Gordonibacter faecis sp. nov., producing urolithin C from ellagic acid, isolated from feces of healthy Korean subjects

A Gram-stain-positive, anaerobic, motile, and short rod-shaped bacterium, designated KGMB12511 T , was isolated from the feces of healthy Koreansubjects. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain KGMB12511 T was closely related to Gordonibacter pamelaeae 7-10-1-b T...

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Published inArchives of microbiology Vol. 206; no. 3; p. 108
Main Authors Kim, Han Sol, Kim, Ji-Sun, Suh, Min Kuk, Eom, Mi Kyung, Do, Hyo Eun, Lee, Ju Huck, Park, Seung-Hwan, Kang, Se Won, Lee, Dong Ho, Yoon, Hyuk, Lee, Je Hee, Lee, Jung-Sook
Format Journal Article
LanguageEnglish
Published Berlin/Heidelberg Springer Berlin Heidelberg 01.03.2024
Springer Nature B.V
Subjects
Archives & records
bacteria
Biochemistry
Biomedical and Life Sciences
Biotechnology
Cell Biology
chemotaxonomy
Dimethyl acetals
DNA
Ecology
Ellagic Acid
Fatty acids
Feces
Gene sequencing
Genes
genome
Genomes
genus
Glycolipids
Humans
Hydrolyzable Tannins
Life Sciences
Lipids
Menaquinones
Microbial Ecology
Microbiology
New species
Nucleotide sequence
nucleotide sequences
Original Paper
phenotype
Phospholipids
Phylogenetics
Phylogeny
Polyphenols
Quinones
Republic of Korea
RNA, Ribosomal, 16S - genetics
rRNA 16S
species
Republic of Korea
Gut microbiota
Urolithin C
Human feces
Ellagic acid
Gordonibacter
Online AccessGet full text
ISSN0302-8933
1432-072X
1432-072X
DOI10.1007/s00203-024-03844-5

