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1.
Antonie Van Leeuwenhoek ; 117(1): 80, 2024 May 22.
Article in English | MEDLINE | ID: mdl-38772982

ABSTRACT

A novel strictly anaerobic bacterium, strain JBNU-10 T, was isolated from BALB/c mouse feces. Cells of the strain JBNU-10 T were Gram-stain positive, non-motile and rod-shaped. Optimum growth occurred at 37℃, with 1% (w/v) NaCl and at pH 7. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain JBNU-10 T belonged to the genus Adlercreutzia and were closely related to Adlercreutzia muris WCA-131-CoC-2 T (95.90%). The genome sequencing of strain JBNU-10 T revealed a genome size of 2,790,983 bp, a DNA G + C content of 69.4 mol%. It contains a total of 2,266 CDSs, 5 rRNA genes and 49 tRNA genes. According to the data obtained strain JBNU-10 T shared ANI value below 77.6- 67.7%, dDDH value below 23.8% with the closely type species. Strain JBNU-10 T possessed iso-C16:0 DMA, C18:1 CIS 9 FAME, and C18:0 DMA as the major fatty acids and had DMMK-6. The major end products of fermentation is propionate and acetate. Based on phylogenetic, physiological and chemotaxonomic characteristics, strain JBNU-10 T represent a novel species of the genus Adlercreutzia. The type strain is JBNU-10 T (= KCTC 25028 T = CCUG 75610 T).


Subject(s)
Acetates , Base Composition , Feces , Mice, Inbred BALB C , Phylogeny , Propionates , RNA, Ribosomal, 16S , Animals , Feces/microbiology , Mice , RNA, Ribosomal, 16S/genetics , Acetates/metabolism , Propionates/metabolism , DNA, Bacterial/genetics , Fatty Acids/metabolism , Fatty Acids/analysis , Bacterial Typing Techniques , Sequence Analysis, DNA , Genome, Bacterial
2.
Arch Microbiol ; 206(3): 108, 2024 Feb 18.
Article in English | MEDLINE | ID: mdl-38368591

ABSTRACT

A Gram-stain-positive, anaerobic, motile, and short rod-shaped bacterium, designated KGMB12511T, was isolated from the feces of healthy Koreansubjects. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain KGMB12511T was closely related to Gordonibacter pamelaeae 7-10-1-bT (95.2%). The draft genome of KGMB12511T comprised 33 contigs and 2,744 protein-coding genes. The DNA G + C content was 59.9% based on whole-genome sequences. The major cellular fatty acids (>10%) of strain KGMB12511T were C18:1 cis9, C18:1 cis9 DMA (dimethylacetal), and C16:0 DMA. The predominant polar lipids included a diphosphatydilglycerol, four glycolipids, and an unidentified phospholipid. The major respiratory quinones were menaquinone 6 (MK-6) and monomethylmenaquinone 6 (MMK-6). Furthermore, HPLC analysis demonstrated the ability of strain KGMB12511T to convert ellagic acid into urolithin. Based on a comprehensive analysis of phenotypic, chemotaxonomic, and phylogenetic data, strain KGMB12511T represents a novel species in the genus Gordonibacter. The type strain is KGMB12511T (= KCTC 25343T = NBRC 116190T).


Subject(s)
Ellagic Acid , Hydrolyzable Tannins , Humans , Phylogeny , RNA, Ribosomal, 16S/genetics , Feces , Republic of Korea
3.
Antonie Van Leeuwenhoek ; 117(1): 30, 2024 Feb 01.
Article in English | MEDLINE | ID: mdl-38302626

ABSTRACT

An obligately anaerobic, non-motile, Gram-stain-negative, and rod-shaped strain KGMB11183T was isolated from the feces of healthy Koreans. The growth of strain KGMB11183T occurred at 30-45 °C (optimum 37 °C), at pH 6-9 (optimum pH 7), and in the presence of 0-0.5% NaCl (optimum 0%). Strain KGMB11183T showed 16S rRNA gene sequence similarities of 95.4% and 94.2% to the closest recognized species, Phocaeicola plebeius M12T, and Phocaeicola faecicola AGMB03916T. Phylogenetic analysis showed that strain KGMB11183T is a member of the genus Phocaeiocla. The major end products of fermentation are acetic acid and isobutyric acid. The major cellular fatty acids (> 10%) of this isolate were C18:1 cis 9, anteiso-C15:0, and summed feature 11 (iso-C17:0 3-OH and/or C18:2 DMA). The assembled draft genome sequences of strain KGMB11183T consisted of 3,215,271 bp with a DNA G + C content of 41.4%. According to genomic analysis, strain KGMB11183T has a number of genes that produce acetic acid. The genome of strain KGMB11183T encoded the starch utilization system (Sus) operon, SusCDEF suggesting that strain uses many complex polysaccharides that cannot be digested by humans. Based on the physiological, chemotaxonomic, phenotypic, and phylogenetic data, strain KGMB11183T is regarded a novel species of the genus Phocaeicola. The type strain is KGMB11183T (= KCTC 25284T = JCM 35696T).


