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Allen-Vercoe E, Daigneault MC, Vancuren SJ, Cochrane K, O'Neal LL, Sankaranarayanan K, Lawson PA. Holtiella tumoricola gen. nov. sp. nov., isolated from a human clinical sample. Int J Syst Evol Microbiol 2023; 73. [PMID: 37436807 DOI: 10.1099/ijsem.0.005958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023] Open
Abstract
The diversity of bacteria associated with biopsy material obtained from patients with colorectal cancer was investigated using culture techniques. A novel bacterium, strain CC70AT, was isolated by diluting a sample of homogenized tissue in anaerobic medium, and then plating to yield a pure culture. Strain CC70AT was a Gram-positive, strictly anaerobic, motile, rod-shaped bacterium. Formate, but not acetate, was a fermentative end-product from growth in peptone-yeast extract and peptone-yeast-glucose broth. The G+C content of DNA from strain CC70AT was 34.9 mol%. 16S rRNA gene sequence analysis revealed that the isolate was part of the phylum Bacillota. The closest described relatives of strain CC70AT were Cellulosilyticum lentocellum (93.3 %) and Cellulosilyticum ruminicola (93.3 and 91.9% sequence similarity across 16S rRNA gene, respectively). According to the data obtained in this work, strain CC70AT represents a novel bacterium belonging to a new genus for which the name Holtiella tumoricola gen. nov., sp. nov. is proposed. The type strain for our described novel species is CC70AT (=DSM 27931T= JCM 30568T).
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Affiliation(s)
- Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, Ontario, Canada
| | | | - Sarah J Vancuren
- Department of Molecular and Cellular Biology, University of Guelph, Ontario, Canada
| | - Kyla Cochrane
- Department of Molecular and Cellular Biology, University of Guelph, Ontario, Canada
| | - Lindsey L O'Neal
- Department of Microbiology and Plant Biology, University of Oklahoma, Oklahoma, USA
| | - Krithivasan Sankaranarayanan
- Department of Microbiology and Plant Biology, University of Oklahoma, Oklahoma, USA
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Oklahoma 73019, USA
| | - Paul A Lawson
- Department of Microbiology and Plant Biology, University of Oklahoma, Oklahoma, USA
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Gianetto-Hill CM, Vancuren SJ, Daisley B, Renwick S, Wilde J, Schroeter K, Daigneault MC, Allen-Vercoe E. The Robogut: A Bioreactor Model of the Human Colon for Evaluation of Gut Microbial Community Ecology and Function. Curr Protoc 2023; 3:e737. [PMID: 37093893 DOI: 10.1002/cpz1.737] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
The human colon is inhabited by a complex community of microbes. These microbes are integral to host health and physiology. Understanding how and when the microbiome causally influences host health will require microbiome models that can be tightly controlled and manipulated. While in vivo models are unrivalled in their ability to study host-microbial interplay, in vitro models are gaining in popularity as methods to study the ecology and function of the gut microbiota, and benefit from tight controllability and reproducibility, as well as reduced ethical constraints. In this set of protocols, we describe the Robogut, a single-stage bioreactor system designed to replicate the conditions of the distal human colon, to culture whole microbial communities derived from stool and/or colonic biopsy samples, with consideration of methods to create culture medium formulations and to build, run, and sample the bioreactor apparatus. Cleaning and maintenance of the bioreactor system are also described. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Growth medium preparation Support Protocol 1: Preparing medium supplements Basic Protocol 2: Preparing the bioreactor vessels Support Protocol 2: Making acid and base bottles Support Protocol 3: Preparing the effluent bottles Support Protocol 4: Making acid solution Support Protocol 5: Making base solution Basic Protocol 3: Preparing inoculum and inoculating bioreactors Alternate Protocol 1: Preparing inoculum less than 0.5% (w/v) of vessel volume Alternate Protocol 2: Preparing synthetic community aliquots and inoculation via the septum Alternate Protocol 3: Preparing inoculum from a tissue sample Basic Protocol 4: Sampling the bioreactor vessel Basic Protocol 5: Harvesting bioreactor vessel contents at end of experiment Support Protocol 6: Cleaning and sterilizing sampling needles Basic Protocol 6: Cleaning the bioreactor vessel Support Protocol 7: Cleaning bioreactor support bottles.
