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Benoit SL, Maier RJ. d-aspartate, an amino-acid important for human health, supports anaerobic respiration in several Campylobacter species. Res Microbiol 2024; 175:104219. [PMID: 38945250 DOI: 10.1016/j.resmic.2024.104219] [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: 05/10/2024] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 07/02/2024]
Abstract
Despite being classified as microaerophilic microorganisms, most Campylobacter species can grow anaerobically, using formate or molecular hydrogen (H2) as electron donors, and various nitrogenous and sulfurous compounds as electron acceptors. Herein, we showed that both l-asparagine (l-Asn) and l-aspartic acid (l-Asp) bolster H2-driven anaerobic growth in several Campylobacter species, whereas the d-enantiomer form of both asparagine (d-Asn) and aspartic acid (d-Asp) only increased anaerobic growth in Campylobacter concisus strain 13826 and Campylobacter ureolyticus strain NCTC10941. A gene annotated as racD encoding for a putative d/l-Asp racemase was identified in the genome of both strains. Disruption of racD in Cc13826 resulted in the inability of the mutant strain to use either d-enantiomer during anaerobic growth. Hence, our results suggest that the racD gene is required for campylobacters to use either d-Asp or d-Asn. The use of d-Asp by various human opportunistic bacterial pathogens, including C. concisus, C. ureolyticus, and also possibly select strains of Campylobacter gracilis, Campylobacter rectus and Campylobacter showae, is significant, because d-Asp is an important signal molecule for both human nervous and neuroendocrine systems. To our knowledge, this is the first report of pathogens scavenging a d-amino acid essential for human health.
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Affiliation(s)
- Stéphane L Benoit
- Department of Microbiology, University of Georgia, Athens, GA, 30602, United States; Center for Metalloenzyme Studies, University of Georgia, Athens, GA, 30602, United States.
| | - Robert J Maier
- Department of Microbiology, University of Georgia, Athens, GA, 30602, United States; Center for Metalloenzyme Studies, University of Georgia, Athens, GA, 30602, United States
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2
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Luk CYM, Lee SA, Naidovski N, Liu F, Tay ACY, Wang L, Riordan S, Zhang L. Investigation of Campylobacter concisus gastric epithelial pathogenicity using AGS cells. Front Microbiol 2024; 14:1289549. [PMID: 38274743 PMCID: PMC10808343 DOI: 10.3389/fmicb.2023.1289549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
Campylobacter concisus is an oral bacterium. Recent studies suggest that C. concisus may be involved in human gastric diseases. The mechanisms, however, by which C. concisus causes human gastric diseases have not been investigated. Here we examined the gastric epithelial pathogenicity of C. concisus using a cell culture model. Six C. concisus strains and the human gastric epithelial cell line AGS cells were used. IL-8 produced by AGS cells after incubation with C. concisus was measured using enzyme-linked immunosorbent assay (ELISA), and AGS cell apoptosis was determined by caspase 3/7 activities. The effects of C. concisus on actin arrangement in AGS cells was determined using fluorescence staining. The effects of C. concisus on global gene expression in AGS cells was determined by transcriptomic analysis and quantitative real-time PCR (qRT-PCR). The role of the upregulated CYP1A1 gene in gastric cancer survival was assessed using the Kaplan-Meier method. C. concisus induced production of IL-8 by AGS cells with strain variation. Significantly increased caspase 3/7 activities were observed in AGS cells incubated with C. concisus strains when compared to AGS cells without bacteria. C. concisus induced actin re-arrangement in AGS cells. C. concisus upregulated 30 genes in AGS cells and the upregulation of CYP1A1 gene was confirmed by qRT-PCR. The Kaplan-Meier analysis showed that upregulation of CYP1A1 gene is associated with worse survival in gastric cancer patients. Our findings suggest that C. concisus may play a role in gastric inflammation and the progression of gastric cancer. Further investigation in clinical studies is warranted.
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Affiliation(s)
- Christopher Yau Man Luk
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Seul A. Lee
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Nicholas Naidovski
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Fang Liu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Alfred Chin Yen Tay
- Helicobacter Research Laboratory, School of Pathology and Laboratory Medicine, Marshall Centre for Infectious Diseases Research and Training, University of Western Australia, Perth, WA, Australia
| | - Liang Wang
- Laboratory Medicine, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
- The Center for Precision Health, School of Medical and Health Sciences, Edith Cowan University, Perth, WA, Australia
- Department of Medical Informatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Stephen Riordan
- Gastrointestinal and Liver Unit, Prince of Wales Hospital, University of New South Wales, Sydney, NSW, Australia
| | - Li Zhang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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Benoit SL, Maier RJ. The Campylobacter concisus BisA protein plays a dual role: oxide-dependent anaerobic respiration and periplasmic methionine sulfoxide repair. mBio 2023; 14:e0147523. [PMID: 37607056 PMCID: PMC10653797 DOI: 10.1128/mbio.01475-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 06/26/2023] [Indexed: 08/24/2023] Open
Abstract
IMPORTANCE Campylobacter concisus is an excellent model organism to study respiration diversity, including anaerobic respiration of physiologically relevant N-/S-oxides compounds, such as biotin sulfoxide, dimethyl sulfoxide, methionine sulfoxide (MetO), nicotinamide N-oxide, and trimethylamine N-oxide. All C. concisus strains harbor at least two, often three, and up to five genes encoding for putative periplasmic Mo/W-bisPGD-containing N-/S-oxide reductases. The respective role (substrate specificity) of each enzyme was studied using a mutagenesis approach. One of the N/SOR enzymes, annotated as "BisA", was found to be essential for anaerobic respiration of both N- and S-oxides. Additional phenotypes associated with disruption of the bisA gene included increased sensitivity toward oxidative stress and elongated cell morphology. Furthermore, a biochemical approach confirmed that BisA can repair protein-bound MetO residues. Hence, we propose that BisA plays a role as a periplasmic methionine sulfoxide reductase. This is the first report of a Mo/W-bisPGD-enzyme supporting both N- or S-oxide respiration and protein-bound MetO repair in a pathogen.
