. The type strain is CBA3647T (=KACC 22891T= JCM 35846T).


Subject(s)
Fatty Acids , Peptostreptococcus , Animals , Horses , Base Composition , Fatty Acids/chemistry , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , DNA, Bacterial/genetics , Bacterial Typing Techniques , Feces
2.
J Microbiol Biotechnol ; 34(4): 757-764, 2024 Apr 28.
Article in English | MEDLINE | ID: mdl-38379289

ABSTRACT

Despite considerable advancements achieved using next-generation sequencing technologies in exploring microbial diversity, several species of the gut microbiome remain unknown. In this transformative era, culturomics has risen to prominence as a pivotal approach in unveiling realms of microbial diversity that were previously deemed inaccessible. Utilizing innovative strategies to optimize growth and culture medium composition, scientists have successfully cultured hard-to-cultivate microbes. This progress has fostered the discovery and understanding of elusive microbial entities, highlighting their essential role in human health and disease paradigms. In this review, we emphasize the importance of culturomics research on the gut microbiome and provide new theories and insights for expanding microbial diversity via the optimization of cultivation conditions.


Subject(s)
Bacteria , Gastrointestinal Microbiome , Humans , Bacteria/genetics , Bacteria/classification , Bacteria/growth & development , Biodiversity , Culture Media/chemistry , High-Throughput Nucleotide Sequencing
3.
Int J Syst Evol Microbiol ; 73(11)2023 Nov.
Article in English | MEDLINE | ID: mdl-37910171

ABSTRACT

Strain CBA3108T is a Gram-positive, non-spore-forming, obligately anaerobic bacterium isolated from horse faecal samples obtained in Jeju Island, Republic of Korea. The cells of CBA3108T are non-motile short rods that have been assessed as catalase-positive and oxidase-negative. Growth of the strain occurs under the following conditions: 25-45 °C (optimum, 35 °C); pH 6-9 (optimum, pH 6); and in the presence of 0-6 % (w/v) NaCl (optimum, 2%). Major fatty acids in the strain include C15 : 0 iso and C15 : 0 iso DMA, while major polar lipids include phosphatidylglycerol, diphosphatidylglycerol and phosphatidylcholine. Based on phylogenetic analysis using 16S rRNA gene sequences, strain CBA3108T forms a phyletic lineage distinct from other closely related species within the genus Cutibacterium. It was found to be most closely related to Cutibacterium avidum ATCC 25577T (98.27 % 16S rRNA gene sequence similarity) and other strains within the genus (≤98.0 %). The genomic DNA G+C content of strain CBA3108T was 63.2 mol%. The in silico DNA-DNA hybridization values of strain CBA3108T with C. avidum ATCC 25577T, C. porci WCA-380-WT-3AT and C. acnes subsp. acnes DSM 1897T were 33.6, 21.7 and 22.7 %, respectively. Its phenotypic, chemotaxonomic and molecular properties support the hypothesis that strain CBA3108T represents a novel species in the genus Cutibacterium, for which we propose the name Cutibacterium equinum sp. nov. The type strain is CBA3108T (=KACC 22889T=JCM 35966T).


Subject(s)
Fatty Acids , Animals , Horses , Base Composition , Fatty Acids/chemistry , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , DNA, Bacterial/genetics , Bacterial Typing Techniques , Feces
4.
Article in English | MEDLINE | ID: mdl-37750780

ABSTRACT

A novel, anaerobic, Gram-stain-positive coccoid strain, CBA3646T, was isolated from the faeces of a thoroughbred racehorse. Phylogenetic analysis based on 16S rRNA gene sequencing yielded results indicative of CBA3646T representing a member of the genus Peptoniphilus, with the species most closely related to it being Peptoniphilus asaccharolyticus DSM 20463T, with a similarity of 94.79 %. DNA-DNA relatedness and average nucleotide identity values between CBA3646T and P. asaccharolyticus DSM 20463T were 21.4 and 67.6 %, respectively. CBA3646T has a circular chromosomal genome of 1 709 189 bp (45.5 mol% DNA G+C content), containing 1652 genes in total, 1584 predicted protein-coding genes, 3 complete rRNA loci and 47 tRNA genes. The cells were non-motile diplococci, catalase-positive and oxidase-negative. Growth of CBA3646T was observed at 20-40 °C (optimal temperature, 35 °C) and in the presence of 0-4 % (w/v) NaCl (optimum concentration, 1 %). The major fatty acids (>10 %) of CBA3646T were C16 : 0, C18 : 1ω9c and C18 : 1ω9c dimethyl acetal, with its major polar lipids being diphosphatidylglycerol and phosphatidylglycerol. The elucidated phylogenetic, physiological, chemotaxonomic and molecular properties are indicative of strain CBA3646T representing a novel species of the genus Peptoniphilus, or which the name Peptoniphilus equinus sp. nov. is proposed. The type strain is CBA3646T (= KACC 22890T = JCM 35845T).