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Abstract A Gram-stain-positive, anaerobic, motile, and short rod-shaped bacterium, designated KGMB12511 T , was isolated from the feces of healthy Koreansubjects. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain KGMB12511 T was closely related to Gordonibacter pamelaeae 7-10-1-b T (95.2%). The draft genome of KGMB12511 T 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 KGMB12511 T were C 18:1 cis 9, C 18:1 cis 9 DMA (dimethylacetal), and C 16:0 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 KGMB12511 T to convert ellagic acid into urolithin. Based on a comprehensive analysis of phenotypic, chemotaxonomic, and phylogenetic data, strain KGMB12511 T represents a novel species in the genus Gordonibacter . The type strain is KGMB12511 T (= KCTC 25343 T  = NBRC 116190 T ).
AbstractList 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).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).
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).
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 C18:1cis9, C18:1cis9 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).
A Gram-stain-positive, anaerobic, motile, and short rod-shaped bacterium, designated KGMB12511 , was isolated from the feces of healthy Koreansubjects. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain KGMB12511 was closely related to Gordonibacter pamelaeae 7-10-1-b (95.2%). The draft genome of KGMB12511 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 KGMB12511 were C cis9, C cis9 DMA (dimethylacetal), and C 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 KGMB12511 to convert ellagic acid into urolithin. Based on a comprehensive analysis of phenotypic, chemotaxonomic, and phylogenetic data, strain KGMB12511 represents a novel species in the genus Gordonibacter. The type strain is KGMB12511 (= KCTC 25343  = NBRC 116190 ).
A Gram-stain-positive, anaerobic, motile, and short rod-shaped bacterium, designated KGMB12511 T , was isolated from the feces of healthy Koreansubjects. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain KGMB12511 T was closely related to Gordonibacter pamelaeae 7-10-1-b T (95.2%). The draft genome of KGMB12511 T 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 KGMB12511 T were C 18:1 cis 9, C 18:1 cis 9 DMA (dimethylacetal), and C 16:0 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 KGMB12511 T to convert ellagic acid into urolithin. Based on a comprehensive analysis of phenotypic, chemotaxonomic, and phylogenetic data, strain KGMB12511 T represents a novel species in the genus Gordonibacter . The type strain is KGMB12511 T (= KCTC 25343 T  = NBRC 116190 T ).
ArticleNumber 108
Author Eom, Mi Kyung
Lee, Jung-Sook
Kim, Ji-Sun
Kim, Han Sol
Lee, Ju Huck
Do, Hyo Eun
Lee, Dong Ho
Lee, Je Hee
Kang, Se Won
Suh, Min Kuk
Park, Seung-Hwan
Yoon, Hyuk
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  givenname: Ji-Sun
  surname: Kim
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  organization: Korean Collection for Type Cultures, (KCTC), Korea Research Institute of Bioscience and Biotechnology, (KRIBB)
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  givenname: Min Kuk
  surname: Suh
  fullname: Suh, Min Kuk
  organization: Korean Collection for Type Cultures, (KCTC), Korea Research Institute of Bioscience and Biotechnology, (KRIBB), Department of Lifestyle Medicine, Jeonbuk National University
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  organization: Korean Collection for Type Cultures, (KCTC), Korea Research Institute of Bioscience and Biotechnology, (KRIBB)
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  email: jslee@kribb.re.kr
  organization: Korean Collection for Type Cultures, (KCTC), Korea Research Institute of Bioscience and Biotechnology, (KRIBB), University of Science and Technology (UST)
BackLink https://www.ncbi.nlm.nih.gov/pubmed/38368591$$D View this record in MEDLINE/PubMed
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CitedBy_id crossref_primary_10_1099_ijsem_0_006398
crossref_primary_10_1016_j_tifs_2024_104622
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1432-072X
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Fri Sep 05 04:17:43 EDT 2025
Fri Jul 25 19:13:43 EDT 2025
Mon Jul 21 06:05:41 EDT 2025
Tue Jul 01 03:50:29 EDT 2025
Thu Apr 24 23:08:23 EDT 2025
Fri Feb 21 02:40:17 EST 2025
IsPeerReviewed true
IsScholarly true
Issue 3
Keywords Gut microbiota
Urolithin C
Human feces
Ellagic acid
Gordonibacter
Language English
License 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.
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Snippet A Gram-stain-positive, anaerobic, motile, and short rod-shaped bacterium, designated KGMB12511 T , was isolated from the feces of healthy Koreansubjects....
A Gram-stain-positive, anaerobic, motile, and short rod-shaped bacterium, designated KGMB12511 , was isolated from the feces of healthy Koreansubjects....
A Gram-stain-positive, anaerobic, motile, and short rod-shaped bacterium, designated KGMB12511T, was isolated from the feces of healthy Koreansubjects....
A Gram-stain-positive, anaerobic, motile, and short rod-shaped bacterium, designated KGMB12511ᵀ, was isolated from the feces of healthy Koreansubjects....
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StartPage 108
SubjectTerms Archives & records
bacteria
Biochemistry
Biomedical and Life Sciences
Biotechnology
Cell Biology
chemotaxonomy
Dimethyl acetals
DNA
Ecology
Ellagic Acid
Fatty acids
Feces
Gene sequencing
Genes
genome
Genomes
genus
Glycolipids
Humans
Hydrolyzable Tannins
Life Sciences
Lipids
Menaquinones
Microbial Ecology
Microbiology
New species
Nucleotide sequence
nucleotide sequences
Original Paper
phenotype
Phospholipids
Phylogenetics
Phylogeny
Polyphenols
Quinones
Republic of Korea
RNA, Ribosomal, 16S - genetics
rRNA 16S
species
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Title Gordonibacter faecis sp. nov., producing urolithin C from ellagic acid, isolated from feces of healthy Korean subjects
URI https://link.springer.com/article/10.1007/s00203-024-03844-5
https://www.ncbi.nlm.nih.gov/pubmed/38368591
https://www.proquest.com/docview/2928067581
https://www.proquest.com/docview/2928242542
https://www.proquest.com/docview/3153607731
Volume 206
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