1
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Bivand JM, Dyrhovden R, Sivertsen A, Tellevik MG, Patel R, Kommedal Ø. Broad-range amplification and sequencing of the rpoB gene: a novel assay for bacterial identification in clinical microbiology. J Clin Microbiol 2024; 62:e0026624. [PMID: 38884485 PMCID: PMC11324016 DOI: 10.1128/jcm.00266-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 05/21/2024] [Indexed: 06/18/2024] Open
Abstract
The rpoB gene has been proposed as a promising phylogenetic marker for bacterial identification, providing theoretically improved species-level resolution compared to the 16S rRNA gene for a range of clinically important taxa. However, its utility in diagnostic microbiology has been limited by the lack of broad-range primers allowing for its amplification from most species with a single PCR assay. Here, we present an assay for broad-range partial amplification and Sanger sequencing of the rpoB gene. To reduce cross-reactivity and allow for rpoB amplification directly from patient samples, primers were based on the dual priming oligonucleotide principle. The resulting amplicon is ~550 base pairs in length and appropriate for species-level identification. Systematic in silico evaluation of a wide selection of taxa demonstrated improved resolution within multiple important genera, including Enterococcus, Fusobacterium, Mycobacterium, Streptococcus, and Staphylococcus species and several genera within the Enterobacteriaceae family. Broad-range rpoB amplification and Sanger sequencing of 115 bacterial isolates provided unambiguous species-level identification for 97 (84%) isolates, as compared to 57 (50%) using a clinical 16S rRNA gene assay. Several unresolved taxonomic matters disguised by the low resolution of the 16S rRNA gene were revealed using the rpoB gene. Using a collection of 33 clinical specimens harboring bacteria and assumed to contain high concentrations of human DNA, the rpoB assay identified the pathogen in 29 specimens (88%). Broad-range rpoB amplification and sequencing provides a promising tool for bacterial identification, improving discrimination between closely related species and making it amenable for use in culture-based and culture-independent diagnostic approaches.
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Affiliation(s)
- Joanna Małgorzata Bivand
- Department of
Microbiology, Haukeland University
Hospital, Bergen,
Norway
- Department of Clinical
Science, University of Bergen,
Bergen, Norway
| | - Ruben Dyrhovden
- Department of
Microbiology, Haukeland University
Hospital, Bergen,
Norway
| | - Audun Sivertsen
- Department of
Microbiology, Haukeland University
Hospital, Bergen,
Norway
| | | | - Robin Patel
- Division of Clinical
Microbiology, Department of Laboratory Medicine and Pathology, Mayo
Clinic, Rochester,
Minnesota, USA
- Division of Public
Health, Infectious Diseases, and Occupational Medicine, Department of
Medicine, Mayo Clinic,
Rochester, Minnesota,
USA
| | - Øyvind Kommedal
- Department of
Microbiology, Haukeland University
Hospital, Bergen,
Norway
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2
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Fernández Vecilla D, Urrutikoetxea Gutiérrez MJ, Roche Matheus MP, Angulo López I, Aspichueta Vivanco C, Calvo Muro FE, Díaz de Tuesta Del Arco JL. Description of eight human infections caused by Bacteroides pyogenes in a tertiary hospital of northern Spain. Anaerobe 2023; 82:102759. [PMID: 37419176 DOI: 10.1016/j.anaerobe.2023.102759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/09/2023]
Abstract
Bacteroides pyogenes is a Gram-negative obligate anaerobe, saccharolytic, non-motile, non-pigment-producing and non-spore-forming rod. Reports of human infections caused by B. pyogenes are scarce, with approximately 30 cases documented in scientific literature. The aim of this study was to describe the clinical characteristics of 8 different patients and to study the in vitro antibiotic susceptibility of the strains, as well as to evaluate the in vivo activity of the prescribed treatments. We conducted a descriptive retrospective study by searching all B. pyogenes isolates from January 2010 to March 2023 at the Basurto University Hospital. This included all cases, both in monomicrobial or polymicrobial cultures. Among the eight patients, three experienced severe infections such as bacteremia and osteomyelitis. All the strains were susceptible to amoxicillin/clavulanic acid, piperacillin/tazobactam, imipenem, meropenem, clindamycin, metronidazole and moxifloxacin.
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Affiliation(s)
| | - Mikel Joseba Urrutikoetxea Gutiérrez
- Basurto University Hospital, Clinical Microbiology Service, Bilbao, Basque Country, Spain; Biocruces Bizkaia Health Research Institute, Barakaldo, Basque Country, Spain
| | - Mary Paz Roche Matheus
- Basurto University Hospital, Clinical Microbiology Service, Bilbao, Basque Country, Spain; Biocruces Bizkaia Health Research Institute, Barakaldo, Basque Country, Spain
| | - Itziar Angulo López
- Basurto University Hospital, Clinical Microbiology Service, Bilbao, Basque Country, Spain; Biocruces Bizkaia Health Research Institute, Barakaldo, Basque Country, Spain
| | - Cristina Aspichueta Vivanco
- Basurto University Hospital, Clinical Microbiology Service, Bilbao, Basque Country, Spain; Biocruces Bizkaia Health Research Institute, Barakaldo, Basque Country, Spain
| | - Felicitas Elena Calvo Muro
- Basurto University Hospital, Clinical Microbiology Service, Bilbao, Basque Country, Spain; Biocruces Bizkaia Health Research Institute, Barakaldo, Basque Country, Spain
| | - José Luis Díaz de Tuesta Del Arco
- Basurto University Hospital, Clinical Microbiology Service, Bilbao, Basque Country, Spain; Biocruces Bizkaia Health Research Institute, Barakaldo, Basque Country, Spain
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3
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Uzma B, Alia F, Qureshi NA, Shakeela Q, Asima B, Ahmed S, Hayat A, Rehman MU. Isolation and characterization of synthetic pyrethroids-degrading bacterial strains from agricultural soil. BRAZ J BIOL 2023; 83:e271790. [PMID: 37132742 DOI: 10.1590/1519-6984.271790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/29/2023] [Indexed: 05/04/2023] Open
Abstract
Pyrethroid pesticides are commonly used for pest control in agriculture setup, veterinary and home garden. They are now posing increased risks to non-targeted organisms associated to human beings due to their considerable use. The present work deals with the isolation of bacteria with tolerance to high concentrations of bifenthrin and cypermethrin from contaminated soil. Enrichment culture technique (bifenthrin concentration = 50-800 mg/L) was used for bacterial isolation. Bacteria that showed growth on minimal media with bifenthrin were also sub-cultured on minimal media with cypermethrin. Bacteria showing luxurious growth on both the pyrethroid, were screened out based on their morphological, biochemical parameters and by API 20NE Kit. Phylogenetic studies revealed that, one bacterial isolate (MG04) belonging to Acinetobacter lwoffii and other five bacterial isolates (MG06, MG05, MG01, MG03 and MG02) cluster with Pseudomonas aeruginosa, Pseudomonas putida respectively. Isolated members of genera Pseudomonas and Acinetobacter could be used for further detailed degradation studies by using FTIR, HPLC-MS or GC-MS analysis.
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Affiliation(s)
- B Uzma
- Hazara University, Department of Microbiology, Mansehra, Khyber Pakhtunkhwa, Pakistan
| | - F Alia
- University of Swabi, Department of Microbiology, Swabi, Khyber Pakhtunkhwa, Pakistan
| | - N A Qureshi
- Quaid-i-Azam University, Faculty of Biological Science, Department of Animal Sciences, Islamabad, Pakistan
| | - Q Shakeela
- Abbottabad University of Science & Technology, Department of Microbiology, Abbottabad, Khyber Pakhtunkhwa, Pakistan
| | - B Asima
- Hazara University, Department of Microbiology, Mansehra, Khyber Pakhtunkhwa, Pakistan
| | - S Ahmed
- Hazara University, Department of Microbiology, Mansehra, Khyber Pakhtunkhwa, Pakistan
| | - A Hayat
- Abbottabad University of Science & Technology, Department of Microbiology, Abbottabad, Khyber Pakhtunkhwa, Pakistan
| | - M U Rehman
- Abbottabad University of Science & Technology, Department of Microbiology, Abbottabad, Khyber Pakhtunkhwa, Pakistan
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4
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Shukla I, Hill JE. cpn60 barcode sequences accurately identify newly defined genera within the Lactobacillaceae. Can J Microbiol 2022; 68:457-464. [PMID: 35230911 DOI: 10.1139/cjm-2021-0296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The cpn60 barcode sequence is established as an informative target for microbial species identification. Applications of cpn60 barcode sequencing are supported by the availability of "universal" PCR primers for its amplification and a curated reference database of cpn60 sequences, cpnDB. A recent reclassification of lactobacilli involving the definition of 23 new genera provided an opportunity to update cpnDB and to determine if the cpn60 barcode could be used for accurate identification of species consistent with the new framework. Analysis of 275 cpn60 sequences representing 258/269 of the validly named species in Lactobacillus, Paralactobacillus and the 23 newer genera showed that cpn60-based sequence relationships were generally consistent with the whole-genome-based phylogeny. Aligning or mapping full length barcode sequences or a 150 bp subsequence resulted in accurate and unambiguous species identification in almost all cases. Taken together, our results show that the combination of available reference sequence data, "universal" barcode amplification primers, and the inherent sequence diversity within the cpn60 barcode make it a useful target for the detection and identification of lactobacilli as defined by the latest taxonomic framework.
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Affiliation(s)
- Ishika Shukla
- University of Saskatchewan, 7235, Veterinary Microbiology, Saskatoon, Saskatchewan, Canada;
| | - Janet E Hill
- University of Saskatchewan, 7235, Veterinary Microbiology, Saskatoon, Saskatchewan, Canada;
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5
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Tikhomirova TS, Matyunin MA, Lobanov MY, Galzitskaya OV. In-depth analysis of amino acid and nucleotide sequences of Hsp60: how conserved is this protein? Proteins 2021; 90:1119-1141. [PMID: 34964171 DOI: 10.1002/prot.26294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/21/2021] [Accepted: 12/23/2021] [Indexed: 11/07/2022]
Abstract
Chaperonin Hsp60, as a protein found in all organisms, is of great interest in medicine, since it is present in many tissues and can be used both as a drug and as an object of targeted therapy. Hence, Hsp60 deserves a fundamental comparative analysis to assess its evolutionary characteristics. It was found that the percent identity of Hsp60 amino acid sequences both within and between phyla was not high enough to identify Hsp60s as highly conserved proteins. However, their ATP binding sites are largely conserved. The amino acid composition of Hsp60s remained relatively constant. At the same time, the analysis of the nucleotide sequences showed that GC content in the Hsp60 genes was comparable to or greater than the genomic values, which may indicate a high resistance to mutations due to tight control of the nucleotide composition by DNA repair systems. Natural selection plays a dominant role in the evolution of Hsp60 genes. The degree of mutational pressure affecting the Hsp60 genes is quite low, and its direction does not depend on taxonomy. Interestingly, for the Hsp60 genes from Chordata, Arthropoda, and Proteobacteria the exact direction of mutational pressure could not be determined. However, upon further division into classes, it was found that the direction of the mutational pressure for Hsp60 genes from Fish differs from that for other chordates. The direction of the mutational pressure affects the synonymous codon usage bias. The number of high and low represented codons increases with increasing GC content, which can improve codon usage. Special server has been created for bioinformatics analysis of Hsp60: http://oka.protres.ru:4202/.