Subject(s)
Acetic Acid , Fatty Acids , Humans , Butyric Acid , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Bacterial Typing Techniques , DNA, Bacterial/genetics , Fatty Acids/chemistry , Bacteroidetes/genetics , Feces
4.
Antonie Van Leeuwenhoek ; 117(1): 19, 2024 Jan 08.
Article in English | MEDLINE | ID: mdl-38189847

ABSTRACT

A novel actinobacterial strain, SB3-54T was isolated from rhizosphere soil of Cynanchum wilfodill, Jaecheon, Chungcheongbuk-do, Republic of Korea. Cells of strain SB3-54T were Gram-stain-positive, aerobic, rod-shaped, and flagellated which formed pale yellow colonies on Reasoner's 2A (R2A) agar. Growth occurred at 15-30 °C (optimum 25 °C), pH 5-8 (optimum pH 7), and 0-2.5% NaCl (optimum 0%). Phylogenetic and phylogenomic analyses showed that strain SB3-54T formed a separate lineage in the genus Jatrophihabitans with Jatrophihabitans telluris N237T. Strain SB3-54T was positive for catalase activity. Genomic analysis showed that SB3-54T has plant-beneficial function contributing (referred to as PBFC) genes such as root colonization and plant protection from oxidative stress. Furthermore, genome of SB3-54T contained gene clusters related to cytokinin biosynthesis, auxin response, tryptophan biosynthesis, siderophore biosynthesis and bacterial toxin-antitoxin systems. Strain SB3-54T contained iso-C16:0 as the major fatty acid and MK-9(H4) and MK-9(H6) as the predominant quinones. The organism had meso-diaminopimelic acid as the diagnostic diamino acid in the peptidoglycan. The major polar lipids were diphosphatidylglycerol, phosphatidylinositol polymannosides, two unidentified aminoglycophospholipids and three unidentified phospholipids. Based on phylogenetic, physiological and chemotaxonomic characteristics, strain SB3-54T represents a novel species of the genus Jatrophihabitans. The type strain is SB3-54T (= KCTC 49134T = NBRC 114108T).


Subject(s)
Actinomycetales , Cynanchum , Phylogeny , Rhizosphere , Agar
5.
Sci Rep ; 14(1): 1038, 2024 01 10.
Article in English | MEDLINE | ID: mdl-38200134

ABSTRACT

The rhizosphere microbial community is closely associated with plant disease by regulating plant growth, agricultural production, nutrient availability, plant hormone and adaptation to environmental changes. Therefore, it is very important to identify the rhizosphere microbes around plant roots and understand their functions. While studying the differences between the rhizosphere microbiota of healthy and diseased apple trees to find the cause of apple tree disease, we isolated a novel strain, designated as B3-10T, from the rhizosphere soil of a healthy apple tree. The genome relatedness indices between strain B3-10T and other type species of family Chitinophagaceae were in the ranges of 62.4-67.0% for ANI, 18.6-32.1% for dDDH, and 39.0-56.6% for AAI, which were significantly below the cut­off values for the species delineation, indicating that strain B3-10T could be considered to represent a novel genus in family Chitinophagaceae. Interestingly, the complete genome of strain B3-10T contained a number of genes encoding ACC-deaminase, siderophore production, and acetoin production contributing to plant-beneficial functions. Furthermore, strain B3-10T was found to significantly promote the growth of shoots and roots of the Nicotiana benthamiana, which is widely used as a good model for plant biology, demonstrating that strain B3-10T, a rhizosphere microbe of healthy apple trees, has the potential to promote growth and reduce disease. The phenotypic, chemotaxonomic, phylogenetic, genomic, and physiological properties of this plant growth-promoting (rhizo)bacterium, strain B3-10T supported the proposal of a novel genus in the family Chitinophagaceae, for which the name Rhizosphaericola mali gen. nov., sp. nov. (= KCTC 72123T = NBRC 114178T).