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Affiliation(s)
- Stéphane L. Benoit
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
- Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia, USA
| | - Robert J. Maier
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
- Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia, USA
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Kannan S, Sharma S, Ciufo S, Clark K, Turner S, Kitts PA, Schoch CL, DiCuccio M, Kimchi A. Collection and curation of prokaryotic genome assemblies from type strains at NCBI. Int J Syst Evol Microbiol 2023; 73. [PMID: 36748495 DOI: 10.1099/ijsem.0.005707] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The public sequence databases are entrusted with the dual responsibility of providing an accessible archive to all submitters and supporting data reliability and its re-use to all users. Genomes from type materials can act as an unambiguous reference for a taxonomic name and play an important role in comparative genomics, especially for taxon verification or reclassification. The National Center for Biotechnology Information (NCBI) collects and curates information on prokaryotic type strains and genomes from type strains. The average nucleotide identity (ANI)-based quality control processes introduced at NCBI to verify the genomes from type strains and improve related sequence records are detailed here. Using the curated genomes from type strains as reference, the taxonomy of over 1.1 million GenBank genomes were verified and the taxonomy of over 7000 new submissions before acceptance to GenBank and over 1800 existing genomes in GenBank were reclassified.
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Affiliation(s)
- Sivakumar Kannan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD, 20892, USA
| | - Shobha Sharma
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD, 20892, USA
| | - Stacy Ciufo
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD, 20892, USA
| | - Karen Clark
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD, 20892, USA
| | - Seán Turner
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD, 20892, USA
| | - Paul A Kitts
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD, 20892, USA
| | - Conrad L Schoch
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD, 20892, USA
| | - Michael DiCuccio
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD, 20892, USA
| | - Avi Kimchi
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 9600 Rockville Pike, Bethesda, MD, 20892, USA
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Nielsen OH, Fernandez-Banares F, Sato T, Pardi DS. Microscopic colitis: Etiopathology, diagnosis, and rational management. eLife 2022; 11:e79397. [PMID: 35913459 PMCID: PMC9342949 DOI: 10.7554/elife.79397] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 07/19/2022] [Indexed: 01/09/2023] Open
Abstract
Microscopic colitis is an inflammatory bowel disease divided into two subtypes: collagenous colitis and lymphocytic colitis. With an increasing incidence of microscopic colitis exceeding those of ulcerative and Crohn's disease among elderly people in some countries, microscopic colitis is a debilitating life experience. Therefore, physicians should be familiar with its clinical features and management strategies because the disease deserves the same attention as the classical inflammatory bowel diseases. Here, state-of-the-art knowledge of microscopic colitis is provided from a global perspective with reference to etiopathology and how to establish the diagnosis with the overall aim to create awareness and improve rational management in clinical practice. The immune system and a dysregulated immune response seem to play a key role combined with risk factors (e.g. cigarette smoking) in genetically predisposed individuals. The symptoms are characterized by recurrent or chronic nonbloody, watery diarrhea, urgency, weight loss, and a female preponderance. As biomarkers are absent, the diagnosis relies on colonoscopy with a histological assessment of biopsy specimens from all parts of the colon. Although the disease is not associated with a risk of colorectal cancer, a recent nationwide, population-based cohort study found an increased risk of lymphoma and lung cancer. Budesonide is the first-line therapy for management, whereas immunomodulatory drugs (including biologics) and drugs with antidiarrheal properties may be indicated in those failing, dependent, or intolerant to budesonide. In microscopic colitis induced by checkpoint inhibitors, a drug class used increasingly for a wide range of malignancies, a more aggressive therapeutic approach with biologics introduced early seems reasonable. However, particular attention needs to be drawn to the existence of incomplete forms of microscopic colitis with the risk of being overlooked in routine clinical settings.