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Affiliation(s)
- Tatyana S Tikhomirova
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region, Russia
| | - Maxim A Matyunin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Michail Yu Lobanov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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6
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Bacteroides pyogenes isolated from appendiceal abscess in a patient without animal contact. New Microbes New Infect 2021; 44:100933. [PMID: 34631109 PMCID: PMC8488308 DOI: 10.1016/j.nmni.2021.100933] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/10/2021] [Accepted: 08/16/2021] [Indexed: 11/23/2022] Open
Abstract
Bacteroides pyogenes is a member of the oral flora of cats and dogs. We report a case of B. pyogenes isolated from an appendiceal abscess in a patient without a history of animal contact. This species was identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and sequencing of 16S rRNA, rpoB, gyrB and hsp60 genes.
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7
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Shenoy PA, Vishwanath S, Nagaraj RT, Banerjee B, Krishna MS. Diabetic Foot Infection with Bacteroides pyogenes. J Glob Infect Dis 2021; 13:186-188. [PMID: 35017877 PMCID: PMC8697825 DOI: 10.4103/jgid.jgid_345_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/06/2020] [Accepted: 03/22/2021] [Indexed: 12/02/2022] Open
Abstract
>Diabetic foot infections are the most common serious diabetes-related complication posing significant socioeconomic burden on the health-care system. Diabetic foot microbiota consists of polymicrobial flora with predominance of Gram-negative aerobes and anaerobes. Here, we report a rare case of diabetic foot infection by Bacteroides pyogenes, an obligate Gram-negative anaerobic bacillus which is commonly encountered in polymicrobial animal bite wound infections.
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Affiliation(s)
- Padmaja Ananth Shenoy
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Shashidhar Vishwanath
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Ravikumar Terikere Nagaraj
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Barnini Banerjee
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - M Sunil Krishna
- Department of Surgery, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
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8
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Sakamoto M, Ikeyama N, Toyoda A, Murakami T, Mori H, Morohoshi S, Kunihiro T, Iino T, Ohkuma M. Coprobacter secundus subsp. similis subsp. nov. and Solibaculum mannosilyticum gen. nov., sp. nov., isolated from human feces. Microbiol Immunol 2021; 65:245-256. [PMID: 33913539 DOI: 10.1111/1348-0421.12886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/08/2021] [Accepted: 04/19/2021] [Indexed: 01/15/2023]
Abstract
An obligately anaerobic, Gram-stain-negative, rod-shaped bacterium, designated strain 2CBH44T , was isolated from the fecal sample of a healthy Japanese man. This strain was initially assigned as a novel species of the genus Coprobacter based on the 16S rRNA gene sequence similarities compared with other Coprobacter species. The 16S rRNA gene sequence analysis revealed strain 2CBH44T had relatively low 16S rRNA gene sequence similarity (97.5%) to Coprobacter secundus 177T . However, strain 2CBH44T showed 96.9% average nucleotide identity value with C. secundus 177T , indicating that strain 2CBH44T and C. secundus 177T belong to the same species. On the other hand, the digital DNA-DNA hybridization value between strain 2CBH44T and C. secundus 177T was 73.5%, indicating that strain 2CBH44T is a subspecies of C. secundus. Another anaerobic, Gram-stain-variable, rod-shaped bacterium, designated strain 12CBH8T , was also isolated from human feces. Strain 12CBH8T had significantly low 16S rRNA gene sequence similarities (<92.0%) to the validated bacterial species within the family Oscillospiraceae. The percentage of conserved protein values between the genome of strain 12CBH8T and that of the validated related taxa were <50%, suggesting that strain 12CBH8T belongs to a novel genus. On the basis of the collected data, strain 2CBH44T represents a novel subspecies of C. secundus, for which the name Coprobacter secundus subsp. similis subsp. nov. (type strain 2CBH44T = JCM 34079T = DSM 111570T ) is proposed. Strain 12CBH8T represents a novel species of a novel genus, for which the name Solibaculum mannosilyticum gen. nov., sp. nov. (type strain 12CBH8T = JCM 34081T = DSM 111571T ) is proposed.
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Affiliation(s)
- Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan.,PRIME, Japan Agency for Medical Research and Development (AMED), Tsukuba, Ibaraki, Japan
| | - Nao Ikeyama
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Takumi Murakami
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Hiroshi Mori
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Sho Morohoshi
- TechnoSuruga Laboratory Co. Ltd, Shizuoka-shi, Shizuoka, Japan
| | - Tadao Kunihiro
- TechnoSuruga Laboratory Co. Ltd, Shizuoka-shi, Shizuoka, Japan
| | - Takao Iino
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
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9
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Majewska A, Kierzkowska M, Kawecki D. What we actually know about the pathogenicity of Bacteroides pyogenes. Med Microbiol Immunol 2021; 210:157-163. [PMID: 33934237 PMCID: PMC8137477 DOI: 10.1007/s00430-021-00709-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/18/2021] [Indexed: 11/26/2022]
Abstract
The aim of the study was to evaluate the pathogenic potential of Bacteroides pyogenes, rarely identified in clinical laboratories anaerobic bacteria. To increase the knowledge about this poorly understood anaerobic microorganism, the study also includes cases of infections described so far in the literature. Only the use of 16S rRNA sequencing and mass spectrometry technique allowed the identification of B. pyogenes from clinical specimens. We reported 13 severe human infections caused by B. pyogenes. Bacteria were cultured from the wound after biting by animals, chronic infections within the oral cavity, from patients with histologically or radiological proven osteomyelitis, surgical site infection, and from urine sample collected after a urological procedure. Most (9/13) of the patients required hospitalization. Almost 70% of them needed urgent admission via the emergency room. Two inpatients due to a life-threatening condition were admitted to the intensive care unit. Almost 50% of isolates were resistant to penicillin. All resistant to penicillin strains were isolated from skin and mucous membrane infections.
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Affiliation(s)
- Anna Majewska
- Department of Medical Microbiology, Medical University of Warsaw, Chalubinskiego 5 Str, 02-004, Warsaw, Poland.
| | - Marta Kierzkowska
- Department of Medical Microbiology, Medical University of Warsaw, Chalubinskiego 5 Str, 02-004, Warsaw, Poland
| | - Dariusz Kawecki
- Department of Medical Microbiology, Medical University of Warsaw, Chalubinskiego 5 Str, 02-004, Warsaw, Poland
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10
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Wang C, Zhao J, Zhang H, Lee YK, Zhai Q, Chen W. Roles of intestinal bacteroides in human health and diseases. Crit Rev Food Sci Nutr 2020; 61:3518-3536. [PMID: 32757948 DOI: 10.1080/10408398.2020.1802695] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Bacteroides, an abundant genus in the intestines of mammals, has been recently considered as the next generation probiotics (NGP) candidate due to its potential role in promoting host health. However, the role of Bacteroides in the development of intestinal dysfunctions such as diarrhea, inflammatory bowel disease, and colorectal cancer should not be overlooked. In the present study, we focused on nine most widely occurred and abundant Bacteroides species and discussed their roles in host immunity, glucose and lipid metabolism and the prevention or induction of diseases. Besides, we also discussed the current methods used in the safety evaluation of Bacteroides species and key opinions about the concerns of these strains for the future use.
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Affiliation(s)
- Chen Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, P.R. China.,School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, P.R. China.,School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, P.R. China.,School of Food Science and Technology, Jiangnan University, Wuxi, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China.,Research Institute, Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine, Wuxi, China.,(Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou, China
| | - Yuan-Kun Lee
- Department of Microbiology & Immunology, National University of Singapore, Singapore, Singapore
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, P.R. China.,School of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Research Laboratory for Probiotics, Jiangnan University, Wuxi, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, P.R. China.,School of Food Science and Technology, Jiangnan University, Wuxi, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China.,Beijing Innovation Centre of Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, P.R. China
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11
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Ikeyama N, Toyoda A, Morohoshi S, Kunihiro T, Murakami T, Mori H, Iino T, Ohkuma M, Sakamoto M. Amedibacterium intestinale gen. nov., sp. nov., isolated from human faeces, and reclassification of Eubacterium dolichum Moore et al. 1976 (Approved Lists 1980) as Amedibacillus dolichus gen. nov., comb. nov. Int J Syst Evol Microbiol 2020; 70:3656-3664. [PMID: 32416738 DOI: 10.1099/ijsem.0.004215] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Four strains (9CBEGH2T, 9BBH35, 6BBH38 and 6EGH11) of Gram-stain-positive, obligately anaerobic, rod-shaped bacteria were isolated from faecal samples from healthy Japanese humans. The results of 16S rRNA gene sequence analysis indicated that the four strains represented members of the family Erysipelotrichaceae and formed a monophyletic cluster with 'Absiella argi' strain N6H1-5 (99.4% sequence similarity) and Eubacterium sp. Marseille-P5640 (99.3 %). Eubacterium dolichum JCM 10413T (94.2 %) and Eubacterium tortuosum ATCC 25548T (93.7 %) were located near this monophyletic cluster. The isolates, 9CBEGH2T, 'A. argi' JCM 30884 and Eubacterium sp. Marseille-P5640 shared 98.7-99.1% average nucleotide identity (ANI) with each other. Moreover, the in silico DNA-DNA hybridization (DDH) values among three strains were 88.4-90.6%, indicating that these strains represent the same species. Strain 9CBEGH2T showed 21.5-24.1 % in silico DDH values with other related taxa. In addition, the ANI values between strain 9CBEGH2T and other related taxa ranged from 71.2 % to 73.5 %, indicating that this strain should be considered as representing a novel species on the basis of whole-genome relatedness. Therefore, we formally propose a novel name for 'A. argi' strains identified because the name 'A. argi' has been effectively, but not validly, published since 2017. On the basis of the collected data, strain 9CBEGH2T represents a novel species of a novel genus, for which the name Amedibacterium intestinale gen. nov., sp. nov. is proposed. The type strain of A. intestinale is 9CBEGH2T (=JCM 33778T=DSM 110575T).