Subject(s)
Malus , Soil , Mali , Phylogeny , Plant Development , Bacteroidetes
6.
Int J Syst Evol Microbiol ; 73(12)2023 Dec.
Article in English | MEDLINE | ID: mdl-38047902

ABSTRACT

Two novel Pseudomonas strains, SA3-5T and SA3-6, were isolated from a tidal flat (getbol) in the Republic of Korea. Strains SA3-5T and SA3-6 were subjected to polyphasic characterization to determine their taxonomic affiliations. Cells were Gram-stain-negative, aerobic, rod-shaped and motile by using peritrichous flagella. Based on their 16S rRNA gene sequences, strains SA3-5T and SA3-6 exhibited a high degree of similarity (100 %) and were classified within the genus Pseudomonas. Furthermore, the closest related species to SA3-5T and SA3-6 were Pseudomonas taeanensis MS-3T (98.3 %). The ranges of average nucleotide identity and digital DNA-DNA hybridization values between SA3-5T and closely related species were 75.9-89.1% and 21.3-38.7%, respectively, both of which being below the thresholds for delineating novel strains. Strain SA3-5T and SA3-6 contained C16 : 1 ω6с and/or C16 : 1 ω7с (summed feature 3), C16 : 0 and C18 : 1 ω6с and/or C18 : 1 ω7с (summed feature 8) as the major fatty acids. The predominant respiratory quinone was Q-9. The DNA G+C content of strain SA3-5T was 62.5 mol%. Based on their combined phenotypic, chemotaxonomic and phylogenetic characterisitics, strains SA3-5T and SA3-6 represent a novel species of the genus Pseudomonas for which the name Pseudomonas aestuarii sp. nov. is proposed. The type strain is SA3-5T (=KCTC 92395T=JCM 35697T).


Subject(s)
Fatty Acids , Pseudomonas , Base Composition , Fatty Acids/chemistry , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , DNA, Bacterial/genetics , Bacterial Typing Techniques , Pseudomonas/genetics
7.
Arch Microbiol ; 204(7): 357, 2022 Jun 03.
Article in English | MEDLINE | ID: mdl-35657444

ABSTRACT

Two obligately anaerobic, Gram-stain-negative, non-motile, non-spore-forming and short rod shaped bacteria, designated KGMB07931T and KGMB10229, were isolated from faeces of two Korean persons. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains KGMB07931T and KGMB10229 were very similar to each other (99.9%) and grouped within the genus Bacteroides, displaying the highest similarity with Bacteroides uniformis ATCC 8492T (97.5%), Bacteroides rodentium JCM 16496T (96.6%), and Bacteroides fluxus YIT 12057T (94.5%). Both strains grew optimally at 37 °C and pH 7.5 in the presence of 0.5% (w/v) NaCl. The complete genome of KGMB07931T comprises 3,335 protein-coding genes with a total of 4,240,638 bp and an average G + C content of 46.3 mol%. The major fatty acids were C18:1 cis9, anteiso-C15:0, iso-C15:0, and Summed Feature 11 (iso-C17:0 3OH and/or C18:2 DMA); the predominant respiratory quinones were MK-9 and MK-10; the major fermentation end products were acetate and isobutyrate. The genome of strain KGMB07931T encoded the starch utilization system (Sus) operon, susABCDEFG, suggesting that this strain uses many complex polysaccharides that cannot be digested by humans. Based on polyphasic taxonomic data, strains KGMB07931T and KGMB10229 represent a novel species within the genus Bacteroides, for which the name Bacteroides humanifaecis sp. nov. is proposed. The type strain is KGMB07931T (= KCTC 25160T = NBRC 115005T).


Subject(s)
Bacteroides , Fatty Acids , Bacterial Typing Techniques , Bacteroides/genetics , DNA, Bacterial/genetics , Fatty Acids/chemistry , Feces/microbiology , Humans , Phylogeny , RNA, Ribosomal, 16S/genetics , Republic of Korea , Sequence Analysis, DNA , Vitamin K 2/chemistry
8.
Article in English | MEDLINE | ID: mdl-35103586