Subject(s)
Coloring Agents , Gram-Positive Cocci , Horses , Animals , Anaerobiosis , Base Composition , Fatty Acids/chemistry , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , DNA, Bacterial/genetics , Bacterial Typing Techniques , Feces , Clostridiales
5.
Article in English | MEDLINE | ID: mdl-36748507

ABSTRACT

A novel bacterial strain, CBA7301T, was isolated from human faeces and was characterised using a polyphasic taxonomic approach. A phylogenetic analysis based on 16S rRNA gene sequences revealed that CBA7301T represented a member of the genus Bacteroides, in the family Bacteroidaceae. The similarity between the 16S rRNA gene sequence of CBA7301T and that of its most closely related species, Bacteroides faecichinchillae JCM 17102T, was 96.2 %, and the average nucleotide identity between these two strains was 77.9 %. The genome size was 6 782 182 bp, and the DNA G+C content was 42.5 mol%. Cells of CBA7301T were Gram-stain-negative, strictly anaerobic and rod-shaped. The optimal growth of this organism occurred at 30-35 °C, pH 7.0 and 0.5 % (w/v) NaCl. The respiratory quinone was menaquinone 10. The predominant polar lipids were phosphatidylethanolamine, phospholipids and aminophospholipids. The major cellular fatty acid was anteiso-C15 : 0. According to the results of the polyphasic taxonomic analysis, CBA7301T represents a novel species of the genus Bacteroides, which we named Bacteroides faecium sp. nov. The type strain is CBA7301T (=KCCM 43355T=ATCC TSD-227T).


Subject(s)
Fatty Acids , Phospholipids , Humans , Fatty Acids/chemistry , Sequence Analysis, DNA , Phylogeny , RNA, Ribosomal, 16S/genetics , DNA, Bacterial/genetics , Base Composition , Bacterial Typing Techniques , Phospholipids/chemistry , Bacteroides , Feces/microbiology
6.
J Microbiol ; 60(9): 899-904, 2022 Sep.
Article in English | MEDLINE | ID: mdl-35835956

ABSTRACT

Two novel halophilic archaeal strains, CBA1133T and CBA1134, were isolated from solar salt in South Korea. The 16S rRNA gene sequences of the isolates were identical to each other and were closely related to the genera Natronomonas (92.3-93.5%), Salinirubellus (92.2%), Halomarina (91.3-92.0%), and Haloglomus (91.4%). The isolated strains were coccoid, Gram-stain-negative, aerobic, oxidase-positive, and catalase-negative. Growth occurred under temperatures of 25-50°C (optimum, 45°C), NaCl levels of 10-30% (optimum, 15%), pH levels of 6.0-8.5 (optimum, 7.0), and MgCl2 concentrations of 0-500 mM (optimum, 100 mM). Digital DNA-DNA hybridization values between the strains and related genera ranged from 18.3% to 22.7%. The major polar lipids of the strains were phosphatidyl glycerol, phosphatidyl glycerol phosphate methyl ester, and phosphatidyl glycerol sulfate. Genomic, phenotypic, physiological, and biochemical analyses of the isolates revealed that they represent a novel genus and species in the family Halobacteriaceae. The type strain is CBA1133T (= KACC 22148T = JCM 34265T), for which the name Sala cibi gen. nov., sp. nov. is proposed.