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Affiliation(s)
- Nao Ikeyama
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Sho Morohoshi
- TechnoSuruga Laboratory Co. Ltd, 330 Nagasaki, Shimizu-ku, Shizuoka-shi, Shizuoka 424-0065, Japan
| | - Tadao Kunihiro
- TechnoSuruga Laboratory Co. Ltd, 330 Nagasaki, Shimizu-ku, Shizuoka-shi, Shizuoka 424-0065, Japan
| | - Takumi Murakami
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Hiroshi Mori
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Takao Iino
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Mitsuo Sakamoto
- PRIME, Japan Agency for Medical Research and Development (AMED), Tsukuba, Ibaraki 305-0074, Japan.,Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
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12
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Sakamoto M, Ikeyama N, Ogata Y, Suda W, Iino T, Hattori M, Ohkuma M. Alistipes communis sp. nov., Alistipes dispar sp. nov. and Alistipes onderdonkii subsp. vulgaris subsp. nov., isolated from human faeces, and creation of Alistipes onderdonkii subsp. onderdonkii subsp. nov. Int J Syst Evol Microbiol 2020; 70:473-480. [PMID: 31633480 DOI: 10.1099/ijsem.0.003778] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three groups of Gram-stain-negative, obligately anaerobic, rod or coccoid-shaped bacteria, which were phylogenetically assigned in the genus Alistipes belonging to the family Rikenellaceae in the phylum Bacteroidetes, were isolated from the faecal samples of healthy Japanese humans. Group I (strains 5CBH24T and 6CPBBH3) showed highest 16S rRNA gene sequence similarity to 'Alistipes obesi' ph8T (99.73 %). Group II (strain 5CPEGH6T) was related to Alistipes shahii WAL 8301T (96.82 %). Ten strains of group III (3BBH6T, 5CPYCFAH4, 5NYCFAH2 and others) were related to Alistipes onderdonkii DSM 19147T (98.96 %). Group I could be differentiated from other strains by the ability to hydrolyse aesculin and the lack of catalase activity. Strain 5CPEGH6T could be differentiated from A. shahii JCM 16773T by the inability to hydrolyse aesculin and the lack of catalase activity, and so on. Phenotypic characteristics of group III were similar to those of A. onderdonkii JCM 16771T. Strains 5CBH24T, 6CPBBH3 and 'A. obesi' ph8T shared 98.8-98.9 % average nucleotide identity (ANI) with each other. In addition, the in silico DNA-DNA hybridization (DDH) values among three strains were 86.7-89.4 %. Strain 5CPEGH6T showed relatively low values (≤ 84.4 % for ANI ; ≤26.2 % for DDH) with other strains. Three strains in the group III (3BBH6T, 5CPYCFAH4 and 5NYCFAH2) shared 97.9-99.9% ANI with each other. These three strains showed 96.9-97.3 % ANI with A. onderdonkii DSM 19147T. The DDH values of strains 3BBH6T, 5CPYCFAH4 and 5NYCFAH2 among themselves were 80.5-99.8 %, while those compared to A. onderdonkii DSM 19147T were 71.0-73.4 %. On the basis of the collected data, three novel species, Alistipes communis sp. nov. (5CBH24T=JCM 32850T=DSM 108979T), Alistipes dispar sp. nov. (5CPEGH6T=JCM 32848T=DSM 108978T) and Alistipes onderdonkii subsp. vulgaris subsp. nov. (3BBH6T=JCM 32839T=DSM 108977T), are proposed.
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Affiliation(s)
- Mitsuo Sakamoto
- PRIME, Japan Agency for Medical Research and Development (AMED), Tsukuba, Ibaraki 305-0074, Japan.,Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Nao Ikeyama
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Yusuke Ogata
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Wataru Suda
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takao Iino
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Masahira Hattori
- Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan.,Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
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Gut Microbiota Alterations from Three-Strain Yogurt Formulation Treatments in Slow-Transit Constipation. CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY 2020; 2020:4583973. [PMID: 32148595 PMCID: PMC7049856 DOI: 10.1155/2020/4583973] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 12/28/2019] [Accepted: 01/27/2020] [Indexed: 02/07/2023]
Abstract
The objective of this study was to evaluate the effects of a three-strain yogurt formulation in slow-transit constipation (STC) patients. Each individual in both treatment groups consumed 250 mL of the formulated yogurt daily for a week (7 days), and fecal samples were collected for gut microbiota and short-chain fatty acid (SCFA) analyses. A significant increase in the defection frequency (p < 0.001) and bacterial diversity (p=0.027) at the 100% sequence homology level and a decrease in the concentrations of acetic acid (p=0.014), propionic acid (p=0.019), and butanoic acid (p=0.005) were observed after the STC patients consumed three-strain yogurt formulation. In addition, the consumption of the three-strain yogurt formulation significantly altered the composition of the intestinal bacteria in the STC patients. The relative abundances of 23 genera in the top dominating genera were altered significantly after the STC patients consumed the yogurt. In summary, the consumption of 250 mL day− the three-strain yogurt formulation described in this study can play a role in improving the symptoms of STC.
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14
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Sakamoto M, Ikeyama N, Toyoda A, Murakami T, Mori H, Iino T, Ohkuma M. Dialister hominis sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2020; 70:589-595. [DOI: 10.1099/ijsem.0.003797] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
- PRIME, Japan Agency for Medical Research and Development (AMED), Tsukuba, Ibaraki 305-0074, Japan
| | - Nao Ikeyama
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Takumi Murakami
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Hiroshi Mori
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Takao Iino
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
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Draft Genome Sequences of Bacteroides pyogenes Strains Isolated from the Uterus of Holstein Dairy Cows with Metritis. Microbiol Resour Announc 2019; 8:8/41/e01043-19. [PMID: 31601669 PMCID: PMC6787326 DOI: 10.1128/mra.01043-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Bacteroides pyogenes is found in the human and animal gut and is implicated in the pathogenesis of metritis in cows. We report the draft genome sequences of four Bacteroides pyogenes isolates obtained from the uterus of metritic cows. This will increase the understanding of its pathogenicity, antimicrobial resistance, and differentiation across hosts. Bacteroides pyogenes is found in the human and animal gut and is implicated in the pathogenesis of metritis in cows. We report the draft genome sequences of four Bacteroides pyogenes isolates obtained from the uterus of metritic cows. This will increase the understanding of its pathogenicity, antimicrobial resistance, and differentiation across hosts.
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16
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Le Roy T, Van der Smissen P, Paquot A, Delzenne N, Muccioli GG, Collet JF, Cani PD. Butyricimonas faecalis sp. nov., isolated from human faeces and emended description of the genus Butyricimonas. Int J Syst Evol Microbiol 2019; 69:833-838. [PMID: 30698516 DOI: 10.1099/ijsem.0.003249] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
A Gram-negative, strictly anaerobic, non-spore forming, non-motile, non-pigmented bacterial strain, designated H184T, was isolated from human faeces. 16S rRNA gene sequence analysis showed that strain H184T represents a member of the genus Butyricimonas. Strain H184T is related to but distinct from Butyricimonasvirosa JCM 15149T and Butyricimonasparavirosa JCM 18677T, with 16S rRNA gene sequence similarities of 96.32 and 96.24 %, respectively. Strain H184T shared 90.50 % hsp60 gene sequence similarity to B. virosa JCM 15149T and B. paravirosa JCM 18677T. Growth occurs between 25 and 42 °C with an optimum at 37 °C. Bile and NaCl concentration range allowing growth are 0-3.75 % and 0-1.8 %, respectively. pH range for growth is 5.5-8. The strain produced propionate as the major end product from glucose. The major cellular fatty acids of strain H184T were iso-C15 : 0 (63.5 %) and iso-C17 : 0 3-OH (12.8%). The major menaquinone of the strain was MK-10 (86 %). DNA G+C content of the isolate H184T was 44.2 mol%. The genome-based comparison between strain H184T and B. virosa JCM 15149T by pairwise average nucleotide identity indicated a clear distinction with a score of 87.22. On the basis of these data, strain H184T represents a novel species of the genus Butyricimonas, for which the name Butyricimonas faecalis sp. nov. is proposed. The type strain of B. faecalis is H184T (DSM 106867T, LMG 30602T).
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Affiliation(s)
- Tiphaine Le Roy
- 1UCLouvain, Université Catholique de Louvain, WELBIO - Walloon Excellence in Life Sciences and Biotechnology, Louvain Drug Research Institute (LDRI), Metabolism and Nutrition Research Group, Brussels, Belgium
| | | | - Adrien Paquot
- 3UCLouvain, Université Catholique de Louvain, Louvain Drug Research Institute (LDRI), Bioanalysis and Pharmacology of Bioactive Lipids Research Group (BPBL), Brussels, Belgium
| | - Nathalie Delzenne
- 1UCLouvain, Université Catholique de Louvain, WELBIO - Walloon Excellence in Life Sciences and Biotechnology, Louvain Drug Research Institute (LDRI), Metabolism and Nutrition Research Group, Brussels, Belgium
| | - Giulio G Muccioli
- 3UCLouvain, Université Catholique de Louvain, Louvain Drug Research Institute (LDRI), Bioanalysis and Pharmacology of Bioactive Lipids Research Group (BPBL), Brussels, Belgium
| | - Jean-François Collet
- 4UCLouvain, Université Catholique de Louvain, WELBIO - Walloon Excellence in Life Sciences and Biotechnology, de Duve Institute, Brussels Center for Redox Biology, Brussels, Belgium
| | - Patrice D Cani
- 1UCLouvain, Université Catholique de Louvain, WELBIO - Walloon Excellence in Life Sciences and Biotechnology, Louvain Drug Research Institute (LDRI), Metabolism and Nutrition Research Group, Brussels, Belgium
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Tkadlec J, Krutova M, Matejkova J, Nyc O, Drevinek P. Bloodstream infection caused by Bacteroides denticanum, a close relative of Bacteroides pyogenes, misidentified by MALDI TOF- mass spectrometry. Anaerobe 2018; 54:23-25. [DOI: 10.1016/j.anaerobe.2018.06.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 06/08/2018] [Accepted: 06/20/2018] [Indexed: 10/28/2022]
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18
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Sakamoto M, Ikeyama N, Kunihiro T, Iino T, Yuki M, Ohkuma M. Mesosutterella multiformis gen. nov., sp. nov., a member of the family Sutterellaceae and Sutterella megalosphaeroides sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2018; 68:3942-3950. [PMID: 30394865 DOI: 10.1099/ijsem.0.003096] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Two novel, obligately anaerobic, Gram-stain-negative, rod or coccoid-shaped bacteria, designated strains 4NBBH2T and 6FBBBH3T, were isolated from faecal samples of a healthy Japanese woman and man. The 16S rRNA gene sequence analysis showed that these strains represent a distinct lineage within the family Sutterellaceae. Strain 4NBBH2T formed a monophyletic branch between the genera Parasutterella and Sutterella, with sequence similarity to Sutterella stercoricanis CCUG 47620T (92.6 %), followed by Sutterella wadsworthensis WAL 7877 (92.4 %), Sutterella parvirubra YIT 11816T (92.1 %) and Parasutterella secunda YIT 12071T (91.8 %). Strain 6FBBBH3T was affiliated to the genus Sutterella, with highest similarity to S. stercoricanis CCUG 47620T (97.1 %), followed by S. parvirubra YIT 11816T (96.6 %) and S. wadsworthensis WAL 7877 (95.2 %). Strains 4NBBH2T and 6FBBBH3T were asaccharolytic. Analysis of fatty acids revealed that strain 4NBBH2T could be differentiated from Sutterella species (including strain 6FBBBH3T) by the presence of a low concentration of C16 : 1ω7c. The major respiratory quinones of strain 4NBBH2T were menaquinone (MK)-6 and methylmenaquinone (MMK)-6, whereas those of strain 6FBBBH3T were MK-5 and MMK-5. The G+C content of the genomic DNA of strains 4NBBH2T and 6FBBBH3T were 56.9 and 62.8 mol%, respectively. On the basis of the collected data, strain 4NBBH2T represents a novel species in a novel genus of the family Sutterellaceae, for which the name Mesosutterella multiformis gen. nov., sp. nov. is proposed. The type strain is 4NBBH2T (=JCM 32464T=DSM 106860T). We also propose a novel Sutterella species, Sutterellamegalosphaeroides sp. nov., for strain 6FBBBH3T (=JCM 32470T=DSM 106861T).