ABSTRACT

A novel bacterium, designated CAU 1612T, was isolated from coastal sediment sampled in the Republic of Korea. Cells of the strain were Gram-stain-negative, rod-shaped and motile. Optimum growth occurred at 30 °C, at pH 7.0 and with 1.0 % (w/v) NaCl. Based on 16S rRNA gene sequences, phylogenetic analysis revealed that strain CAU 1612T belonged to the genus Sneathiella and showed highest similarity to 'Sneathiella litorea' JCM 33810T (98.5 %), followed by Sneathiella chungangensis KCTC 32476T (97.7 %), Sneathiella aquimaris KCTC 12842T (96.0 %), Sneathiella chinensis LMG 23452T (95.5 %), Sneathiella limimaris KCTC 52846T (95.5 %) and Sneathiella glossodoripedis KCTC 12842T (95.4 %). The average nucleotide identity and digital DNA-DNA hybridization values of strain CAU 1612T were estimated to be 68.5-81.7 % and ≤23.7 %, respectively, to members of the genus Sneathiella. The DNA G+C content was 54.1 mol%. The major cellular fatty acids (>10 %) were C16:0, C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The major menaquinone was Q-10 and the predominant polar lipids were phosphatidylmethylethanolamine, phosphatidylethanolamine and phosphatidylglycerol. On the basis of taxonomic evidence, strain CAU 1612T represents a novel species, for which the name Sneathiella sedimenti sp. nov. is proposed. The type strain is CAU 1612T (=KCTC 82427T=MCCC 1K06082T).


Subject(s)
Alphaproteobacteria/classification , Geologic Sediments/microbiology , Phylogeny , Seawater , Alphaproteobacteria/isolation & purification , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , Nucleic Acid Hybridization , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Republic of Korea , Seawater/microbiology , Sequence Analysis, DNA , Vitamin K 2/chemistry
9.
Arch Microbiol ; 204(2): 155, 2022 Jan 30.
Article in English | MEDLINE | ID: mdl-35094174

ABSTRACT

A Gram-negative, rod-shaped, motile bacterium, designated strain CAU 1620T, was isolated from a tidal flat sediment in Incheon, Republic of Korea. Strain CAU 1620T grew optimally at 30 °C and pH 8.0 in the presence of 6.0% (w/v) NaCl. The results of 16S rRNA gene sequence analysis revealed that strain CAU 1620T showed the highest similarity to Marinobacter adhaerens DSM 23420T (98.5%), followed by Marinobacter algicola DSM 16394T (98.3%) and Marinobacter maroccanus LMG 30465T (98.2%). The average nucleotide identity and digital DNA-DNA hybridisation values between strain CAU 1620T and related strains were estimated as 75.6-78.1% and 19.5-20.9%, respectively. The DNA G + C content based on the draft genome sequence was 59.2%, and the major respiratory quinone was ubiquinone-9. The predominant cellular fatty acids were C12:0, C16:0, C18:1 ω9c, and C12:0 3OH. The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol. According to phenotypic, genotypic, and chemotaxonomic analyses, strain CAU 1620T represents a novel species of the genus Marinobacter, for which the name Marinobacter arenosus sp. nov. is proposed. The type strain is CAU 1620T (= KCTC 82431T = MCCC 1K06079T).


Subject(s)
Marinobacter , Bacterial Typing Techniques , DNA, Bacterial/genetics , Marinobacter/genetics , Phospholipids/analysis , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA
10.
Arch Microbiol ; 204(2): 147, 2022 Jan 20.
Article in English | MEDLINE | ID: mdl-35059852

ABSTRACT

A Gram-negative, non-motile, short rod-shaped aerobic bacterial strain CAU 1593T was isolated from a coastal sand sample collected in the Republic of Korea. Cells of strain CAU 1593T grew optimally at 30 °C and pH 7.5 in 4% (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain CAU 1593T had the highest similarity to Arenibacterium halophilum (97.5%). The whole genome of strain CAU 1593T was 3,979,826 bp with 26 contigs, and the DNA G + C content was 64.3 mol%. The major fatty acid of strain CAU 1593 T was summed feature 8 (C18:1 ω7c/C18:1 ω6c). Q-10 was the only respiratory quinone. The polar lipids were composed of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two phosphoglycolipids, an unidentified glycolipid, and an unidentified lipid. Based on the results of chemotaxonomic, phylogenetic, and phenotypic analyses, strain CAU 1593T represents a novel species in the genus Arenibacterium, which is named Arenibacterium arenosum sp. nov. The type strain is CAU 1593T (= KCTC 82402T = MCCC 1K05671T).