Subject(s)
Sodium Chloride , Base Composition , DNA, Archaeal/genetics , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA
7.
Food Res Int ; 158: 111533, 2022 08.
Article in English | MEDLINE | ID: mdl-35840231

ABSTRACT

A high-fat diet (HFD) induces low-grade, chronic inflammation throughout the body including the hypothalamus, a key brain region involved in the control of satiety and energy expenditure in central nervous system (CNS). Kimchi is a traditional fermented Korean food, which is recognized as a healthy food. In this study, we evaluated its ability to suppress the obesity-induced inflammation in mice fed an HFD. Male C57BL/6 mice were fed an HFD or HFD with kimchi (pH 5.2 âˆ¼ 5.8). Oral administration of kimchi significantly reduced the body weight, fat mass gain, and levels of pro-inflammatory cytokines in serum. Furthermore, kimchi diminished the HFD-induced activation of astrocyte and microglial cells (reactive gliosis, a hallmark of CNS injury and inflammation) in hypothalamus region. IgG accumulation assay showed that kimchi ingestion suppressed HFD-induced breakage of the blood brain barrier (BBB) via upregulating the expression of tight junction molecules in cerebrovascular endothelial cells. In addition, kimchi modulated gut microbiome profiles, which showed an increase in the abundance of Akkermansia muciniphila. Moreover, kimchi enhanced acetate level and BBB integrity in A. muciniphila-colonized gnotobiotic mice. These results suggest that kimchi may exert beneficial effects to prevent and ameliorate obesity and associated neuroinflammation by changing gut microbiota composition and short-chain fatty acids production.


Subject(s)
Brain-Gut Axis , Fermented Foods , Animals , Endothelial Cells/metabolism , Inflammation/metabolism , Male , Mice , Mice, Inbred C57BL , Neuroinflammatory Diseases , Obesity/prevention & control
9.
Food Res Int ; 149: 110668, 2021 11.
Article in English | MEDLINE | ID: mdl-34600670

ABSTRACT

Kimchi is a fermented food prepared via spontaneous fermentation by lactic acid bacteria originating from raw ingredients. To investigate the effect of these ingredients on food fermentation, four types of food that differed only in their main raw ingredients (kimchi cabbage, green onion, leaf mustard, and young radish) were evaluated. The major microorganisms were Leuconostoc gelidum, Weissella kandleri, and Lactobacillus sakei groups. The distribution of these species depended on the sample type. All three species were primarily distributed in the food prepared from kimchi cabbage and young radish; however, the Lac. sakei group was hardly found in the food prepared using green onion and leaf mustard. Metabolite analysis results showed that the free sugar, organic acid, ethanol, and amino acid profiles differed with the sample type. This study indicates that the main ingredients could be an important factor in determining the composition of the microbial community and the metabolite composition.


Subject(s)
Fermented Foods , Food Microbiology , Fermentation , Leuconostoc , Weissella
10.
Nutrients ; 13(9)2021 Aug 27.
Article in English | MEDLINE | ID: mdl-34578867

ABSTRACT

Dietary habits and gut microbiota play an essential role in non-alcoholic fatty liver disease (NAFLD) and related factors such as insulin resistance and de novo lipogenesis. In this study, we investigated the protective effects of Bacteroides uniformis CBA7346, isolated from the gut of healthy Koreans, on mice with high-fat diet (HFD)-induced NAFLD. Administration of B. uniformis CBA7346 reduced body and liver weight gain, serum alanine aminotransferase and aspartate aminotransferase levels, liver steatosis, and liver triglyceride levels in mice on an HFD; the strain also decreased homeostatic model assessment for insulin resistance values, as well as serum cholesterol, triglyceride, lipopolysaccharide, leptin, and adiponectin levels in mice on an HFD. Moreover, B. uniformis CBA7346 controlled fatty liver disease by attenuating steatosis and inflammation and regulating de novo lipogenesis-related proteins in mice on an HFD. Taken together, these findings suggest that B. uniformis CBA7346 ameliorates HFD-induced NAFLD by reducing insulin resistance and regulating de novo lipogenesis in obese mice.


Subject(s)
Bacteroides , Diet, High-Fat/adverse effects , Fatty Liver/prevention & control , Gastrointestinal Microbiome/physiology , Insulin Resistance/physiology , Lipogenesis/physiology , Animals , Disease Models, Animal , Fatty Liver/blood , Fatty Liver/etiology , Humans , Liver , Male , Mice , Mice, Inbred C57BL
11.
Arch Microbiol ; 203(7): 4693-4703, 2021 Sep.
Article in English | MEDLINE | ID: mdl-34189594