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Affiliation(s)
- Mitsuo Sakamoto
- 1Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan.,2PRIME, Japan Agency for Medical Research and Development (AMED), Tsukuba, Ibaraki 305-0074, Japan
| | - Nao Ikeyama
- 1Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Tadao Kunihiro
- 3TechnoSuruga Laboratory Co. Ltd, 330 Nagasaki, Shimizu-ku, Shizuoka-shi, Shizuoka 424-0065, Japan
| | - Takao Iino
- 1Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Masahiro Yuki
- 1Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- 1Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
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Jo Y, Kim J, Hwang K, Lee C. A comparative study of single- and two-phase anaerobic digestion of food waste under uncontrolled pH conditions. WASTE MANAGEMENT (NEW YORK, N.Y.) 2018; 78:509-520. [PMID: 32559939 DOI: 10.1016/j.wasman.2018.06.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 04/11/2018] [Accepted: 06/09/2018] [Indexed: 06/11/2023]
Abstract
This study compared single- versus two-phase systems for semi-continuous anaerobic digestion of food waste without pH control at varying organic loading rates (OLRs). The methanogenic reactors of both systems required trace element supplementation for stable operation at 3.0 g VS (volatile solids)/L∙d or higher OLRs. Under trace-element supplemented conditions, both systems achieved stable and efficient performance at OLRs up to 4.0 g VS/L∙d. The two-phase system outperformed the single-phase system at 1.0-4.0 g VS/L∙d OLRs, but it failed at an OLR of 5.0 g VS/L∙d. Meanwhile, the single-phase system maintained the stable performance and reached its maximum methane production at this OLR. These results suggest that a single-phase configuration is more advantageous for robust treatment of food waste without pH control at high organic and hydraulic loads. Hydrogenotrophic methanogens dominated the methanogen community throughout the experiment in both systems. Microbial community structure shifts correlated with reactor operation and performance characteristics.
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Affiliation(s)
- Yeadam Jo
- School of Urban and Environmental Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan 44919, Republic of Korea
| | - Jaai Kim
- School of Urban and Environmental Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan 44919, Republic of Korea
| | - Kwanghyun Hwang
- Environmental Process Engineering Team, Global Engineering Division, GS E&C, GRAN SEOUL, 33 Jong-ro, Jongno-gu, Seoul 03159, Republic of Korea
| | - Changsoo Lee
- School of Urban and Environmental Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan 44919, Republic of Korea.
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Sakamoto M, Iino T, Yuki M, Ohkuma M. Lawsonibacter asaccharolyticus gen. nov., sp. nov., a butyrate-producing bacterium isolated from human faeces. Int J Syst Evol Microbiol 2018; 68:2074-2081. [PMID: 29745868 DOI: 10.1099/ijsem.0.002800] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
An obligately anaerobic, Gram-positive, non-spore-forming, straight rod-shaped bacterium, designated strain 3BBH22T, was isolated from a faecal sample of a healthy Japanese woman. The 16S rRNA gene sequence analysis showed that strain 3BBH22T formed a monophyletic cluster with species in the genera Pseudoflavonifractor and Flavonifractor within the family Ruminococcaceae and had highest similarity to Pseudoflavonifractor capillosus ATCC 29799T (96.7 % sequence similarity), followed by Flavonifractor plautii ATCC 29863T (96.4 %). Acetate and butyrate were produced by strain 3BBH22T as metabolic end-products. The major cellular fatty acids were C14 : 0, C16 : 0, C18 : 1ω9c, C16 : 0 dimethyl acetal, C18 : 0 and C18 : 2ω6,9c. No respiratory quinones were detected. In contrast to F. plautii JCM 32125T, strain 3BBH22T did not degrade quercetin, one of the flavonoids. P. capillosus JCM 32126T also did not. Strain 3BBH22T was differentiated from P. capillosus JCM 32126T by its inability to hydrolyse aesculin. The G+C content of the genomic DNA was 61.2±1.0 mol%. On the basis of these data and the phylogenetic tree based on 89 proteins, strain 3BBH22T represents a novel species in a novel genus of the family Ruminococcaceae, for which the name Lawsonibacter asaccharolyticus gen. nov., sp. nov. is proposed. The type strain of L. asaccharolyticus is 3BBH22T (=JCM 32166T=DSM 106493T).
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Affiliation(s)
- Mitsuo Sakamoto
- PRIME, Japan Agency for Medical Research and Development (AMED), Tsukuba, Ibaraki 305-0074, Japan.,Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Takao Iino
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Masahiro Yuki
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
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21
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Sakamoto M, Iino T, Hamada M, Ohkuma M. Parolsenella catena gen. nov., sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2018; 68:1165-1172. [PMID: 29458507 DOI: 10.1099/ijsem.0.002645] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Strain 2CBEGH3T, which is an obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-stain-positive coccobacillus, was isolated from a faecal sample of a healthy Japanese man. The 16S rRNA gene sequence analysis showed that strain 2CBEGH3T represented a member of the family Atopobiaceae and formed a monophyletic cluster with Olsenella uli DSM 7084T (93.6 % sequence similarity), Olsenella umbonata strain lac31T (93.0 %), Olsenella profusa JCM 14553T (92.7 %) and Olsenella scatoligenes strain SK9K4T (92.7 %) as closest neighbours and Atopobium species. The hsp60 gene sequence analysis supported the phylogenetic relationships based on the 16S rRNA gene sequences, with sequence similarity values of 82.1-84.7 % to the four species described above. A unique three-base (one amino acid residue) insertion was found in the alignment regions of the hsp60 gene sequence of strain 2CBEGH3T. The major end products from d-glucose were d- and l-lactic acids produced at the ratio of 75 : 25, while four species of the genus Olsenella produced d- and l-lactic acids at ratios of 94-98 : 2-6. The isolate formed characteristic crater-like colonies on Eggerth-Gagnon agar plates. The major cellular fatty acids were C18 : 1ω9c, C18 : 1ω9c dimethyl acetal (DMA) and C16 : 0 DMA. The G+C content of the genomic DNA was 68.4 mol%. On the basis of these data, strain 2CBEGH3T represents a novel species in a novel genus of the family Atopobiaceae, for which the name Parolsenella catena gen. nov., sp. nov. is proposed. The type strain of P. catena is 2CBEGH3T (=JCM 31932T=DSM 105194T).
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Affiliation(s)
- Mitsuo Sakamoto
- PRIME, Japan Agency for Medical Research and Development (AMED), Tsukuba, Ibaraki 305-0074, Japan
- MicrobeDivision/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Takao Iino
- MicrobeDivision/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriyuki Hamada
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Moriya Ohkuma
- MicrobeDivision/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
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The gut bacterium and pathobiont Bacteroides vulgatus activates NF-κB in a human gut epithelial cell line in a strain and growth phase dependent manner. Anaerobe 2017; 47:209-217. [DOI: 10.1016/j.anaerobe.2017.06.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 05/17/2017] [Accepted: 06/01/2017] [Indexed: 01/06/2023]
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Sakamoto M, Iino T, Ohkuma M. Faecalimonas umbilicata gen. nov., sp. nov., isolated from human faeces, and reclassification of Eubacterium contortum, Eubacterium fissicatena and Clostridium oroticum as Faecalicatena contorta gen. nov., comb. nov., Faecalicatena fissicatena comb. nov. and Faecalicatena orotica comb. nov. Int J Syst Evol Microbiol 2017; 67:1219-1227. [PMID: 28556772 DOI: 10.1099/ijsem.0.001790] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Two bacterial strains, designated EGH7T and TSAH33, were isolated from human faeces and characterized by using a polyphasic taxonomic approach that included analysis of morphology, phenotypic and biochemical features, cellular fatty acid profiles and phylogenetic position based on 16S rRNA and hsp60 gene sequence analyses. The results of 16S rRNA gene sequence analysis indicated that these strains represented members of the family Lachnospiraceae and formed a monophyletic cluster near Eubacterium contortum JCM 6483T (95 % sequence similarity), Ruminococcus gnavus JCM 6515T (95 %), Clostridium oroticum JCM 1429T (95 %), Eubacterium fissicatena JCM 31501T (95 %) and Clostridium nexile JCM 31500T (94 %). The results of a hsp60 gene sequence analysis supported the phylogenetic tree based on the 16S rRNA gene sequence, with a sequence similarity value of between 77.9 and 84.8 % to the five strains listed above. The novel strains were obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-stain-positive cocco-bacilli. The strains formed characteristic umbilicated colonies on EG agar plates. The major cellular fatty acids were C18 : 1ω9c, C16 : 0 and C18 : 1ω9c dimethyl acetal (DMA). EGH7T and TSAH33 have DNA G+C contents of 46.9 and 45.5 mol%, respectively. On the basis of these data, strains EGH7T and TSAH33 represent a novel species of a novel genus, for which the name Faecalimonas umbilicata gen. nov., sp. nov. is proposed. The type strain of F. umbilicata is EGH7T (=JCM 30896T=DSM 103426T).
