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Stoll DA, Danylec N, Soukup ST, Hetzer B, Kulling SE, Huch M. Adlercreutzia rubneri sp. nov., a resveratrol-metabolizing bacterium isolated from human faeces and emended description of the genus Adlercreutzia. Int J Syst Evol Microbiol 2021; 71. [PMID: 34495823 PMCID: PMC8549271 DOI: 10.1099/ijsem.0.004987] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The novel, anaerobic, Gram-positive, rod-shaped bacterial strain, ResAG-91T, was isolated from a faecal sample of a male human volunteer. Analysis of the 16S rRNA gene sequence revealed that strain ResAG-91T showed high similarity to the type strains of Adlercreutzia equolifaciens subsp. equolifaciens and Adlercreutzia equolifaciens subsp. celatus. Analysis of the whole draft genome sequences, i.e. digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI), of strain ResAG-91T and the type strains of Adlercreutzia species revealed that strain ResAG-91T represents a novel species of the genus Adlercreutzia. The genome size of strain ResAG-91T is 2.8 Mbp and the G+C content is 63.3 mol%. The major respiratory quinone of strain ResAG-91T was MMK-5 (methylmenaquinone). Major cellular fatty acids were C15 : 0 anteiso, C14 : 0 iso and C14 : 0 2-OH. Galactose and ribose were detected as major whole cell sugars. Furthermore, the peptidoglycan type of strain ResAG-91T was A1γ with meso-diaminopimelic acid. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, one unidentified lipid, three unidentified phospholipids and five unidentified glycolipids. Strain ResAG-91T was able to metabolize the stilbene resveratrol into dihydroresveratrol. On the basis of this polyphasic approach, including phenotypical, molecular (16S rRNA gene and whole genome sequencing) and biochemical (fatty acids, quinones, polar lipids, peptidoglycan, whole cell sugars, Rapid ID32A and API20A) analyses, we propose the novel species Adlercreutzia rubneri sp. nov. with the type and only strain ResAG-91T (=DSM 111416T=JCM 34176T=LMG 31897T).
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Affiliation(s)
- Dominic A Stoll
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Karlsruhe, Germany
| | - Nicolas Danylec
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Karlsruhe, Germany
| | - Sebastian T Soukup
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Karlsruhe, Germany
| | - Birgit Hetzer
- Department of Food Technology and Bioprocess Engineering, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Karlsruhe, Germany
| | - Sabine E Kulling
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Karlsruhe, Germany
| | - Melanie Huch
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Karlsruhe, Germany
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Guo Y, Zhao L, Fang X, Zhong Q, Liang H, Liang W, Wang L. Isolation and identification of a human intestinal bacterium capable of daidzein conversion. FEMS Microbiol Lett 2021; 368:6261181. [PMID: 33930123 DOI: 10.1093/femsle/fnab046] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/28/2021] [Indexed: 12/21/2022] Open
Abstract
Equol, which produced from daidzein (one of the principal isoflavones), is recognized to be the most resultful in stimulating an estrogenic and antioxidant response. The daidzein transformation was studied during fermentation of five growth media inoculated with feces from a healthy human, and a daidzein conversion strain was isolated. To enrich the bacterial population involved in daidzein metabolism in a complex mixture, fecal samples were treated with antibiotics. The improved propidium monoazide combined with the quantitative polymerase chain reaction (PMAxx-qPCR) assay showed that the ampicillin treatment of samples did result in a reduction of the total visible bacteria counts by 52.2% compared to the treatment without antibiotics. On this basis, the newly isolated rod-shaped, Gram-positive anaerobic bacterium, named strain Y11 (MN560033), was able to metabolize daidzein to equol under anaerobic conditions, with a conversion ratio (equol ratio: the amount of equol produced/amount of supplemented daizein) of 0.56 over 120 h. The 16S rRNA partial sequence of the strain Y11 exhibited 99.8% identity to that of Slackia equolifaciens strain DZE (NR116295). This study will provide new insights into the biotransformation of equol from daidzein by intestinal microbiota from the strain-level and explore the possibility of probiotic interventions.