Subject(s)
Phospholipids , Sand , Bacterial Typing Techniques , DNA, Bacterial/genetics , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Silicon Dioxide , Ubiquinone
11.
Int J Syst Evol Microbiol ; 71(11)2021 Nov.
Article in English | MEDLINE | ID: mdl-34846293

ABSTRACT

A novel bacterium, designated strain CAU 1637T, was isolated from a tidal mudflat. Cells of strain CAU 1637T were Gram-stain-negative, aerobic, motile with single flagellum and rod-shaped. The optimum conditions for growth were observed at 30 °C, pH 6.0 and in the presence of 2 % (w/v) NaCl. The respiratory quinone was ubiquinone-10. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CAU 1637T was closely related to the genus Roseibium, with the highest similarity to Roseibium aestuarii NRBC 112946T (97.4 %), followed by Roseibium hamelinense NRBC 16783T (96.8 %), Roseibium aquae JCM 19310T (96.4 %), Roseibium sediminis KCTC 52373T (95.8 %) and Roseibium denhamense JCM 10543T (95.3 %). The predominant cellular fatty acids were C18 : 1 ω7c 11-methyl and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The major polar lipids consisted of diphosphatidylglycerol and phosphatidylglycerol. The average nucleotide identity values between the novel isolate and related strains ranged from 71.0 to 76.4 %, and the DNA-DNA hybridization values ranged from 19.3 to 20.3 %. The G+C content was 58.4 mol% and the whole-genome size was 4.6 Mb, which included 17 contigs and 3931 protein-coding genes. Based on the taxonomic data, strain CAU 1637T represents a novel species of the genus Roseibium, for which the name Roseibium limicola sp. nov. is proposed. The type strain is CAU 1637T (=KCTC 82429T=MCCC 1K06080T).


Subject(s)
Alphaproteobacteria/classification , Geologic Sediments/microbiology , Phylogeny , Seawater , Alphaproteobacteria/isolation & purification , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , Nucleic Acid Hybridization , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Republic of Korea , Seawater/microbiology , Sequence Analysis, DNA , Ubiquinone/analogs & derivatives , Ubiquinone/chemistry
12.
Curr Microbiol ; 78(10): 3667-3673, 2021 Oct.
Article in English | MEDLINE | ID: mdl-34382101

ABSTRACT

A novel actinobacterial strain, Gram-positive, anaerobic, non-motile, and rod-shaped, designated KGMB02528T, was isolated from healthy human feces. Cells of strain KGMB02528T grew optimally at pH 7.0 and 37 °C and in the presence of 0% (w/v) NaCl. Based on 16S rRNA gene sequence similarity, strain KGMB04489T belonged to the genus Collinsella and was most closely related to Collinsella aerofaciens DSM 17552T (95.8%). The DNA G + C content was 58.0 mol%. The major cellular fatty acids (> 10%) were C16:0 DMA, C16:0 ALDE, C14:0 DMA, and C12:0. The predominant end product of fermentation was acetic acid. The cell wall peptidoglycan of strain KGMB02528T contained alanine, glutamic acid, and lysine, while diaminopimelic acid was not detected. The polar lipids were composed of two unidentified phospholipids and unidentified nine glycolipids. Based on the phenotypic, chemotaxonomic, and phylogenetic properties, strain KGMB02528T represents a novel species of the genus Collinsella, for which the name Collinsella acetigenes sp. nov. is proposed. The type strain is Collinsella acetigenes KGMB02528T (= KCTC 15847T = CCUG 73987T). The description of the genus Collinsella is emended to accommodate the new species.The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of Collinsella acetigenes KGMB02528T is MT117838. The whole-genome shotgun BioProject number is PRJNA623694 with the accession number JABBCP000000000.


Subject(s)
Fatty Acids , Phospholipids , Actinobacteria , Anaerobiosis , Bacterial Typing Techniques , DNA, Bacterial/genetics , Feces , Humans , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA
13.
Article in English | MEDLINE | ID: mdl-33470927

ABSTRACT

A novel actinobacterial strain, SB3-45T, was isolated from soil of Cynanchum wilfordii rhizosphere, Jaecheon-si, Chungcheongbuk-do, Republic of Korea. Strain SB3-45T, was Gram-stain-positive, aerobic and coccoid to short rod-shaped bacterium. Growth occurred at 4-37 °C (optimum 28 °C), pH 5-8 (optimum pH 7) and 0-2.5 % NaCl (optimum 0%). Phylogenetic analysis based on 16S rRNA gene sequence showed that strain SB3-45T belonged to the genus Nocardioides and was closely related to Nocardioides opuntiae OS-21T (96.2%) and Nocardioides panacihumi Gsoil 616T (95.9%). ll-DAP as the diamino acid in the peptidoglycan and the menaquinone MK-8(H4) as the predominant isoprenoid quinone were detected. The polar lipids of strain SB3-45T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and unidentified phospholipid. The major cellular fatty acids (>5%) of strain SB3-45T were iso-C16 : 0, C18 : 1 ω9c and C17 : 0. Based on phylogenetic, physiological and chemotaxonomic characteristics, strain SB3-45T represents a novel species of the genus Nocardioides, for which the name Nocardioides cynanchi sp.nov. is proposed. The type strain is SB3-45T (=KCTC 49133T=NBRC 114107T).