ABSTRACT

Six different fermented vegetables were collected from Zhejiang Province, China, to explore the associated bacterial community using a high-throughput sequencing platform. A total of 24 phyla, 274 families and 569 genera were identified from 6 samples. Firmicutes and Proteobacteria were the main phyla in all of the samples. Brevibacterium was the major genus in Xiaoshan pickled radish. Lactobacillus-related genera and Vibrio were the major genera in fermented potherb mustard and its brine. Enterobacter and Cobetia were the major genera in fermented radish and its brine. Chromohalobacter was the major genus in the tuber mustard. These results indicated clear differences were there between the bacterial genera present in Xiaoshan pickled radish, fermented potherb mustard, fermented radish, and tuber mustard. This demonstrated the possible influences of raw materials and manufacturing processes. Furthermore, a large number of lactic acid bacteria were isolated and identified by culture-dependent and 16S rRNA gene sequence analysis, which accounted for more than 68% of all the isolates. In addition, whole-genome analysis of Levilactobacillus suantsaii, Latilactobacillus sakei subsp. sakei, and Weissella cibaria showed that they had large numbers of genes associated with carbohydrate metabolism. This may explain why these three bacterial strains can grow in fermented vegetable environments.


Subject(s)
Fermented Foods , Food Microbiology , Lactobacillales , Microbiota , Vegetables , China , Fermented Foods/microbiology , Genome, Bacterial/genetics , Genomics , Lactobacillales/genetics , Microbiota/genetics , RNA, Ribosomal, 16S/genetics , Vegetables/microbiology
12.
Arch Microbiol ; 203(6): 3163-3169, 2021 Aug.
Article in English | MEDLINE | ID: mdl-33821299

ABSTRACT

In this study, aimed at investigating and characterizing river sediment bacteria, we isolated a Gram-stain-positive, rod-shaped, obligate anaerobic bacterium, strain CBA3637T, from the sediment of the Geum River. This strain grew at 10-40 °C (optimum, 30 °C), 0-1% NaCl (optimum, 0%), and pH 7-8 (optimum, pH 7). The 16S rRNA gene sequence comparison revealed Aminipila butyrica DSM 103574T to be the closest relative of strain CBA3637T (96.6-96.7% similarity); and both strains clustered together in phylogenetic analysis. The genome of strain CBA3637T was found to consist of a single chromosome (3.51 Mbp; 36.98% G + C content). Comparative genomic analysis of the strain CBA3637T with A. butyrica DSM 103574T revealed that strain CBA3637T possessed five unique pathways related to polyamine biosynthesis, lipopolysaccharide metabolism, pyrimidine metabolism, and cofactor and vitamin metabolism. Strain CBA3637T contained C14:0, C16:0, and C18:1 ω9c as the major fatty acids, and diphosphatidylglycerol as the major polar lipid. No respiratory quinone was observed. Biochemical, chemotaxonomic, and genotypic data revealed that the strain CBA3637T is a representative of a novel species within the genus Aminipila, for which the name Aminipila terrae is proposed. The type strain is CBA3637T (= KACC 21651T = DSM 110662T).


Subject(s)
Clostridiales , Geologic Sediments , Phospholipids , Rivers , Anaerobiosis , Base Composition , Clostridiales/classification , Clostridiales/genetics , Clostridiales/isolation & purification , Fatty Acids/analysis , Geologic Sediments/microbiology , Phospholipids/analysis , Phylogeny , RNA, Ribosomal, 16S/genetics , Rivers/microbiology
13.
Antonie Van Leeuwenhoek ; 114(5): 507-513, 2021 May.
Article in English | MEDLINE | ID: mdl-33730291

ABSTRACT

Strain CBA3638T was isolated from the Geum River sediment, Republic of Korea. The cells of strain CBA3638T were Gram-stain-positive, strictly anaerobic, rod-shaped, and 0.5-1.0 µm wide, and 4.0-4.5 µm long. Optimal growth occurred at 37 °C, pH 7.0, and 1.0% (w/v) NaCl. Based on the 16S rRNA gene sequence, the phylogenetic analysis showed that strain CBA3638T belongs to the genus Anaerocolumna in the family Lachnospiraceae, and is most closely related to Anaerocolumna cellulosilytica (94.6-95.0%). The DDH value with A. cellulosilytica SN021T showed 15.0% relatedness. The genome of strain CBA3638T consisted of one circular chromosome that is 5,500,435 bp long with a 36.7 mol% G + C content. The genome contained seven 16S-5S-23S rRNA operons and one antibiotic resistance-related transporter gene (mefA). Quinones were not detected. The predominant cellular fatty acids were C16:0 and C14:0 and the polar lipids were diphosphatidylglycerol, phosphatidylcholine, and uncharacterised polar lipids. Based on the polyphasic taxonomic analysis, we propose strain CBA3638T as a novel species in the genus Anaerocolumna, with the name Anaerocolumna sedimenticola sp. nov. The type strain is CBA3638T (= KACC 21652T = DSM 110663T).