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Affiliation(s)
- Yingyu Guo
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Lichao Zhao
- College of Food Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
| | - Xiang Fang
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Qingping Zhong
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Huijun Liang
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Wenou Liang
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Li Wang
- College of Food Science, South China Agricultural University, Guangzhou, China
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A case of severe empyema with acute respiratory distress syndrome caused by Slackia exigua requiring veno-venous extracorporeal membrane oxygenation. Anaerobe 2017; 48:7-11. [DOI: 10.1016/j.anaerobe.2017.06.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 06/20/2017] [Accepted: 06/27/2017] [Indexed: 11/19/2022]
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Two New Cyclohexenone Derivatives from a Novel Actinobacterium, Enteractinococcus coprophilus. Chem Nat Compd 2015. [DOI: 10.1007/s10600-015-1495-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Selma MV, Tomás-Barberán FA, Beltrán D, García-Villalba R, Espín JC. Gordonibacter urolithinfaciens sp. nov., a urolithin-producing bacterium isolated from the human gut. Int J Syst Evol Microbiol 2014; 64:2346-2352. [PMID: 24744017 DOI: 10.1099/ijs.0.055095-0] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Urolithins are dibenzopyranone metabolites that exert anti-inflammatory activity in vivo and are produced by the gut microbiota from the dietary polyphenols ellagic acid (EA) and ellagitannins. However, the bacteria involved in this process remain unknown. We report here a novel bacterium, strain CEBAS 1/15P(T), capable of metabolizing EA to urolithins, that was isolated from healthy human faeces and characterized by determining phenotypic, biochemical and molecular methods. The strain was related to Gordonibacter pamelaeae 7-10-1-b(T), the type and only reported strain of the only species of the genus Gordonibacter, with about 97% 16S rRNA gene sequence similarity; they were both obligately anaerobic, non-spore-forming, Gram-stain-positive, short-rods/coccobacilli and metabolized only small numbers of carbon sources. L-Fucose, D-fructose, turanose, D-galacturonic acid and α-ketobutyric acid were metabolized by strain CEBAS 1/15P(T), while G. pamelaeae was negative for metabolism of these compounds. The whole-cell fatty acids consisted predominantly of saturated fatty acids (70%); strain CEBAS 1/15P(T) differed significantly from G. pamelaeae in the major fatty acid, which was C18 : 1ω9c, while anteiso-C15 : 0 was the major component for G. pamelaeae. The presence of a number of different fatty acid peaks, especially C19 : 0 cyclo and C18 : 1ω6c, was also indicative of distinct species. Six glycolipids (GL1-6) were recognized, while, in G. pamelaeae, only four glycolipids were described. On the basis of these data, the novel species Gordonibacter urolithinfaciens sp. nov. is described, with strain CEBAS 1/15P(T) ( = DSM 27213(T) = CCUG 64261(T)) as the type strain.
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Affiliation(s)
- María V Selma
- Research Group on Quality, Safety and Bioactivity of Plant Foods, Department of Food Science and Technology, CEBAS-CSIC, 30100 Campus de Espinardo, Murcia, Spain
| | - Francisco A Tomás-Barberán
- Research Group on Quality, Safety and Bioactivity of Plant Foods, Department of Food Science and Technology, CEBAS-CSIC, 30100 Campus de Espinardo, Murcia, Spain
| | - David Beltrán
- Research Group on Quality, Safety and Bioactivity of Plant Foods, Department of Food Science and Technology, CEBAS-CSIC, 30100 Campus de Espinardo, Murcia, Spain
| | - Rocio García-Villalba
- Research Group on Quality, Safety and Bioactivity of Plant Foods, Department of Food Science and Technology, CEBAS-CSIC, 30100 Campus de Espinardo, Murcia, Spain
| | - Juan C Espín
- Research Group on Quality, Safety and Bioactivity of Plant Foods, Department of Food Science and Technology, CEBAS-CSIC, 30100 Campus de Espinardo, Murcia, Spain