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Affiliation(s)
- Mitsuo Sakamoto
- PRIME, Japan Agency for Medical Research and Development (AMED), Tsukuba, Ibaraki 305-0074, Japan.,Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Takao Iino
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
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Jeon SJ, Cunha F, Ma X, Martinez N, Vieira-Neto A, Daetz R, Bicalho RC, Lima S, Santos JEP, Jeong KC, Galvão KN. Uterine Microbiota and Immune Parameters Associated with Fever in Dairy Cows with Metritis. PLoS One 2016; 11:e0165740. [PMID: 27802303 PMCID: PMC5089738 DOI: 10.1371/journal.pone.0165740] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 10/17/2016] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVE This study aimed to evaluate bacterial and host factors causing a fever in cows with metritis. For that, we investigated uterine microbiota using a metagenomic sequencing of the 16S rRNA gene (Study 1), and immune response parameters (Study 2) in metritic cows with and without a fever. PRINCIPAL FINDINGS (STUDY1) Bacterial communities were similar between the MNoFever and MFever groups based on distance metrics of relative abundance of bacteria. Metritic cows showed a greater prevalence of Bacteroidetes, and Bacteroides and Porphyromonas were the largest contributors to that difference. A comparison of relative abundance at the species level pointed to Bacteroides pyogenes as a fever-related species which was significantly abundant in the MFever than the MNoFever and Healthy groups; however, absolute abundance of Bacteroides pyogenes determined by droplet digital PCR (ddPCR) was similar between MFever and MNoFever groups, but higher than the Healthy group. The same trend was observed in the total number of bacteria. PRINCIPAL FINDINGS (STUDY2) The activity of polymorphonuclear leukocyte (PMN) and the production of TNFα, PGE2 metabolite, and PGE2 were evaluated in serum, before disease onset, at 0 and 3 DPP. Cows in the MNoFever had decreased proportion of PMN undergoing phagocytosis and oxidative burst compared with the MFever. The low PMN activity in the MNoFever was coupled with the low production of TNFα, but similar PGE2 metabolite and circulating PGE2. CONCLUSION/SIGNIFICANCE Our study is the first to show a similar microbiome between metritic cows with and without a fever, which indicates that the host response may be more important for fever development than the microbiome. Bacteroides pyogenes was identified as an important pathogen for the development of metritis but not fever. The decreased inflammatory response may explain the lack of a febrile response in the MNoFever group.
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Affiliation(s)
- Soo Jin Jeon
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Federico Cunha
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Xiaojie Ma
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Natalia Martinez
- Department of Animal Sciences, University of Florida, Gainesville, Florida, United States of America
| | - Achilles Vieira-Neto
- Department of Animal Sciences, University of Florida, Gainesville, Florida, United States of America
| | - Rodolfo Daetz
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Rodrigo C. Bicalho
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York, United States of America
| | - Svetlana Lima
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York, United States of America
| | - Jose E. P. Santos
- Department of Animal Sciences, University of Florida, Gainesville, Florida, United States of America
| | - K. Casey Jeong
- Department of Animal Sciences, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Klibs N. Galvão
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida, United States of America
- D. H. Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville, Florida, United States of America
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25
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Lau JSY, Korman TM, Yeung A, Streitberg R, Francis MJ, Graham M. Bacteroides pyogenes causing serious human wound infection from animal bites. Anaerobe 2016; 42:172-175. [PMID: 27771394 DOI: 10.1016/j.anaerobe.2016.10.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/06/2016] [Accepted: 10/18/2016] [Indexed: 10/20/2022]
Abstract
Bacteroides pyogenes is part of the normal oral flora of domestic animals. There is one previous report of human infection, with B. pyogenes bacteremia following a cat bite (Madsen 2011). We report seven severe human infections where B. pyogenes was identified by Bruker matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDTI-TOF MS), but not by VITEK MS and was misidentified by VITEK ANC card.
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Affiliation(s)
- Jillian S Y Lau
- Monash Infectious Diseases, Monash University, Monash Health, Clayton, Australia.
| | - Tony M Korman
- Monash Infectious Diseases, Monash University, Monash Health, Clayton, Australia; Department of Microbiology, Monash Health, Clayton, Australia
| | - Alex Yeung
- Monash Infectious Diseases, Monash University, Monash Health, Clayton, Australia
| | | | | | - Maryza Graham
- Monash Infectious Diseases, Monash University, Monash Health, Clayton, Australia; Department of Microbiology, Monash Health, Clayton, Australia
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26
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Park JE, Park SY, Song DJ, Huh HJ, Ki CS, Peck KR, Lee NY. A case of Bacteroides pyogenes bacteremia secondary to liver abscess. Anaerobe 2016; 42:78-80. [PMID: 27614214 DOI: 10.1016/j.anaerobe.2016.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/05/2016] [Accepted: 09/06/2016] [Indexed: 11/17/2022]
Abstract
Bacteroides pyogenes, a non-spore-forming, anaerobic, gram-negative rod, is a component of the oral flora of animals and has, on occasion, been reported to cause human infection through dog or cat bites. We report the first case of B. pyogenes bacteremia secondary to liver abscess with no history of an animal bite. The microorganism was identified by 16S rRNA sequencing.
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Affiliation(s)
- Jong Eun Park
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - So-Young Park
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Dong Joon Song
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Chang-Seok Ki
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kyong Ran Peck
- Division of Infectious Diseases, Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
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27
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Irisawa T, Saputra S, Kitahara M, Sakamoto M, Sulistiani, Yulineri T, Dinoto A, Ohkuma M. Bacteroides caecicola sp. nov. and Bacteroides gallinaceum sp. nov., isolated from the caecum of an Indonesian chicken. Int J Syst Evol Microbiol 2016; 66:1431-1437. [DOI: 10.1099/ijsem.0.000899] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Tomohiro Irisawa
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Sugiyono Saputra
- Microbiology Division, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jl. Raya Jakarta-Bogor Km. 46, Cibinong 16911, Indonesia
| | - Maki Kitahara
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Sulistiani
- Microbiology Division, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jl. Raya Jakarta-Bogor Km. 46, Cibinong 16911, Indonesia
| | - Titin Yulineri
- Microbiology Division, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jl. Raya Jakarta-Bogor Km. 46, Cibinong 16911, Indonesia
| | - Achmad Dinoto
- Microbiology Division, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jl. Raya Jakarta-Bogor Km. 46, Cibinong 16911, Indonesia
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
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28
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Saputra S, Irisawa T, Sakamoto M, Kitahara M, Sulistiani, Yulinery T, Ohkuma M, Dinoto A. Bacteroides caecigallinarum sp. nov., isolated from caecum of an Indonesian chicken. Int J Syst Evol Microbiol 2015; 65:4341-4346. [PMID: 26345419 DOI: 10.1099/ijsem.0.000573] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three strains of anaerobic Gram-stain-negative, short to longer rod-shaped bacteria isolated from the caecum of chicken in Indonesia were studied using a polyphasic taxonomic approach. These strains belonged to the genus Bacteroides, based on sequence analysis of 16S rRNA and hsp60 (groEL) genes, with similarities of 93.2-94.1 and 89.8-90.8 %, respectively, to the closest recognized species, Bacteroides coprocola JCM 17929T. Sugar fermentation and enzyme characteristics, cellular fatty acid profiles, menaquinone profiles and metabolic end products were also investigated. Furthermore, DNA-DNA hybridization studies confirmed that the three novel strains are different from the closest related species. The strains were also found to be distinct from each other on the basis of ribotype profiles. The DNA G+C contents of the three strains were 41.1-41.8 mol%. Based on phenotypic and phylogenetic characteristics, a novel species, Bacteroides caecigallinarum sp. nov., is proposed (type strain C13EG111T = LIPI12-4-Ck773T = JSAT12-4-Ck773T = InaCC B455T = NBRC 110959T).
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Affiliation(s)
- Sugiyono Saputra
- Microbiology Division, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jl. Raya Bogor Km. 46, Cibinong, 16911, Indonesia
| | - Tomohiro Irisawa
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Maki Kitahara
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Sulistiani
- Microbiology Division, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jl. Raya Bogor Km. 46, Cibinong, 16911, Indonesia
| | - Titin Yulinery
- Microbiology Division, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jl. Raya Bogor Km. 46, Cibinong, 16911, Indonesia
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Achmad Dinoto
- Microbiology Division, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jl. Raya Bogor Km. 46, Cibinong, 16911, Indonesia
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29
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Sakamoto M, Li D, Shibata Y, Takeshita T, Yamashita Y, Ohkuma M. Porphyromonas pasteri sp. nov., isolated from human saliva. Int J Syst Evol Microbiol 2015; 65:2511-2515. [PMID: 25933621 DOI: 10.1099/ijs.0.000294] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain, designated KUFDS01T, isolated from human saliva was characterized using a polyphasic taxonomic approach that included analysis of physiological and biochemical features, cellular fatty acid profiles and phylogenetic position based on 16S rRNA gene sequence analysis. Cells of the strain were obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-stain-negative rods. Growth of the strain was inhibited on medium containing 20% bile. The 16S rRNA gene sequence analysis showed that the strain was a member of the genus Porphyromonas. Strain KUFDS01T was closely related to Porphyromonas catoniae JCM 13863T (96.6% sequence similarity). An hsp60 gene sequence analysis indicated that strain KUFDS01T was different from P. catoniae JCM 13863T, with a sequence similarity value of 87.8%. The major cellular fatty acids of strain KUFDS01T were C16 : 0, iso-C15 : 0, anteiso-C15 : 0, C18 : 2ω6, 9c and C18 : 1ω9c. The DNA G+C content of strain KUFDS01T was 57.7 ± 0.66 mol%. On the basis of these data, strain KUFDS01T represents a novel species of the genus Porphyromonas, for which the name Porphyromonas pasteri sp. nov. is proposed. The type strain of P. pasteri is KUFDS01T ( = JCM 30531T = CCUG 66735T).