Subject(s)
Fresh Water , Phospholipids , Bacterial Typing Techniques , Base Composition , Clostridiales , DNA, Bacterial/genetics , Fatty Acids/analysis , Phospholipids/analysis , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA
14.
Arch Microbiol ; 203(1): 261-268, 2021 Jan.
Article in English | MEDLINE | ID: mdl-32918097

ABSTRACT

Extremely halophilic archaea (haloarchaea) belonging to the phylum Euryarchaeota have been found in high-salinity environments. In this study, Halarchaeum sp. CBA1220, Halorubrum sp. CBA1229, and Halolamina sp. CBA1230, which are facultatively oligotrophic haloarchaea, were isolated from solar salt by culture under oligotrophic culture conditions. The complete genomes of strains CBA1220, CBA1229, and CBA1230 were sequenced and were found to contain 3,175,875, 3,582,278, and 3,465,332 bp, with a G + C content of 68.25, 67.66, and 66.75 mol %, respectively. In total, 60, 36, and 33 carbohydrate-active enzyme genes were determined in the respective strains. The strains harbored various genes encoding stress-tolerance proteins, including universal stress proteins, cold-shock proteins, and rubrerythrin and rubrerythrin-related proteins. The genome data produced in this study will facilitate further research to improve our understanding of other halophilic strains and promote their industrial application.


Subject(s)
Euryarchaeota/genetics , Genome, Archaeal/genetics , Base Composition , Genomics , Halobacteriaceae/classification , Halobacteriaceae/genetics , Halorubrum/classification , Halorubrum/genetics , Salinity , Stress, Physiological/genetics
15.
Int J Syst Evol Microbiol ; 70(7): 4298-4304, 2020 Jul.
Article in English | MEDLINE | ID: mdl-32589569

ABSTRACT

A novel, facultatively anaerobic actinobacterium, designated strain CBA3103T, was isolated from sediment of the Geum River in South Korea. Phylogenetic analysis indicated that strain CBA3103T is most closely related to Raineyella antarctica LZ-22T (98.47 % 16S rRNA gene sequence similarity). The genome of strain CBA3103T was 3 649 865 bp with a DNA G+C content of 69.6 mol%. The average nucleotide identity value between strain CBA3103T and R. antarctica LZ-22T was 79.22 %. Cells of strain CBA3103T were Gram-positive, rod-shaped, 0.6-0.9 µm wide and 1.4-2.4 µm long. Growth occurred at 15-40 °C (optimum, 35 °C), at pH 6.0-7.0 (optimum, pH 7.0) and with 0-2 % NaCl (w/v) (optimum, 0-1 %, w/v). The major cellular fatty acids in strain CBA3103T were anteiso-C15 : 0, anteiso-C15 : 1 A and iso-C14 : 0. The major respiratory quinone was menaquinone-9(H4). The polar lipids of strain CBA3103T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, five unidentified glycolipids and three unidentified phospholipids. Based on the genotypic, phenotypic and chemotaxonomic analyses, strain CBA3103T represents a novel species of the genus Raineyella, for which the name Raineyella fluvialis sp. nov. (type strain CBA3103T=KACC 21446T=DSM 110288T) is proposed.