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Nagai F, Watanabe Y, Morotomi M. Slackia piriformis sp. nov. and Collinsella tanakaei sp. nov., new members of the family Coriobacteriaceae, isolated from human faeces. Int J Syst Evol Microbiol 2010; 60:2639-2646. [DOI: 10.1099/ijs.0.017533-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three Gram-positive, strictly anaerobic, non-spore-forming, rod-shaped organisms (strains YIT 12062T, YIT 12063T and YIT 12064) were isolated from human faeces. Strain YIT 12062T was asaccharolytic and possessed a DNA G+C content of 58.3 mol%. Cells of strain YIT 12062T were negative for catalase, oxidase, urease, hydrolysis of aesculin and gelatin, nitrate reduction and indole production. Based on 16S rRNA gene sequence analysis, strain YIT 12062T was assigned to the genus Slackia (91.7–96.0 % sequence similarities to type strains of Slackia species). Biochemical data showed that the isolate was phenotypically distinct from all recognized species of the genus Slackia. Strain YIT 12062T therefore represents a novel species in the genus Slackia, for which the name Slackia piriformis sp. nov. is proposed. The type strain is YIT 12062T (=DSM 22477T=JCM 16070T). Following 16S rRNA gene sequence analysis, strains YIT 12063T and YIT 12064, which were isolated from different subjects, were shown to be most closely related to species of the genus Collinsella (93.8–95.1 % similarities to type strains). Although their phenotypic characteristics were very similar and they shared >99 % 16S rRNA gene sequence similarity and >97±1.8 % DNA–DNA relatedness, the two isolates could be discriminated by RAPD fingerprints. The DNA G+C contents of strains YIT 12063T and YIT 12064 were 60.8 and 61.0 mol%, respectively. They were saccharolytic in API test systems, positive for aesculin hydrolysis and negative for catalase, oxidase, urease, indole production, nitrate reduction and gelatin hydrolysis. The major end products of glucose fermentation of these strains were lactate, acetate and formate. Biochemical data supported the affiliation of strains YIT 12063T and YIT 12064 to the genus Collinsella and showed that they were phenotypically distinct from all recognized species of the genus Collinsella. Strains YIT 12063T and YIT 12064 therefore represent a novel species of the genus Collinsella, for which the name Collinsella tanakaei sp. nov. is proposed. The type strain is YIT 12063T (=DSM 22478T=JCM 16071T).
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Affiliation(s)
- Fumiko Nagai
- Yakult Central Institute for Microbiological Research, 1796 Yaho, Kunitachi, 186-8650 Tokyo, Japan
| | - Yohei Watanabe
- Yakult Central Institute for Microbiological Research, 1796 Yaho, Kunitachi, 186-8650 Tokyo, Japan
| | - Masami Morotomi
- Yakult Central Institute for Microbiological Research, 1796 Yaho, Kunitachi, 186-8650 Tokyo, Japan
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Characterization of Slackia exigua isolated from human wound infections, including abscesses of intestinal origin. J Clin Microbiol 2010; 48:1070-5. [PMID: 20107092 DOI: 10.1128/jcm.01576-09] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Eleven clinical strains isolated from infected wound specimens were subjected to polyphasic taxonomic analysis. Sequence analysis of the 16S rRNA gene showed that all 11 strains were phylogenetically related to Slackia exigua. Additionally, conventional and biochemical tests of 6 of the 11 strains were performed as supplementary methods to obtain phenotypic identification by comparison with the phenotypes of the relevant type strains. S. exigua has been considered an oral bacterial species in the family Coriobacteriaceae. This organism is fastidious and grows poorly, so it may easily be overlooked. The 16S rRNA gene sequences and the biochemical characteristics of four of the S. exigua strains isolated for this study from various infections indicative of an intestinal source were almost identical to those of the validated S. exigua type strain from an oral source and two of the S. exigua strains from oral sources evaluated in this study. Thus, we show for the first time that S. exigua species can be isolated from extraoral infections as well as from oral infections. The profiles of susceptibility to selected antimicrobials of this species were also investigated for the first time.