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Affiliation(s)
| | - Sarah J Vancuren
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario
| | - Brendan Daisley
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario
| | - Simone Renwick
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario
| | - Jacob Wilde
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario
| | - Kathleen Schroeter
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario
| | - Michelle C Daigneault
- NuBiyota, Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario
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Vogt SL, Serapio-Palacios A, Woodward SE, Santos AS, de Vries SP, Daigneault MC, Brandmeier LV, Grant AJ, Maskell DJ, Allen-Vercoe E, Finlay BB. Enterohemorrhagic Escherichia coli responds to gut microbiota metabolites by altering metabolism and activating stress responses. Gut Microbes 2023; 15:2190303. [PMID: 36951510 PMCID: PMC10038027 DOI: 10.1080/19490976.2023.2190303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 03/08/2023] [Indexed: 03/24/2023] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) is a major cause of severe bloody diarrhea, with potentially lethal complications, such as hemolytic uremic syndrome. In humans, EHEC colonizes the colon, which is also home to a diverse community of trillions of microbes known as the gut microbiota. Although these microbes and the metabolites that they produce represent an important component of EHEC's ecological niche, little is known about how EHEC senses and responds to the presence of gut microbiota metabolites. In this study, we used a combined RNA-Seq and Tn-Seq approach to characterize EHEC's response to metabolites from an in vitro culture of 33 human gut microbiota isolates (MET-1), previously demonstrated to effectively resolve recurrent Clostridioides difficile infection in human patients. Collectively, the results revealed that EHEC adjusts to growth in the presence of microbiota metabolites in two major ways: by altering its metabolism and by activating stress responses. Metabolic adaptations to the presence of microbiota metabolites included increased expression of systems for maintaining redox balance and decreased expression of biotin biosynthesis genes, reflecting the high levels of biotin released by the microbiota into the culture medium. In addition, numerous genes related to envelope and oxidative stress responses (including cpxP, spy, soxS, yhcN, and bhsA) were upregulated during EHEC growth in a medium containing microbiota metabolites. Together, these results provide insight into the molecular mechanisms by which pathogens adapt to the presence of competing microbes in the host environment, which ultimately may enable the development of therapies to enhance colonization resistance and prevent infection.
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Affiliation(s)
- Stefanie L. Vogt
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Sarah E. Woodward
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andrew S. Santos
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Stefan P.W. de Vries
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Michelle C. Daigneault
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Lisa V. Brandmeier
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andrew J. Grant
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Duncan J. Maskell
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - B. Brett Finlay
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
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Paun A, Yau C, Meshkibaf S, Daigneault MC, Marandi L, Mortin-Toth S, Bar-Or A, Allen-Vercoe E, Poussier P, Danska JS. Association of HLA-dependent islet autoimmunity with systemic antibody responses to intestinal commensal bacteria in children. Sci Immunol 2020; 4:4/32/eaau8125. [PMID: 30709843 DOI: 10.1126/sciimmunol.aau8125] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 12/13/2018] [Indexed: 12/11/2022]
Abstract
Microbiome sequence analyses have suggested that changes in gut bacterial composition are associated with autoimmune disease in humans and animal models. However, little is known of the mechanisms through which the gut microbiota influences autoimmune responses to distant tissues. Here, we evaluated systemic antibody responses against cultured human gut bacterial strains to determine whether observed patterns of anticommensal antibody (ACAb) responses are associated with type 1 diabetes (T1D) in two cohorts of pediatric study participants. In the first cohort, ACAb responses in sera collected from participants within 6 months of T1D diagnosis were compared with age-matched healthy controls and also with patients with recent onset Crohn's disease. ACAb responses against multiple bacterial species discriminated among these three groups. In the second cohort, we asked whether ACAb responses present before diagnosis were associated with later T1D development and with HLA genotype in participants who were discordant for subsequent progression to diabetes. Serum IgG2 antibodies against Roseburia faecis and against a bacterial consortium were associated with future T1D diagnosis in an HLA DR3/DR4 haplotype-dependent manner. These analyses reveal associations between antibody responses to intestinal microbes and HLA-DR genotype and islet autoantibody specificity and with a future diagnosis of T1D. Further, we present a platform to investigate antibacterial antibodies in biological fluids that is applicable to studies of autoimmune diseases and responses to therapeutic interventions.