Subject(s)
Cynanchum/microbiology , Nocardioides/classification , Phylogeny , Rhizosphere , Soil Microbiology , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Diaminopimelic Acid/chemistry , Fatty Acids/chemistry , Nocardioides/isolation & purification , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Republic of Korea , Sequence Analysis, DNA , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistry
14.
Article in English | MEDLINE | ID: mdl-33464201

ABSTRACT

A novel Gram-negative bacterium, designated G2-14T, was isolated from rhizosphere soil sample collected from apple orchard in Chungju-si, Chungcheongbuk-do, Republic of Korea. Strain G2-14T was a strictly aerobic, non-spore-forming, non-motile and short-rod-shaped bacterium. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain G2-14T was closely related to Mucilaginibacter myungsuensis HMD1056T (96.9 %) and Mucilaginibacter boryungensis BDR-9T (96.8 %). The major cellular fatty acids (>10 %) of strain G2-14T were summed feature 3 (C16:1 ω6с and/or C16:1 ω7с) and iso-C15:0. The predominant quinone and the major polar lipid were menaquinone-7 and phosphatidylethanolamine, respectively. Strain G2-14T produced acetic acid. The DNA G+C content based on whole genome sequences was 46.4 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain G2-14T represents a novel species in the genus Mucilaginibacter, for which the name Mucilaginibacter mali sp. nov. is proposed. The type strain is G2-14T (=KCTC 72533T=NBRC 114179T).


Subject(s)
Bacteroidetes/classification , Malus/microbiology , Phylogeny , Rhizosphere , Soil Microbiology , Bacterial Typing Techniques , Bacteroidetes/isolation & purification , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , Phosphatidylethanolamines/chemistry , RNA, Ribosomal, 16S/genetics , Republic of Korea , Sequence Analysis, DNA , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistry
15.
Curr Microbiol ; 77(8): 1902-1908, 2020 Aug.
Article in English | MEDLINE | ID: mdl-32170406

ABSTRACT

A Gram-negative, aerobic, non-motile, rod-shaped, floc-forming, and non-spore-forming bacterium, designated as NLF-7-7T, was isolated from the biofilm of a sample collected from a livestock wastewater treatment plant in Nonsan, Republic of Korea. Strain NLF-7-7T, forms a visible floc and grows in the flocculated state. Cells of strain NLF-7-7T grew optimally at pH 6.5 and 30 °C and in the presence of 0.5% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain NLF-7-7T belonged to the family Comamonadaceae, and was most closely related to Comamonas badia DSM 17552T (95.8% similarity) and Comamonas nitrativorans 23310T (94.0% similarity). The phylogenetic and phenotypic data indicate strain NLF-7-7T is clearly distinguished from the Comamonas lineage. The major cellular fatty acids were C10:0 3OH, C16:0, and summed feature 3 (C16:1 ω6c/C16:1 ω7c). The respiratory quinone was Q-8. The polar lipids were composed of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and an unidentified aminolipid. The DNA G+C content of strain NLF-7-7 was 68.0 mol%. Based on the phenotypic, chemotaxonomic, and phylogenetic properties, strain NLF-7-7T represents a novel species of the genus Comamonas, for which the name Comamonas flocculans sp. nov. is proposed. The type strain is C. flocculans NLF-7-7T (=KCTC 62943T). The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of Comamonas flocculans NLF-7-7T is MN527436. The whole-genome shotgun BioProject Number is PRJNA555370 with the Accession Number CP042344.


Subject(s)
Comamonas/classification , Livestock/microbiology , Phylogeny , Wastewater/microbiology , Animals , Bacterial Typing Techniques , Base Composition , Comamonas/isolation & purification , DNA, Bacterial/genetics , Fatty Acids/chemistry , Genome, Bacterial , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Republic of Korea , Sequence Analysis, DNA , Ubiquinone/chemistry
16.
Int J Syst Evol Microbiol ; 70(3): 2059-2065, 2020 Mar.
Article in English | MEDLINE | ID: mdl-32100703