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Jin JS, Kitahara M, Sakamoto M, Hattori M, Benno Y. Slackia equolifaciens sp. nov., a human intestinal bacterium capable of producing equol. Int J Syst Evol Microbiol 2009; 60:1721-1724. [PMID: 19734283 DOI: 10.1099/ijs.0.016774-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
An equol-producing bacterium, strain DZE(T), which was isolated from human faeces, was characterized by morphological, biochemical and molecular methods. The isolate was Gram-positive, obligately anaerobic, non-spore-forming, asaccharolytic and rod-shaped. 16S rRNA gene sequence analysis showed 92.8, 91.0, 91.1 and 90.6% similarities with Slackia faecicanis, Slackia exigua, Slackia heliotrinireducens and Slackia isoflavoniconvertens, respectively. Based on these data, we propose a novel species of the genus Slackia, Slackia equolifaciens sp. nov. The major cellular fatty acids are C14:0, C18:1omega9c and C18:1omega9c DMA (dimethyl acetal). The DNA G+C content of the strain is 60.8 mol%. The type strain of S. equolifaciens sp. nov. is DZET (=JCM 16059T =CCUG 58231T).
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Affiliation(s)
- Jong-Sik Jin
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Institute of Natural Medicine, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
- Benno Laboratory, Center for Intellectual Property Strategies, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Maki Kitahara
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Masao Hattori
- Institute of Natural Medicine, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Yoshimi Benno
- Benno Laboratory, Center for Intellectual Property Strategies, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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Würdemann D, Tindall BJ, Pukall R, Lünsdorf H, Strömpl C, Namuth T, Nahrstedt H, Wos-Oxley M, Ott S, Schreiber S, Timmis KN, Oxley APA. Gordonibacter pamelaeae gen. nov., sp. nov., a new member of the Coriobacteriaceae isolated from a patient with Crohn's disease, and reclassification of Eggerthella hongkongensis Lau et al. 2006 as Paraeggerthella hongkongensis gen. nov., comb. nov. Int J Syst Evol Microbiol 2009; 59:1405-15. [PMID: 19502325 DOI: 10.1099/ijs.0.005900-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strictly anaerobic, Gram-positive, short-rod/coccobacillus-shaped bacterial strain, designated 7-10-1-b(T), was isolated from the colon of a patient suffering from acute Crohn's disease. The isolate formed small, pale-white, semi-translucent colonies on solid cultivation media. The strain was catalase-positive and metabolized only a small number of carbon sources. Whole-cell fatty acids consisted predominantly of saturated fatty acids (89 %), of which 15 : 0 anteiso was the major component. The polar lipids phosphatidylglycerol and diphosphatidylglycerol as well as four glycolipids were identified. 16S rRNA gene sequence analysis revealed that the isolate represents a distinct lineage within the family Coriobacteriaceae and has 94.6 % identity to the type strain of [Eggerthella] hongkongensis, the phylogenetically closest bacterial species. On the basis of the analyses performed, the new genus and species Gordonibacter pamelaeae gen. nov., sp. nov. is described, with strain 7-10-1-b(T) (=DSM 19378(T) =CCUG 55131(T)) as the type and only strain of Gordonibacter pamelaeae. Also, based on the chemotaxonomic data obtained for all type strains of the neighbouring genus Eggerthella, we propose that Eggerthella hongkongensis Lau et al. 2006 be transferred to a new genus as Paraeggerthella hongkongensis gen. nov., comb. nov.; the type strain of Paraeggerthella hongkongensis is HKU10(T) (=DSM 16106(T) =CCUG 49250(T)).
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Affiliation(s)
- Dieco Würdemann
- Environmental Microbiology Laboratory, Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany.
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Isolation of a human intestinal bacterium capable of daidzein and genistein conversion. Appl Environ Microbiol 2009; 75:1740-4. [PMID: 19139227 DOI: 10.1128/aem.01795-08] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A rod-shaped gram-positive anaerobic bacterium, strain HE8, was isolated from human feces. The isolate was able to convert the isoflavones daidzein and genistein to equol and 5-hydroxy-equol, respectively. Based on phenotypic and phylogenetic analyses, strain HE8 is described as a new species, Slackia isoflavoniconvertens.
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