Subject(s)
Geologic Sediments , Phylogeny , Propionibacteriaceae/classification , Rivers/microbiology , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , Glycolipids/chemistry , Phospholipids/chemistry , Propionibacteriaceae/isolation & purification , RNA, Ribosomal, 16S/genetics , Republic of Korea , Sequence Analysis, DNA , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistry
16.
Syst Appl Microbiol ; 43(3): 126085, 2020 May.
Article in English | MEDLINE | ID: mdl-32381322

ABSTRACT

Two extremely halophilic archaea strains, CBA1112T and CBA1113, were isolated from solar salt in Korea. The genome sizes and G+C content of CBA1112T and CBA1113 were 3.77 and 3.53Mb, and 66.0 and 66.5mol%, respectively. Phylogenetic analysis based on closely related taxa and environmental Haloplanus sequences indicated that both CBA1112T and CBA1113 strains are grouped within the genus Haloplanus. OrthoANI and in silico DNA-DNA hybridization values were below the species delineation threshold. Pan-genomic analysis showed that the two novel strains and four reference strains had 6203 pan-orthologous groups in total. Six Haloplanus strains shared 1728 core pan-genome orthologous groups, which were mainly associated with amino acid transport and metabolism and translation, ribosomal structure and biogenesis categories, and amino acid metabolism and carbohydrate metabolism related categories. The novel strain-specific pan-genome orthologous groups were mainly involved with replication, recombination and repair category and replication and repair pathway or amino acid metabolism pathway. Cells of both strains were Gram-negative and pleomorphic, and colonies were red-pigmented. The major polar lipids of both strains were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate, and one glycolipid, sulfated mannosyl glucosyl diether. Based on genomic, phylogenetic, phenotypic, and chemotaxonomic features, strains CBA1112T and CBA1113 are described as novel species of the genus Haloplanus. Thus, we propose the name Haloplanus rubicundus sp. nov. The type strain is CBA1112T (=KCCM 43224T=JCM 30475T).


Subject(s)
Halobacteriaceae/classification , Halobacteriaceae/genetics , Bacterial Typing Techniques , Base Composition , Gene Library , Genome, Archaeal , Genomics/methods , Halobacteriaceae/isolation & purification , Phenotype , Phylogeny , RNA, Ribosomal, 16S/genetics
17.
Food Chem ; 318: 126481, 2020 Jul 15.
Article in English | MEDLINE | ID: mdl-32126467

ABSTRACT

Fermented foods constitute hubs of microbial consortia differentially affecting nutritional and organoleptic properties, quality, and safety. Here we show the origin source of fermentative microbes and fermentation dynamics of kimchi. We partitioned microbiota by raw ingredient (kimchi cabbage, garlic, ginger, and red pepper) to render kimchi fermented by each source-originated microbe pool and applied multi-omics (metataxonomics and metabolomics), bacterial viability, and physiochemical analyses to longitudinally collected samples. Only kimchi cabbage- and garlic-derived microbial inoculums yielded successful kimchi fermentations. The dominant fermentative microbial taxa and subsequent metabolic outputs differed by raw ingredient type: the genus Leuconostoc, Weissella, and Lactobacillus for all non-sterilized ingredients, garlic, and kimchi cabbage, respectively. Gnotobiotic kimchi inoculated by mono-, di-, and tri- isolated fermentative microbe combinations further revealed W. koreensis-mediated reversible microbial metabolic outputs. The results suggest that the raw ingredient microbial habitat niches selectively affect microbial community assembly patterns and processes during kimchi fermentation.


Subject(s)
Fermented Foods/microbiology , Microbiota , Brassica/microbiology , Capsicum/microbiology , Fermentation , Food Microbiology , Garlic/microbiology , Zingiber officinale/microbiology , Lactobacillus/genetics , Leuconostoc/genetics , Metabolome , Microbial Consortia , Microbiota/genetics , Weissella/genetics
18.
J Microbiol ; 57(6): 444-449, 2019 Jun.
Article in English | MEDLINE | ID: mdl-31054135

ABSTRACT

A Gram-stain-negative and facultatively aerobic bacterium, designated as strain CBA4604T, was isolated from a traditional Korean salted and fermented shrimp food (saeu-jeot). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CBA4604T formed a clearly distinct phyletic lineage from closely related species within the genus Paracoccus. Strain CBA4604T was the most closely related to P. koreensis Ch05T (97.5% 16S rRNA gene sequence similarity) and other type strains (≤ 97.0%). The genome comprised a chromosome and two plasmids of 3,299,166 bp with 66.5% G+C content. The DNA-DNA relatedness values between strain CBA4604T and P. koreensis Ch05T, P. alcaliphilus DSM 8512T, and P. stylophorae KTW-16T were 30.5%, 22.9%, and 16.7%, respectively. Cells of the strain were short rod-shaped and oxidase- and catalase-positive. The growth of strain CBA-4604T was observed at 10-40°C (optimum, 37°C), pH 6.0-10.0 (optimum, pH 7.0), and in the presence of 0-8.0% (w/v) NaCl (optimum, 0-2.0%). Strain CBA4604T contained ubiquinone 10 as the sole isoprenoid quinone and summed feature 8 (C18:1ω7c/C18:1ω6c) and C18:0 as the major cellular fatty acids. The polar lipids consisted of phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phospholipid, an unidentified aminolipid, an unidentified glycolipid, and three unidentified lipids. Based on its phylogenetic, genomic, phenotypic, and chemotaxonomic features, we concluded that strain CBA-4604T represents a novel species in the genus Paracoccus and we propose the name Paracoccus jeotgali sp. nov. The type strain is CBA4604T (= KACC 19579T = JCM 32510T).