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Affiliation(s)
- Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Dan Li
- Section of Preventive and Public Health Dentistry, Division of Oral Health, Growth and Development, Kyushu University Faculty of Dental Science, Fukuoka, Japan
| | - Yukie Shibata
- Section of Preventive and Public Health Dentistry, Division of Oral Health, Growth and Development, Kyushu University Faculty of Dental Science, Fukuoka, Japan
| | - Toru Takeshita
- Section of Preventive and Public Health Dentistry, Division of Oral Health, Growth and Development, Kyushu University Faculty of Dental Science, Fukuoka, Japan
| | - Yoshihisa Yamashita
- Section of Preventive and Public Health Dentistry, Division of Oral Health, Growth and Development, Kyushu University Faculty of Dental Science, Fukuoka, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
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30
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Sakamoto M, Tanaka Y, Benno Y, Ohkuma M. Parabacteroides faecis sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2015; 65:1342-1346. [PMID: 25667391 DOI: 10.1099/ijs.0.000109] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
A bacterial strain, designated 157(T), isolated from human faeces was characterized by using a polyphasic taxonomic approach, which included analysis of physiological and biochemical features, cellular fatty acid profiles, menaquinone profiles and its phylogenetic position, based on 16S rRNA gene sequence analysis. The strain was obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-stain-negative rods. The isolate was able to grown on medium containing 20% (w/v) bile. 16S rRNA gene sequence analysis showed that the strain was a member of the genus Parabacteroides . Strain 157(T) was closely related to Parabacteroides gordonii JCM 15724(T) (96% sequence similarity). The results of hsp60 gene sequence analysis indicated that strain 157(T) was different from P. gordonii JCM 15724(T), with a hsp60 gene sequence similarity of 96.1%. The major cellular fatty acids of strain 157(T) were anteiso-C(15 : 0), iso-C(17 : 0) 3-OH, C(18 : 1)ω9c and anteiso-C(17 : 0) 3-OH. The major menaquinone of the isolate was MK-9. The DNA G+C content of strain 157(T) was 41.8 mol%. On the basis of these data, strain 157(T) represents a novel species of the genus Parabacteroides , for which the name Parabacteroides faecis sp. nov. is proposed; the type strain is 157(T) ( = JCM 18682(T) = CCUG 66681(T)).
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Affiliation(s)
- Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Yoshiki Tanaka
- Biofermin Kobe Research Institute, Nishi-ku, Kobe 651-2242, Japan.,Benno Laboratory, RIKEN Innovation Center, Wako, Saitama 351-0198, Japan
| | - Yoshimi Benno
- Benno Laboratory, RIKEN Innovation Center, Wako, Saitama 351-0198, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
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31
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Improved detection of Staphylococcus intermedius group in a routine diagnostic laboratory. J Clin Microbiol 2014; 53:961-3. [PMID: 25502532 DOI: 10.1128/jcm.02474-14] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The Staphylococcus intermedius group (SIG) includes zoonotic pathogens traditionally associated with dog bites. We describe a simple scheme for improved detection of SIG using routine laboratory methods, report its effect on isolation rates, and use sequencing to confirm that, apart from one atypical SIG strain, most isolates are Staphylococcus pseudintermedius.
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32
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Sakamoto M, Tanaka Y, Benno Y, Ohkuma M. Butyricimonas faecihominis sp. nov. and Butyricimonas paravirosa sp. nov., isolated from human faeces, and emended description of the genus Butyricimonas. Int J Syst Evol Microbiol 2014; 64:2992-2997. [DOI: 10.1099/ijs.0.065318-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two bacterial strains, designated 180-3T and 214-4T, isolated from human faeces were characterized by using a polyphasic taxonomic approach that included analysis of their phenotypic and biochemical features, cellular fatty acid profiles, menaquinone profiles and phylogenetic positions based on 16S rRNA gene sequence analysis. 16S rRNA gene sequence analysis showed that these strains represented members of the genus
Butyricimonas
. These strains shared 97.9 % 16S rRNA gene sequence similarity with each other and were related to
Butyricimonas virosa
JCM 15149T (97 % sequence similarity) and
Butyricimonas synergistica
JCM 15148T (94–95 %). Although strain 180-3T was related to (but distinct from)
B. virosa
JCM 15149T and
B. synergistica
JCM 15148T, with hsp60 gene sequence similarities of 89.4 and 84.6 %, respectively, strain 214-4T exhibited high hsp60 gene sequence similarity (100 %) with
B. virosa
JCM 15149T and was different from
B. synergistica
JCM 15148T (83.5 %). DNA–DNA hybridization experiments demonstrated a genomic distinction of strains 180-3T and 214-4T from
B. virosa
JCM 15149T and
B. synergistica
JCM 15148T. The strains were obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-stain-negative rods. Growth of the strains was inhibited on medium containing 20 % bile. The two strains produced butyric and isobutyric acids as the end products from glucose, as has been observed in the other two species of the genus
Butyricimonas
. The major cellular fatty acid of strains 180-3T and 214-4T was iso-C15 : 0. The major menaquinone of the isolates was MK-10 (>50 %). Strains 180-3T and 214-4T have DNA G+C contents of 45 mol%. On the basis of these data, strains 180-3T and 214-4T represent two novel species of the genus
Butyricimonas
, for which the names Butyricimonas faecihominis sp. nov. and Butyricimonas paravirosa sp. nov., respectively, are proposed. The type strains of B. faecihominis and B. paravirosa are 180-3T ( = JCM 18676T = CCUG 65562T) and 214-4T ( = JCM 18677T = CCUG 65563T), respectively.
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Affiliation(s)
- Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Yoshiki Tanaka
- Biofermin Kobe Research Institute, Nishi-ku, Kobe 651-2242, Japan
- Benno Laboratory, RIKEN Innovation Center, Wako, Saitama 351-0198, Japan
| | - Yoshimi Benno
- Benno Laboratory, RIKEN Innovation Center, Wako, Saitama 351-0198, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
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33
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Hatamoto M, Kaneshige M, Nakamura A, Yamaguchi T. Bacteroides luti sp. nov., an anaerobic, cellulolytic and xylanolytic bacterium isolated from methanogenic sludge. Int J Syst Evol Microbiol 2014; 64:1770-1774. [DOI: 10.1099/ijs.0.056630-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A mesophilic, anaerobic, cellulolytic and xylanolytic strain, UasXn-3T, was isolated from anaerobic granular sludge in a mesophilic upflow anaerobic sludge blanket reactor, which was used to treat municipal sewage. The cells were Gram-stain-negative, non-motile, and non-spore-forming rods. The optimal temperature for growth was 37–40 °C and the optimal pH for growth was pH 6.5–7.0. Strain UasXn-3T could grow on several polysaccharides and sugars, including cellulose, cellobiose, xylan, xylose, glucose, fructose, arabinose, mannose, raffinose, trehalose and starch. The DNA G+C content was 44.4 mol%. On the basis of comparative 16S rRNA gene sequence analysis, strain UasXn-3T was identified as a member of the genus
Bacteroides
and most closely related to
Bacteroides oleiciplenus
,
B. intestinalis
,
B. cellulosilyticus
and
B. graminisolvens
(sequence similarities of 91.3–91.6 %). Since the genetic and phenotypic properties suggest that strain UasXn-3T represents a novel species, we propose the name Bacteroides luti sp. nov. The type strain is UasXn-3T ( = JCM 19020T = DSM 26991T).
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Affiliation(s)
- Masashi Hatamoto
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Masami Kaneshige
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Akinobu Nakamura
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Takashi Yamaguchi
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
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Draft Genome Sequences of Three Strains of Bacteroides pyogenes Isolated from a Cat and Swine. GENOME ANNOUNCEMENTS 2014; 2:2/1/e01242-13. [PMID: 24482517 PMCID: PMC3907732 DOI: 10.1128/genomea.01242-13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we report the draft genome sequences of Bacteroides pyogenes JCM 6294(T), JCM 6292, and JCM 10003, which were isolated from a cat and swine and were recently classified into a single species, B. pyogenes. Comparative analyses of these genomes revealed the diversification of B. pyogenes strains isolated from different animals.
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35
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Tsuchida S, Takahashi S, Nguema PPM, Fujita S, Kitahara M, Yamagiwa J, Ngomanda A, Ohkuma M, Ushida K. Bifidobacterium moukalabense sp. nov., isolated from the faeces of wild west lowland gorilla (Gorilla gorilla gorilla). Int J Syst Evol Microbiol 2013; 64:449-455. [PMID: 24158945 DOI: 10.1099/ijs.0.055186-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gram-staining-positive anaerobic rods were isolated from the faeces of a wild lowland gorilla (Gorilla gorilla gorilla) in Moukalaba-Doudou National Park, Gabon, and strain GG01(T) was taxonomically investigated. Based on phylogenetic analyses and specific phenotypic characteristics, the strain belonged to the genus Bifidobacterium. Phylogenetic analysis of its 16S rRNA gene sequence revealed that strain GG01(T) formed a single monophyletic cluster and had a distinct line of descent. Based on 16S rRNA gene sequence similarity, the type strains of Bifidobacterium catenulatum JCM 1194(T) (98.3%) and Bifidobacterium pseudocatenulatum (98.1%) JCM 1200(T) were the most closely related to this novel strain, although it was clear that they belonged to different species. hsp60 sequences also supported these relationships. The DNA G+C content of this novel strain was 60.1 mol%. Bifidobacterium moukalabense sp. nov. (type strain GG01(T) = JCM 18751(T) = DSM 27321(T)) is proposed.
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Affiliation(s)
- Sayaka Tsuchida
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo, Kyoto 606-8522, Japan
| | | | | | - Shiho Fujita
- Graduate School of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan
| | - Maki Kitahara
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Juichi Yamagiwa
- Graduate School of Science, Kyoto University, Kitashirakawa, Kyoto 606-8502, Japan
| | - Alfred Ngomanda
- Research Institute of Tropical Ecology, Libreville, Bp 13354, Gabon
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Kazunari Ushida
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo, Kyoto 606-8522, Japan
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36
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Kitahara M, Sakamoto M, Tsuchida S, Kawasumi K, Amao H, Benno Y, Ohkuma M. Parabacteroides chinchillae sp. nov., isolated from chinchilla (Chincilla lanigera) faeces. Int J Syst Evol Microbiol 2013; 63:3470-3474. [PMID: 23563230 DOI: 10.1099/ijs.0.050146-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strains of Gram-stain-negative, anaerobic, rod-shaped bacteria were isolated from chinchilla (Chinchilla lanigera) faeces, and strain ST166(T) was investigated taxonomically. Phylogenetic analyses of 16S rRNA gene sequences revealed that strain ST166(T) belonged to the genus Parabacteroides. Strain ST166(T) formed a distinct line of descent, and the highest sequence similarity to ST166(T) was found with Parabacteroides merdae JCM 9497(T) (95.6%) and Parabacteroides johnsonii JCM 13406(T) (95.0%). Analysis of hsp60 gene sequences also supported these relationships. Based on the phenotypic and phylogenetic characteristics, the novel species Parabacteroides chinchillae sp. nov. is proposed. The type strain of P. chinchillae sp. nov. is ST166(T) ( = JCM 17104(T) =CCUG 62154(T)).
