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Miller S, Hendry M, King J, Sankaranarayanan K, Lawson PA. Bacteroides vicugnae sp. nov. isolated from the fecal material of an alpaca. Anaerobe 2024; 88:102862. [PMID: 38718919 DOI: 10.1016/j.anaerobe.2024.102862] [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] [Revised: 04/27/2024] [Accepted: 04/29/2024] [Indexed: 06/10/2024]
Abstract
Two strictly anaerobic, Gram-stain-negative rod-shaped bacterial isolates, A2-P53T and A1-P5, were isolated from an enrichment of fecal material from two alpacas (Vicugna pacos). Based on a comparative 16S rRNA gene sequence analysis, the isolates were assigned to the genus Bacteroides with the highest sequence similarities to Bacteroides koreensis YS-aM39T (A2- P53T 97.7 % and A1-P5 97.9 %). Additionally, the average nucleotide identity and digital DNA-DNA hybridization values between these isolates and their closest relatives within Bacteroides were less than 92.1 % and 49.1 %, respectively. The average nucleotide identity between isolates A2-P53T and A1-P5 was 99.9 %. The predominant cellular fatty acid for isolates A2-P53T and A1-P5 was C15:0 antesio. The G+C % content of the isolates was 41.7 %. Based on biochemical, phylogenetic, genotypic, and chemotaxonomic criteria, these isolates A2-P53T and A1-P5 represent two individual strains of a novel species within the genus Bacteroides for which the name Bacteroides vicugnae sp. nov. is proposed. The type strain of this species is strain A2-P53T (CCUG 77273T = CCM 9377T = NRRL B-65693T).
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Affiliation(s)
- Samuel Miller
- School of Biological Sciences, 730 and 770 Van Vleet Oval, Norman, OK, 73019, USA; Laboratories of Molecular Anthropology and Microbiome Research, Stephenson Research and Technology Center, 101 David L. Boren Blvd, Norman, OK, 73019, USA.
| | - Meredith Hendry
- School of Biological Sciences, 730 and 770 Van Vleet Oval, Norman, OK, 73019, USA.
| | - Jacobey King
- School of Biological Sciences, 730 and 770 Van Vleet Oval, Norman, OK, 73019, USA.
| | - Krithivasan Sankaranarayanan
- School of Biological Sciences, 730 and 770 Van Vleet Oval, Norman, OK, 73019, USA; Laboratories of Molecular Anthropology and Microbiome Research, Stephenson Research and Technology Center, 101 David L. Boren Blvd, Norman, OK, 73019, USA.
| | - Paul A Lawson
- School of Biological Sciences, 730 and 770 Van Vleet Oval, Norman, OK, 73019, USA.
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Miller S, Hendry M, King J, Sankaranarayanan K, Lawson PA. Clostridium tanneri sp. nov., isolated from the faecal material of an alpaca. Int J Syst Evol Microbiol 2024; 74. [PMID: 38728064 DOI: 10.1099/ijsem.0.006372] [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] [Indexed: 05/12/2024] Open
Abstract
A strictly anaerobic, Gram-stain-negative rod-shaped bacterium, designated A1-XYC3T, was isolated from the faeces of an alpaca (Lama pacos). On the basis of the results of a comparative 16S rRNA gene sequence analysis, the isolate was assigned to the genus Clostridium with the highest sequence similarities to Clostridium magnum DSM 2767T (96.8 %), Clostridium carboxidivorans P7T (96.3 %) and Clostridium aciditolerans JW/YJL-B3T (96.1 %). The average nucleotide identity between A1-XYC3T, C. magnum, C. carboxidivorans and C. aciditolerans was 77.4, 76.1 and 76.6 %, respectively. The predominant components of the cellular fatty acids of A1-XYC3T were C14 : 0, C16 : 0 and summed feature 10, containing C18:0/C17:0 cyclo. The DNA G+C content was 32.4 mol%. On the basis of biochemical, phylogenetic, genotypic and chemotaxonomic criteria, this isolate represents a novel species within Clostridium sensu stricto for which the name Clostridium tanneri sp. nov. is proposed. The type strain of this species is strain A1-XYC3T (=CCM 9376T=NRRL B-65691T).