Subject(s)
Fermented Foods/microbiology , Paracoccus/classification , Paracoccus/isolation & purification , Phylogeny , Seafood/microbiology , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/analysis , Fermentation , Genome, Bacterial , Hydrogen-Ion Concentration , Nucleic Acid Hybridization , Paracoccus/genetics , Paracoccus/physiology , RNA, Ribosomal, 16S/genetics , Republic of Korea , Sequence Analysis, DNA , Sodium Chloride , Ubiquinone/analogs & derivatives , Ubiquinone/analysis
19.
J Microbiol ; 57(1): 30-37, 2019 Jan.
Article in English | MEDLINE | ID: mdl-30392155

ABSTRACT

White colony-forming yeasts (WCFYs) often appear in fermented foods, depending on the storage method. Despite the ongoing research on fermented foods, the community and genome features of WCFYs have not been well studied. In this study, the community structures of WCFYs on fermented vegetables (kimchi) prepared with various raw materials were investigated using deep sequencing. Only eight operational taxonomic units (OTUs) were detected, indicating that the community structure of WCFYs on kimchi is very simple. The five most abundant OTUs represented Pichia kluyveri, Yarrowia lipolytica, Candida sake, Hanseniaspora uvarum, and Kazachstania servazzii. Using a culture-dependent method, 41 strains representing the five major OTUs were isolated from the surface of the food samples. Whole genomes of the five major yeast strains were sequenced and annotated. The total genome length for the strains ranged from 8.97 Mbp to 21.32 Mbp. This is the first study to report genome sequences of the two yeasts Pichia kluyveri and Candida sake. Genome analysis indicated that each yeast strain had core metabolic pathways such as oxidative phosphorylation; purine metabolism; glycolysis/gluconeogenesis; aminoacyl-tRNA biosynthesis; citrate cycle; but strain specific pathways were also found. In addition, no toxin or antimicrobial resistance genes were identified. Our study provides genome information for five WCFY strains that may highlight their potential beneficial or harmful metabolic effects in fermented vegetables.


Subject(s)
Fermented Foods/microbiology , Vegetables/microbiology , Yeasts/genetics , Yeasts/metabolism , Fermentation , Genome, Fungal , Genomics , Phylogeny , Yeasts/classification , Yeasts/isolation & purification
20.
Food Chem ; 265: 135-143, 2018 Nov 01.
Article in English | MEDLINE | ID: mdl-29884364

ABSTRACT

We investigated the effects of jeotgal (fermented fish sauce) on kimchi fermentation, with or without saeu-jeot and myeolchi-jeot. Bacterial community analysis showed that Leuconostoc, Weissella, Lactobacillus, and Tetragenococcus were the dominant genera; however, their succession depended on the presence of jeotgal. Leuconostoc gasicomitatum was the dominant species in kimchi without jeotgal, whereas Weissella koreensis and Lactobacillus sakei were the dominant species in kimchi with myeolchi-jeot and saeu-jeot, respectively. Metabolite analysis, using 1H NMR, showed that the amounts of amino acids and gamma-aminobutyric acid (GABA) were higher in kimchi with jeotgal. Increases in acetate, lactate, and mannitol contents depended on fructose consumption and were more rapid in kimchi with jeotgal. Moreover, the consumption of various amino acids affected the increase in kimchi LAB. Thus, the role of jeotgal in kimchi fermentation was related to enhancement of taste, the amino acid source, and the increases in levels of functional metabolites.


Subject(s)
Bacteria/metabolism , Fermentation , Fermented Foods , Fishes/microbiology , Food Microbiology , Metabolomics , Animals , Food Handling
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