ABSTRACT

An obligately anaerobic, Gram-stain-positive, non-motile and coccoid- or oval-shaped bacterium, designated strain KGMB01111T, was isolated from faeces from a healthy Korean. Comparative analysis of 16S rRNA gene sequences indicated that KGMB01111T was closely related to Ruminococcus gauveauii CCRI-16110T (93.9 %) and Blautia stercoris GAM6-1T (93.7 %), followed by Clostridium nexile DSM 1787T (93.5 %), Blautia producta ATCC 27340T (93.4 %), Blautia hydrogenotrophica DSM 10507T (93.1 %) and Blautia coccoides ATCC 29236T (93.1 %) within the family Lachnospiraceae (Clostridium rRNA cluster XIVa). Phylogenetic analysis based on the 16S rRNA gene sequences indicated that KGMB01111T formed a separate branch with species in the genus Blautia. The major cellular fatty acids (>10.0 %) were C16 : 0 and C18 : 1 cis 9 dimethyl acetal (DMA), and the major polar lipids were aminophospholipids and lipids. KGMB01111T contained meso-diaminopimelic acid in cell-wall peptidoglycan. The predominant end product of fermentation produced by KGMB01111T was acetic acid. Based on the whole-genome sequence, the DNA G+C content of the isolate was 44.7 mol%. On the basis of the phenotypic, chemotaxonomic and phylogenetic characteristics, KGMB01111T represents a novel species within the genus Blautia for which the name Blautia faecicola sp. nov. is proposed. The type strain is KGMB01111T (=KCTC 15706T=DSM 107827T).


Subject(s)
Clostridiales/classification , Feces/microbiology , Phylogeny , Acetic Acid/metabolism , Bacterial Typing Techniques , Base Composition , Clostridiales/isolation & purification , DNA, Bacterial/genetics , Diaminopimelic Acid/chemistry , Fatty Acids/chemistry , Fermentation , Humans , Peptidoglycan/chemistry , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Republic of Korea , Sequence Analysis, DNA
17.
J Microbiol ; 58(2): 99-104, 2020 Feb.
Article in English | MEDLINE | ID: mdl-31993985

ABSTRACT

An obligately anaerobic, Gram-stain-negative, non-motile, non-spore-forming, and coccobacilli-shaped bacterial strain, designated KGMB03119T, was isolated from human faeces from a Korean. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolate was a member of the genus Sutterella and most closely related to Sutterlla wadsworthensis KCTC 15691T (96.8% 16S rRNA gene sequence similarity). The DNA G + C content of strain KGMB03119T was 58.3 mol% as determined from its whole genome sequence. Strain KGMB03119T was asaccharolytic, catalase-positive, oxidase- and urease-negative. Furthermore, the isolate was positive for alkaline phosphatase, leucine arylamidase, acid phosphatase, arginine arylamidase, alanine arylamidase, and glycine arylamidase. The major cellular fatty acids (> 10%) of the isolate were C18:1ω9c and C16:0. Methylmenaquinone-5 (MMK-5, 100%) was the predominant isoprenoid quinone in the isolate. Based on the phylogenetic, physiological, and chemotaxonomic characteristics, strain KGMB03119T represents a novel species, for which the name Sutterella faecalis sp. nov. is proposed. The type strain is KGMB03119T (= KCTC 15823T = NBRC 114254T).


Subject(s)
Alcaligenaceae/classification , Alcaligenaceae/isolation & purification , Feces/microbiology , Alcaligenaceae/genetics , Alcaligenaceae/metabolism , Classification , DNA, Bacterial/genetics , Gastrointestinal Microbiome , Humans , Phylogeny , RNA, Ribosomal, 16S/genetics
18.
Int J Syst Evol Microbiol ; 70(3): 1684-1690, 2020 Mar.
Article in English | MEDLINE | ID: mdl-31913113

ABSTRACT

A novel actinobacterial strain, designated KGMB04484T, was isolated from healthy human faeces sampled in the Republic of Korea. Cells of strain KGMB04484T were strictly anaerobic, Gram-stain-positive, catalase-positive, oxidase-negative, non-motile coccobacilli and formed tiny colonies on Columbia agar with 5 % horse blood. On the basis of 16S rRNA gene sequence similarity, strain KGMB04484T was affiliated with the genus Senegalimassilia in the family Coriobacteriaceae and its closest relative was Senegalimassilia anaerobia JC110T (96.28 % sequence similarity). The DNA G+C content of strain KGMB04484T was 61.2 mol%. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, an unidentified phospholipid, an unidentified aminolipid and three unidentified glycolipids. The predominant cellular fatty acids (>10 %) of strain KGMB04484T were C14 : 0, C16 : 0 and C16 : 0 dimethyl acetal. Based on its phylogenetic, physiological and chemotaxonomic characteristics, strain KGMB04484T is considered to represent a novel species within the genus Senegalimassilia, for which the name Senegalimassilia faecalis sp. nov. is proposed. The type strain is KGMB04484T (=KCTC 15721T=CCUG 72347T).