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Affiliation(s)
- Samuel Miller
- School of Biological Sciences, 730-770 Van Vleet Oval Norman, OK 73019, USA
- Laboratories of Molecular Anthropology and Microbiome Research, Stephenson Research and Technology Center 101 David L. Boren Blvd. Norman, OK 73019, USA
| | - Meredith Hendry
- School of Biological Sciences, 730-770 Van Vleet Oval Norman, OK 73019, USA
| | - Jacobey King
- School of Biological Sciences, 730-770 Van Vleet Oval Norman, OK 73019, USA
| | - Krithivasan Sankaranarayanan
- School of Biological Sciences, 730-770 Van Vleet Oval Norman, OK 73019, USA
- Laboratories of Molecular Anthropology and Microbiome Research, Stephenson Research and Technology Center 101 David L. Boren Blvd. Norman, OK 73019, USA
- Wadsworth Center, NYS Department of Health, 120 New Scotland Ave. Albany, New York 12208, USA
| | - Paul A Lawson
- School of Biological Sciences, 730-770 Van Vleet Oval Norman, OK 73019, USA
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Wu X, Li Y, Shang Y, Wang W, Wu L, Han L, Wang Q, Wang Z, Xu H, Liu W. Application of two-dimensional polymerase chain reaction to detect four types of microorganisms in feces for assisted diagnosis of IBD. Clin Chim Acta 2024; 555:117802. [PMID: 38281660 DOI: 10.1016/j.cca.2024.117802] [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: 10/12/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 01/30/2024]
Abstract
BACKGROUND The incidence of inflammatory bowel disease (IBD) continues to increase annually, accounting for about 6.8 million cases in 2017 worldwide. However, there is currently no gold standard for the diagnosis of IBD. METHODS A method for the detection of four microorganisms in feces by two-dimensional polymerase chain reaction (2D-PCR) has been developed. Plasmids were used to validate the sensitivity and specificity of the method. Clinical samples were tested using a 2D-PCR method. Optimal diagnostic thresholds for IBD were determined based on ROC results. RESULTS Of the 112 samples, 78 were from IBD patients and 34 from patients with other gastrointestinal (GI) diseases. Thomasclavelia ramosum and univ907-1062 positivity are necessary, and two or more positives of the three bacteria (Thomasclavelia spiroforme, Thomasclavelia saccharogumia or Clostridium cluster XVIII) are the optimal diagnostic thresholds for IBD. The area under the curve was 0.826 with a 95% confidence interval of 0.735-0.981 and a p-value of 0.000, corresponding to a sensitivity of 0.769 and a specificity of 0.853. CONCLUSIONS Based on the detection results of microorganisms, IBD and GI can be effectively distinguished. The detection of four microorganisms in feces can assist clinicians in the differential diagnosis of IBD. Our experiment aims to provide a better program for early clinical diagnosis and regular dynamic monitoring of IBD.
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Affiliation(s)
- Xuan Wu
- Department of Laboratory Medicine, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China; Central Laboratory and Department of Laboratory Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200070, China
| | - Yueying Li
- Department of Laboratory Medicine, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China; Central Laboratory and Department of Laboratory Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200070, China
| | - Yuanjiang Shang
- Central Laboratory and Department of Laboratory Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200070, China
| | - Weifeng Wang
- Department of Laboratory Medicine, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Lixia Wu
- Central Laboratory and Department of Laboratory Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200070, China
| | - Lin Han
- Central Laboratory and Department of Laboratory Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200070, China
| | - Qiong Wang
- Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu 210029, China; Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210022, China.
| | - Zhujian Wang
- Clinical Laboratory, Eye & ENT Hospital, Shanghai Medical College, Fudan University, Shanghai 200031, China.
| | - Hanchen Xu
- Institute of Digestive Diseases, Longhua Hospital, China-Canada Center of Research for Digestive Diseases (ccCRDD), Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China.
| | - Weiwei Liu
- Department of Laboratory Medicine, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China.
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Blondel CJ, Amaya FA, Bustamante P, Santiviago CA, Pezoa D. Identification and distribution of new candidate T6SS effectors encoded in Salmonella Pathogenicity Island 6. Front Microbiol 2023; 14:1252344. [PMID: 37664116 PMCID: PMC10469887 DOI: 10.3389/fmicb.2023.1252344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 08/03/2023] [Indexed: 09/05/2023] Open
Abstract
The type VI secretion system (T6SS) is a contact-dependent contractile multiprotein apparatus widely distributed in Gram-negative bacteria. These systems can deliver different effector proteins into target bacterial and/or eukaryotic cells, contributing to the environmental fitness and virulence of many bacterial pathogens. Salmonella harbors five different T6SSs encoded in different genomic islands. The T6SS encoded in Salmonella Pathogenicity Island 6 (SPI-6) contributes to Salmonella competition with the host microbiota and its interaction with infected host cells. Despite its relevance, information regarding the total number of effector proteins encoded within SPI-6 and its distribution among different Salmonella enterica serotypes is limited. In this work, we performed bioinformatic and comparative genomics analyses of the SPI-6 T6SS gene cluster to expand our knowledge regarding the T6SS effector repertoire and the global distribution of these effectors in Salmonella. The analysis of a curated dataset of 60 Salmonella enterica genomes from the Secret6 database revealed the presence of 23 new putative T6SS effector/immunity protein (E/I) modules. These effectors were concentrated in the variable regions 1 to 3 (VR1-3) of the SPI-6 T6SS gene cluster. VR1-2 were enriched in candidate effectors with predicted peptidoglycan hydrolase activity, while VR3 was enriched in candidate effectors of the Rhs family with C-terminal extensions with predicted DNase, RNase, deaminase, or ADP-ribosyltransferase activity. A global analysis of known and candidate effector proteins in Salmonella enterica genomes from the NCBI database revealed that T6SS effector proteins are differentially distributed among Salmonella serotypes. While some effectors are present in over 200 serotypes, others are found in less than a dozen. A hierarchical clustering analysis identified Salmonella serotypes with distinct profiles of T6SS effectors and candidate effectors, highlighting the diversity of T6SS effector repertoires in Salmonella enterica. The existence of different repertoires of effector proteins suggests that different effector protein combinations may have a differential impact on the environmental fitness and pathogenic potential of these strains.
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Affiliation(s)
- Carlos J. Blondel
- Facultad de Medicina y Facultad de Ciencias de la Vida, Instituto de Ciencias Biomédicas, Universidad Andrés Bello, Santiago, Chile
| | - Fernando A. Amaya
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Paloma Bustamante
- Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Santiago, Chile
| | - Carlos A. Santiviago
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - David Pezoa
- Núcleo de Investigaciones Aplicadas en Ciencias Veterinarias y Agronómicas, Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Santiago, Chile
- Departamento de Ciencias Químicas y Biológicas, Universidad Bernardo O'Higgins, Santiago, Chile
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