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Affiliation(s)
- Maki Kitahara
- Japan Collection of Microorganisms, RIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Mitsuo Sakamoto
- Japan Collection of Microorganisms, RIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Sayaka Tsuchida
- Laboratory of experimental animal science, Nippon Veterinary and Life Science University, Musashino, Tokyo 180-8602, Japan
| | - Koh Kawasumi
- Laboratory of experimental animal science, Nippon Veterinary and Life Science University, Musashino, Tokyo 180-8602, Japan
| | - Hiromi Amao
- Laboratory of experimental animal science, Nippon Veterinary and Life Science University, Musashino, Tokyo 180-8602, Japan
| | - Yoshimi Benno
- Benno Laboratory, RIKEN Innovation Center, Wako, Saitama 351-0198, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki 305-0074, Japan
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37
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Bacteroides reticulotermitis sp. nov., isolated from the gut of a subterranean termite (Reticulitermes speratus). Int J Syst Evol Microbiol 2013; 63:691-695. [DOI: 10.1099/ijs.0.040931-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
An obligately anaerobic, non-pigmented, non-spore-forming, Gram-staining-negative, rod-shaped bacterium, designated strain Rs-03T, was isolated from the gut of the subterranean termite Reticulitermes speratus. The taxonomic position of the novel strain was determined by following a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Rs-03T was a member of the genus
Bacteroides
and was most closely related to
Bacteroides thetaiotaomicron
JCM 5827T (95.0 % sequence similarity),
Bacteroides faecis
JCM 16478T (94.8 %) and
Bacteroides xylanisolvens
JCM 15633T (94.3 %). The results of hsp60 gene sequence analysis indicated that the novel strain was different from established members of the genus
Bacteroides
. Strain Rs-03T was saccharolytic and produced succinic and acetic acids, with small amounts of propionic acid, as metabolic end products. The major cellular fatty acids of strain Rs-03T were anteiso-C15 : 0, C18 : 1ω9c and iso-C17 : 0 3-OH. The major menaquinones were MK-10 and MK-9 and the genomic DNA G+C content was 44.9 mol%. Based on these data, strain Rs-03T represents a novel species in the genus
Bacteroides
, for which the name Bacteroides reticulotermitis sp. nov. is proposed. The type strain is Rs-03T ( = JCM 10512T = CCUG 62153T).
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38
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Sakamoto M, Ohkuma M. Porphyromonas crevioricanis
is an earlier heterotypic synonym of
Porphyromonas cansulci
and has priority. Int J Syst Evol Microbiol 2013; 63:454-457. [DOI: 10.1099/ijs.0.042531-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A DNA–DNA hybridization experiment was carried out to clarify the relationship between
Porphyromonas crevioricanis
and
Porphyromonas cansulci
. The taxonomic standing of these two species was unclear so far because of the high 16S rRNA gene sequence similarity value (99.9 %). The DNA–DNA relatedness values between
P. crevioricanis
JCM 15906T and
P. cansulci
JCM 13913T were above 91 % (91–99 %). In addition,
P. crevioricanis
JCM 15906T exhibited high hsp60 gene sequence similarity with
P. cansulci
JCM 13913T (100 %). The hsp60 gene sequence analysis and the DNA–DNA relatedness values demonstrated that
P. crevioricanis
JCM 15906T and
P. cansulci
JCM 13913T are a single species. Based on these data, we propose
Porphyromonas cansulci
as a later heterotypic synonym of
Porphyromonas crevioricanis
.
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Affiliation(s)
- Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
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39
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Links MG, Dumonceaux TJ, Hemmingsen SM, Hill JE. The chaperonin-60 universal target is a barcode for bacteria that enables de novo assembly of metagenomic sequence data. PLoS One 2012. [PMID: 23189159 PMCID: PMC3506640 DOI: 10.1371/journal.pone.0049755] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Barcoding with molecular sequences is widely used to catalogue eukaryotic biodiversity. Studies investigating the community dynamics of microbes have relied heavily on gene-centric metagenomic profiling using two genes (16S rRNA and cpn60) to identify and track Bacteria. While there have been criteria formalized for barcoding of eukaryotes, these criteria have not been used to evaluate gene targets for other domains of life. Using the framework of the International Barcode of Life we evaluated DNA barcodes for Bacteria. Candidates from the 16S rRNA gene and the protein coding cpn60 gene were evaluated. Within complete bacterial genomes in the public domain representing 983 species from 21 phyla, the largest difference between median pairwise inter- and intra-specific distances (“barcode gap”) was found from cpn60. Distribution of sequence diversity along the ∼555 bp cpn60 target region was remarkably uniform. The barcode gap of the cpn60 universal target facilitated the faithful de novo assembly of full-length operational taxonomic units from pyrosequencing data from a synthetic microbial community. Analysis supported the recognition of both 16S rRNA and cpn60 as DNA barcodes for Bacteria. The cpn60 universal target was found to have a much larger barcode gap than 16S rRNA suggesting cpn60 as a preferred barcode for Bacteria. A large barcode gap for cpn60 provided a robust target for species-level characterization of data. The assembly of consensus sequences for barcodes was shown to be a reliable method for the identification and tracking of novel microbes in metagenomic studies.
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Affiliation(s)
- Matthew G. Links
- Agriculture and AgriFood Canada, Saskatoon, Saskatchewan, Canada
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Tim J. Dumonceaux
- Agriculture and AgriFood Canada, Saskatoon, Saskatchewan, Canada
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Sean M. Hemmingsen
- National Research Council Canada, Saskatoon, Saskatchewan, Canada
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Janet E. Hill
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- * E-mail:
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40
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Paramel Jayaprakash T, Schellenberg JJ, Hill JE. Resolution and characterization of distinct cpn60-based subgroups of Gardnerella vaginalis in the vaginal microbiota. PLoS One 2012; 7:e43009. [PMID: 22900080 PMCID: PMC3416817 DOI: 10.1371/journal.pone.0043009] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 07/17/2012] [Indexed: 01/28/2023] Open
Abstract
Bacterial vaginosis (BV), characterized by a shift of the vaginal microbiota from a Lactobacillus-dominated community to a dense biofilm containing a complex mixture of organisms, is an important risk factor in poor reproductive health outcomes. The Nugent score, based on Gram stain, is used to diagnose BV and Gardnerella vaginalis abundance in the sample is one factor determining Nugent score. A high Nugent score is indicative of BV but does not always correspond to the presence of clinical symptoms. G. vaginalis is recognized as a heterogeneous group of organisms, which can also be part of the normal, healthy vaginal microbiome. In addition, asymptomatic BV and non-Gardnerella types of BV are being recognized. In an attempt to resolve the heterogeneous group of G. vaginalis, a phylogenetic tree of cpn60 universal target sequences from G. vaginalis isolates was constructed that indicates the existence of four subgroups of G. vaginalis. This subdivision, supported by whole genome similarity calculation of representative strains using JSpecies, demonstrates that these subgroups may represent different species. The cpn60 subgroupings did not correspond with the Piot biotyping scheme, but did show consistency with ARDRA genotyping and sialidase gene presence. Isolates from all four subgroups produced biofilm in vitro. We also investigated the distribution of G. vaginalis subgroups in vaginal samples from Kenyan women with Nugent scores consistent with BV, Intermediate and Normal microbiota (n = 44). All subgroups of G. vaginalis were detected in these women, with a significant difference (z = −3.372, n = 39, p = 0.001) in frequency of G. vaginalis subgroup B between BV and Normal groups. Establishment of a quantifiable relationship between G. vaginalis subgroup distribution and clinical status could have significant diagnostic implications.
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Affiliation(s)
- Teenus Paramel Jayaprakash
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | | | - Janet E. Hill
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- * E-mail:
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41
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Bacteroides sartorii
is an earlier heterotypic synonym of
Bacteroides chinchillae
and has priority. Int J Syst Evol Microbiol 2012; 62:1241-1244. [DOI: 10.1099/ijs.0.035659-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strains of the recently proposed species
Bacteroides chinchillae
share more than 99.4 % 16S rRNA gene sequence similarity with the type strain of
Bacteroides sartorii
although these two species do not appear to be similar from their published descriptions. The aim of this study was to perform phenotypic and genetic analyses of both species to clarify their taxonomic position.
B. chinchillae
JCM 16497T exhibited high hsp60 gene sequence similarity with
B. sartorii
JCM 17136T (100 %) as well as
B. chinchillae
JCM 16498 (100 %). The hsp60 gene sequence analysis and levels of DNA–DNA relatedness observed demonstrated
B. sartorii
JCM 17136T,
B. chinchillae
JCM 16497T, and
B. chinchillae
JCM 16498 are members of a single species. Based on these data, we propose
Bacteroides chinchillae
as a later heterotypic synonym of
Bacteroides sartorii
. An emended description of B. sartorii is provided.
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42
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Chaban B, Links MG, Hill JE. A molecular enrichment strategy based on cpn60 for detection of epsilon-proteobacteria in the dog fecal microbiome. MICROBIAL ECOLOGY 2012; 63:348-57. [PMID: 21881944 DOI: 10.1007/s00248-011-9931-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2011] [Accepted: 08/17/2011] [Indexed: 05/13/2023]
Abstract
Members of the rare microbiome can be important components of complex microbial communities. For example, pet dog ownership is a known risk factor for human campylobacteriosis, and Campylobacter is commonly detected in dog feces by targeted assays. However, these organisms have not been detected by metagenomic methods. The goal of this study was to characterize fecal microbiota from healthy and diarrheic pet dogs using two different levels of molecular detection. PCR amplification and pyrosequencing of the universal cpn60 gene target was used to obtain microbial profiles from each dog. To investigate the relatively rare epsilon-proteobacteria component of the microbiome, a molecular enrichment was carried out using a PCR that first amplified the cpn10-cpn60 region from epsilon-proteobacteria, followed by universal cpn60 target amplification and pyrosequencing. From the non-enriched survey, the major finding was a significantly higher proportion of Bacteroidetes, notably Bacteroides vulgatus, in healthy dogs compared to diarrheic dogs. Epsilon-proteobacteria from the genera Helicobacter and Campylobacter were also detected at a low level in the non-enriched profiles of some dogs. Molecular enrichment increased the proportion of epsilon-proteobacteria sequences detected from each dog, as well as identified novel, presumably rare sequences not seen in the non-enriched profiles. Enriched profiles contained known species of Arcobacter, Campylobacter, Flexispira, and Helicobacter and identified two possibly novel species. These findings add to our understanding of the canine fecal microbiome in general, the epsilon-proteobacteria component specifically, and present a novel modification to traditional metagenomic approaches for study of the rare microbiome.