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Affiliation(s)
- Ole Haagen Nielsen
- Department of Gastroenterology, Herlev Hospital, University of CopenhagenHerlevDenmark
| | - Fernando Fernandez-Banares
- Department of Gastroenterology, Hospital Universitari Mutua TerrassaBarcelonaSpain
- Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivasCIBERehdSpain
| | - Toshiro Sato
- Department of Gastroenterology, Keio University School of MedicineTokyoJapan
| | - Darrell S Pardi
- Division of Gastroenterology and Hepatology, Mayo ClinicRochesterUnited States
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Ferreira EO, Lagacé-Wiens P, Klein J. Campylobacter concisus gastritis masquerading as Helicobacter pylori on gastric biopsy. Helicobacter 2022; 27:e12864. [PMID: 34820966 DOI: 10.1111/hel.12864] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/01/2021] [Accepted: 11/07/2021] [Indexed: 12/09/2022]
Abstract
OBJECTIVE Campylobacter concisus is a Gram-negative rod closely related to Helicobacter pylori. We sought to identify gastric biopsies positive for C. concisus that had been misdiagnosed as H. pylori gastritis in our routine surgical pathology practice. MATERIALS AND METHODS We performed a retrospective review of gastric biopsies in our regional microbiology and pathology electronic records to identify cases that were submitted for H. pylori testing in which C. consicus was identified on culture and how many had concurrent biopsies sent to pathology for histologic assessment over a two-year period (2017-2018). Pathologic findings in the gastric biopsies were reviewed and immunohistochemical staining for H. pylori was performed. RESULTS 50 of 2191 gastric biopsy specimens submitted to microbiology in 2017-18 grew C. concisus (2.3%), compared to 168 in which H. pylori was identified (7.7%). Twenty-eight cases had concurrent histology. A total of four cases (three from 2017 and one from 2018) demonstrated organisms morphologically identical to H. pylori in the H&E sections, of which all were H. pylori immunoreactive. CONCLUSIONS Our case series is the first to demonstrate that C. concisus can mimic H. pylori gastritis in routine biopsy pathology.
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Affiliation(s)
- Elizabeth O Ferreira
- Department of Pathology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Philippe Lagacé-Wiens
- Department of Medical Microbiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Julianne Klein
- Department of Pathology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
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Cornelius AJ, Huq M, On SLW, French NP, Vandenberg O, Miller WG, Lastovica AJ, Istivan T, Biggs PJ. Genetic characterisation of Campylobacter concisus: Strategies for improved genomospecies discrimination. Syst Appl Microbiol 2021; 44:126187. [PMID: 33677170 DOI: 10.1016/j.syapm.2021.126187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 02/03/2021] [Accepted: 02/08/2021] [Indexed: 02/08/2023]
Abstract
Although at least two genetically distinct groups, or genomospecies, have been well documented for Campylobacter concisus, no phenotype has yet been identified for their differentiation and thus formal description as separate species. C. concisus has been isolated from a variety of sites in the human body, including saliva and stool samples from both healthy and diarrhoeic individuals. We evaluated the ability of a range of whole genome-based tools to distinguish between the two C. concisus genomospecies (GS) using a collection of 190 C. concisus genomes. Nine genomes from related Campylobacter species were included in some analyses to provide context. Analyses incorporating sequence analysis of multiple ribosomal genes generated similar levels of C. concisus GS discrimination as genome-wide comparisons. The C. concisus genomes formed two groups; GS1 represented by ATCC 33237T and GS2 by CCUG 19995. The two C. concisus GS were separated from the nine genomes of related species. GS1 and GS2 also differed in G+C content with medians of 37.56% and 39.51%, respectively. The groups are consistent with previously established GS and are supported by DNA reassociation results. Average Nucleotide Identity using MUMmer (ANIm) and Genome BLAST Distance Phylogeny generated in silico DNA-DNA hybridisation (isDDH) (against ATCC 33237T and CCUG 19995), plus G+C content provides cluster-independent GS discrimination suitable for routine use. Pan-genomic analysis identified genes specific to GS1 and GS2. WGS data and genomic species identification methods support the existence of two GS within C. concisus. These data provide genome-level metrics for strain identification to genomospecies level.
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Affiliation(s)
- Angela J Cornelius
- Institute of Environmental Science and Research Ltd, P.O. Box 29181, Christchurch 8540, New Zealand.
| | - Mohsina Huq
- School of Science, RMIT University, G.P.O. Box 2476, Bundoora, Victoria 3001, Australia
| | - Stephen L W On
- Lincoln University, P.O. Box 85084, Lincoln 7647, New Zealand
| | - Nigel P French
- Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
| | - Olivier Vandenberg
- National Reference Centre for Campylobacter, Laboratoire Hospitalier Universitaire de Bruxelles, 322 rue Haute, 1000 Brussels, Belgium; School of Public Health, Campus Erasme - Bâtiment A, Route de Lennik 808 - CP591, Université Libre de Bruxelles, 1070 Bruxelles, Belgium
| | - William G Miller
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, United States Department of Agriculture, 800 Buchanan Street, Albany, CA 94710, USA
| | - Albert J Lastovica
- University of Western Cape, Private Bag X17, Bellville 7535, South Africa
| | - Taghrid Istivan
- School of Science, RMIT University, G.P.O. Box 2476, Bundoora, Victoria 3001, Australia
| | - Patrick J Biggs
- Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
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