Subject(s)
Actinobacteria/classification , Feces/microbiology , Phylogeny , Actinobacteria/isolation & purification , Anaerobiosis , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , Glycolipids/chemistry , Humans , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Republic of Korea , Sequence Analysis, DNA
19.
J Microbiol ; 57(12): 1073-1078, 2019 Dec.
Article in English | MEDLINE | ID: mdl-31680219

ABSTRACT

A strictly anaerobic bacterium, designated as strain KGMB-03357T, was isolated from the faeces of a healthy Korean selected by Bundang Seoul National University based on health status. Cells of strain KGMB03357T are Gram-stain-positive, non-motile, non-spore-forming, and observed as straight or curved rods. The isolate grew at 10-45°C (optimum temperature of 40°C) and a pH range of 5.1-10.5 (optimum pH of 6.8). Analysis of phylogenetic trees based on the 16S rRNA gene sequences revealed that strain KGMB03357T forms a lineage within the genus Anaerotignum, and is most closely related to Anaerotignum lactatifermentans G17T (= KCTC 15066T, 96.1%), Anaerotignum propionicum DSM 1682T (= KCTC 5582T, 94.9%), Anaerotignum neopropionicum DSM 03847T (= KCTC 15564T, 94.9%), and Anaerotignum aminivorans SH021T (= KCTC 15705T, 94.8%). The ANI values between strain KGMB 03357T and members of the genus Anaerotignum were 73.3-71.0%, which are below the ANI criterion for interspecies identity. The DNA G + C content based on the whole-genome sequence is 47.3 mol%. The major cellular fatty acids of strain KGMB03357T are C16:0, C18:0, C18∶1 cis 9, and anteiso-C15∶0. Strain KGMB03357T contains meso-diaminopimelic acid as the diagnostic amino acid in the cell wall peptidoglycan. Based on the phenotypic, phylogenetic, and genomic properties, strain KGMB 03357T represents a novel species of the genus Anaerotignum, for which the name Anaerotignum faecicola sp. nov. is proposed. The type strain is KGMB03357T (= KCTC 15736T = DSM 107953T).


Subject(s)
Clostridiales/classification , Clostridiales/isolation & purification , Feces/microbiology , Microbiota , Phylogeny , Bacterial Typing Techniques , Base Composition , Clostridiales/genetics , Clostridiales/physiology , DNA, Bacterial/genetics , Diaminopimelic Acid/analysis , Fatty Acids/analysis , Humans , Hydrogen-Ion Concentration , Peptidoglycan/analysis , RNA, Ribosomal, 16S/genetics , Seoul , Sequence Analysis, DNA , Temperature
20.
Int J Syst Evol Microbiol ; 69(12): 3824-3829, 2019 Dec.
Article in English | MEDLINE | ID: mdl-31511127

ABSTRACT

A novel Gram-stain-negative and strictly anaerobic bacterial strain, designated KGMB02408T, was isolated from faeces of a healthy human in the Republic of Korea. The isolate was characterized as non-motile, non-spore-forming and rod-shaped (variable in length). The results of phylogenetic analysis based on 16S rRNA gene sequences revealed that strain KGMB02408T belonged to the genus Bacteroides and was most closely related to Bacteroides faecichinchillae JCM 17102T (=KCTC 15666T; 96.5 %). Based on its whole-genome sequence, the DNA G+C content of the isolate was 39.5 mol%. The average nucleotide identity value between strain KGMB02408T and related species, B. faecichinchillae JCM 17102T, was 93.8 %. The major cellular fatty acids (>10 %) of the isolate were anteiso-C15 : 0, iso-C17 : 0-OH, summed feature 11 (iso-C17 : 0-OH and/or C18 : 2 DMA) and C16 : 0. Menaquinone-8 (28.6 %) and menaquinone-10 (47.1 %) were detected as the major respiratory quinones in the isolate. The major end products of glucose fermentation produced by strain KGMB02408T were lactic acid, acetic acid and formic acid. Based on its phylogenetic, phenotypic and chemotaxonomic characteristics, strain KGMB02408T represents a novel species of the genus Bacteroides in the family Bacteroidaceae. The type strain is KGMB02408T (=KCTC 15687T=DSM 107828T).


Subject(s)
Bacteroides/classification , Feces/microbiology , Phylogeny , Bacterial Typing Techniques , Bacteroides/isolation & purification , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , Humans , RNA, Ribosomal, 16S/genetics , Republic of Korea , Sequence Analysis, DNA , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistry
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