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Affiliation(s)
- Bonnie Chaban
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada S7N 5B4
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43
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Sakamoto M, Ohkuma M. Reclassification of Xylanibacter oryzae Ueki et al. 2006 as Prevotella oryzae comb. nov., with an emended description of the genus Prevotella. Int J Syst Evol Microbiol 2011; 62:2637-2642. [PMID: 22199207 DOI: 10.1099/ijs.0.038638-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
16S rRNA gene sequence information has indicated that Xylanibacter oryzae has a close relationship with the genus Prevotella. To clarify the taxonomic position of X. oryzae, we determined the sequence of hsp60 as it represents an alternative phylogenetic marker for identification and classification of Gram-negative anaerobic rods. On the basis of hsp60 sequences, X. oryzae was located within the genus Prevotella, indicating that the species does not represent a distinct taxon at the genus level. Statistical tests (the Shimodaira-Hasegawa test and the approximately unbiased test) supported the finding that X. oryzae is monophyletic with members of the genus Prevotella and thus belongs to the genus. On the basis of the phylogenetic findings, we propose that X. oryzae should be reclassified as Prevotella oryzae comb. nov.; the type strain is KB3(T) (=JCM 13648(T) =DSM 17970(T)). An emended description of the genus Prevotella is also provided.
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Affiliation(s)
- Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan
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44
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Sakamoto M, Ohkuma M. Identification and classification of the genus Bacteroides by multilocus sequence analysis. MICROBIOLOGY-SGM 2011; 157:3388-3397. [PMID: 21948050 DOI: 10.1099/mic.0.052332-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Multilocus sequence analysis (MLSA) was performed on representative species of the genus Bacteroides. Internal fragments of the genes selected, dnaJ, gyrB, hsp60, recA, rpoB and 16S rRNA, were amplified by direct PCR and then sequenced from 38 Bacteroides strains representing 35 species. Neighbour-joining (NJ), maximum-likelihood (ML) and maximum-parsimony (MP) phylogenies of the individual genes were compared. The data confirm that the potential for discrimination of Bacteroides species is greater using MLSA of housekeeping genes than 16S rRNA genes. Among the housekeeping genes analysed, gyrB was the most informative, followed by dnaJ. Analyses of concatenated sequences (4816 bp) of all six genes revealed robust phylogenetic relationships among different Bacteroides species when compared with the single-gene trees. The NJ, ML and MP trees were very similar, and almost fully resolved relationships of Bacteroides species were obtained, to our knowledge for the first time. In addition, analysis of a concatenation (2457 bp) of the dnaJ, gyrB and hsp60 genes produced essentially the same result. Ten distinct clades were recognized using the SplitsTree4 program. For the genus Bacteroides, we can define species as a group of strains that share at least 97.5% gene sequence similarity based on the fragments of five protein-coding housekeeping genes and the 16S rRNA gene. This study demonstrates that MLSA of housekeeping genes is a valuable alternative technique for the identification and classification of species of the genus Bacteroides.
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Affiliation(s)
- Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan
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45
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Kitahara M, Sakamoto M, Tsuchida S, Kawasumi K, Amao H, Benno Y, Ohkuma M. Bacteroides stercorirosoris sp. nov. and Bacteroides faecichinchillae sp. nov., isolated from chinchilla (Chinchilla lanigera) faeces. Int J Syst Evol Microbiol 2011; 62:1145-1150. [PMID: 21724955 DOI: 10.1099/ijs.0.032706-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Strains of gram-negative anaerobic rods were isolated from chinchilla (Chinchilla lanigera) faeces, and three strains, ST161(T), ST33 and ST37(T), were investigated taxonomically. Based on phylogenetic analyses and specific phenotypic characteristics, the three strains were allocated to the genus Bacteroides. Phylogenetic analyses of their 16S rRNA gene sequences revealed that strain ST161(T) formed a distinct line of descent, with highest sequence similarity to strain ST33 (98.7 %) and Bacteroides oleiciplenus JCM 16102(T) (97.7 %). High levels of DNA-DNA relatedness (79-89 %) were found between strains ST161(T) and ST33, but low levels were found between strain ST161(T) and B. oleiciplenus JCM 16102(T) (33-37 %) and between strain ST33 and B. oleiciplenus JCM 16102(T) (33-37 %). These data clearly indicated that strains ST161(T) and ST33 represent a single novel species. 16S rRNA gene sequence analyses showed that strain ST37(T) also formed a distinct line of descent, with highest sequence similarity to Bacteroides acidifaciens JCM 10556(T) (96.5 %) and Bacteroides caccae JCM 9498(T) (95.6 %). Analysis of hsp60 gene sequences also supported these relationships. Based on phenotypic and phylogenetic characteristics, two novel species, Bacteroides stercorirosoris sp. nov. and Bacteroides faecichinchillae sp. nov., are thus proposed. The type strains of B. stercorirosoris and B. faecichinchillae are ST161(T) ( = JCM 17103(T) = CCUG 60872(T)) and ST37(T) ( = JCM 17102(T) = CCUG 60873(T)), respectively. The DNA G+C contents of strains ST161(T) and ST37(T) were 45.7 and 41.0 mol%, respectively.
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Affiliation(s)
- Maki Kitahara
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan
| | - Sayaka Tsuchida
- Laboratory of Experimental Animal Science, Nippon Veterinary and Life Science University, Musashino, Tokyo 180-8602, Japan
| | - Koh Kawasumi
- Laboratory of Experimental Animal Science, Nippon Veterinary and Life Science University, Musashino, Tokyo 180-8602, Japan
| | - Hiromi Amao
- Laboratory of Experimental Animal Science, Nippon Veterinary and Life Science University, Musashino, Tokyo 180-8602, Japan
| | - Yoshimi Benno
- Benno Laboratory, RIKEN Innovation Center, Wako, Saitama 351-0198, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan
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46
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Peeters K, Willems A. The gyrB gene is a useful phylogenetic marker for exploring the diversity of Flavobacterium strains isolated from terrestrial and aquatic habitats in Antarctica. FEMS Microbiol Lett 2011; 321:130-40. [DOI: 10.1111/j.1574-6968.2011.02326.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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47
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Abstract
Animal bite wounds are often infected with bacteria from the animal's oral flora. We report what we believe to be the first case of bacteremia with Bacteroides pyogenes resulting from an infected cat bite.
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48
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Kitahara M, Tsuchida S, Kawasumi K, Amao H, Sakamoto M, Benno Y, Ohkuma M. Bacteroides chinchillae sp. nov. and Bacteroides rodentium sp. nov., isolated from chinchilla (Chinchilla lanigera) faeces. Int J Syst Evol Microbiol 2011; 61:877-881. [DOI: 10.1099/ijs.0.024026-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gram-negative anaerobic rods were isolated from chinchilla (Chinchilla lanigera) faeces and three strains, ST170T, ST180 and ST28T, were investigated taxonomically. On the basis of phylogenetic analyses and specific phenotypic characteristics, the three strains belonged to the genus Bacteroides. Phylogenetic analysis of their 16S rRNA gene sequences revealed that strains ST170T and ST180 formed a single cluster and a distinct line of descent. Strain ST170T exhibited 99.7 % 16S rRNA gene sequence similarity with strain ST180 and 95.1, 94.6 and 94.4 % 16S rRNA gene sequence similarity with Bacteroides massiliensis JCM 13223T, Bacteroides dorei JCM 13471T and Bacteroides vulgatus JCM 5826T, respectively. Strain ST28T also formed a distinct line of descent and exhibited the highest 16S rRNA gene sequence similarity with Bacteroides uniformis JCM 5828T (98.1 %). Low DNA–DNA relatedness (1 %) between strain ST28T and B. uniformis JCM 5828T clearly indicated that they belonged to different species. Analysis of hsp60 sequences also supported these relationships. The DNA G+C contents of strains ST170T and ST28T were 45.2 and 41.0 mol%, respectively. On the basis of phenotypic characteristics and phylogenetic data, two novel species, Bacteroides chinchillae sp. nov. (type strain ST170T = JCM 16497T = CCUG 59335T) and Bacteroides rodentium sp. nov. (type strain ST28T = JCM 16496T = CCUG 59334T), are proposed.
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Affiliation(s)
- Maki Kitahara
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan
| | - Sayaka Tsuchida
- Laboratory of Experimental Animal Science, Nippon Veterinary and Life Science University, Musashino, Tokyo 180-8602, Japan
| | - Koh Kawasumi
- Laboratory of Experimental Animal Science, Nippon Veterinary and Life Science University, Musashino, Tokyo 180-8602, Japan
| | - Hiromi Amao
- Laboratory of Experimental Animal Science, Nippon Veterinary and Life Science University, Musashino, Tokyo 180-8602, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan
| | - Yoshimi Benno
- Benno Laboratory, RIKEN Innovation Center, Wako, Saitama 351-0198, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan
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49
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Sakamoto M, Ohkuma M. Usefulness of the hsp60 gene for the identification and classification of Gram-negative anaerobic rods. J Med Microbiol 2010; 59:1293-1302. [DOI: 10.1099/jmm.0.020420-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The hsp60 gene sequences were determined for 121 strains of Gram-negative anaerobic rods, including the genera Bacteroides, Barnesiella, Butyricimonas, Odoribacter, Parabacteroides, Paraprevotella, Porphyromonas, Prevotella and Tannerella. The mean pairwise hsp60 gene sequence similarity (73.8–97.1 %) between species in each genus, except for the genus Tannerella that comprises one species, was significantly less than that of the 16S rRNA gene sequence (88.3–96.3 %). Only pairwise hsp60 gene sequence similarity (97.1 %) of the genus Paraprevotella was higher than that of the 16S rRNA gene sequence (93.8 %). Each genus formed a distinct clade in the phylogenetic analysis of the hsp60 gene sequence as well as the 16S rRNA gene sequence. The phylogenetic analysis indicated a higher evolutionary rate for the hsp60 gene sequence than the 16S rRNA gene sequence, especially in the genera Porphyromonas and Prevotella. This study suggests that the hsp60 gene is a useful alternative phylogenetic marker for the identification and classification of a broad range of Gram-negative anaerobic rods.
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Affiliation(s)
- Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan
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