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Affiliation(s)
- Alexandra Paun
- Hospital for Sick Children, Toronto, ON, Canada. .,Department of Immunology, University of Toronto, Faculty of Medicine, Toronto, ON, Canada
| | - Christopher Yau
- Hospital for Sick Children, Toronto, ON, Canada. .,Department of Immunology, University of Toronto, Faculty of Medicine, Toronto, ON, Canada
| | | | - Michelle C Daigneault
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | | | | | - Amit Bar-Or
- Montreal Neurological Institute, McGill University, Montreal, QC, Canada.,Department of Neurology, Perelman Center for Advanced Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, U.S.A
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Philippe Poussier
- Department of Immunology, University of Toronto, Faculty of Medicine, Toronto, ON, Canada.,Sunnybrook Research Institute, Toronto, ON Canada
| | - Jayne S Danska
- Hospital for Sick Children, Toronto, ON, Canada. .,Department of Immunology, University of Toronto, Faculty of Medicine, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Faculty of Medicine, Toronto, ON, Canada
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Belik J, Shifrin Y, Arning E, Bottiglieri T, Pan J, Daigneault MC, Allen-Vercoe E. Corrigendum: Intestinal microbiota as a tetrahydrobiopterin exogenous source in hph-1 mice. Sci Rep 2017; 7:44161. [PMID: 28398297 PMCID: PMC5388072 DOI: 10.1038/srep44161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Belik J, Shifrin Y, Arning E, Bottiglieri T, Pan J, Daigneault MC, Allen-Vercoe E. Intestinal microbiota as a tetrahydrobiopterin exogenous source in hph-1 mice. Sci Rep 2017; 7:39854. [PMID: 28079055 PMCID: PMC5227711 DOI: 10.1038/srep39854] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 11/29/2016] [Indexed: 01/07/2023] Open
Abstract
Tetrahydrobiopterin (BH4) is a cofactor of a number of regulatory enzymes. Although there are no known BH4 exogenous sources, the tissue content of this biopterin increases with age in GTP cyclohydrolase 1-deficient hyperphenylalaninemia-1 (hph-1) mice. Since certain bacteria are known to generate BH4, we hypothesize that generation of this biopterin by the intestinal microbiota contributes to its tissue increase in hph-1 adult mice. The goal of this study was to comparatively evaluate hph-1 mice and wild-type C57Bl/6 controls for the presence of intestinal BH4-producing bacteria. Newborn and adult mice fecal material was screened for 6-pyruvoyltetrahydropterin synthase (PTPS-2) an enzyme only present in BH4-generating bacteria. Adult, but not newborn, wild-type control and hph-1 mouse fecal material contained PTPS-2 mRNA indicative of the presence of BH4-generating bacteria. Utilizing chemostat-cultured human fecal bacteria, we identified the PTPS-2-producing bacteria as belonging to the Actinobacteria phylum. We further confirmed that at least two PTPS-2-producing species, Aldercreutzia equolifaciens and Microbacterium schleiferi, generate BH4 and are present in hph-1 fecal material. In conclusion, intestinal Actinobacteria generate BH4. This finding has important translational significance, since manipulation of the intestinal flora in individuals with congenital biopterin deficiency may allow for an increase in total body BH4 content.
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Affiliation(s)
- Jaques Belik
- Physiology & Experimental Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Ontario M5G 1X8, Canada
- Department of Paediatrics and Physiology, University of Toronto, Toronto, Ontario, M5G 1X8 Canada
| | - Yulia Shifrin
- Physiology & Experimental Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Ontario M5G 1X8, Canada
| | - Erland Arning
- Baylor Research Institute, Institute of Metabolic Disease, Dallas, TX, 75226, USA
| | - Teodoro Bottiglieri
- Baylor Research Institute, Institute of Metabolic Disease, Dallas, TX, 75226, USA
| | - Jingyi Pan
- Physiology & Experimental Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Ontario M5G 1X8, Canada
| | | | - Emma Allen-Vercoe
- Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1 Canada
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Santiago-Rodriguez TM, Ly M, Daigneault MC, Brown IHL, McDonald JAK, Bonilla N, Vercoe EA, Pride DT. Chemostat culture systems support diverse bacteriophage communities from human feces. Microbiome 2015; 3:58. [PMID: 26549756 PMCID: PMC4638026 DOI: 10.1186/s40168-015-0124-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 10/27/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND Most human microbiota studies focus on bacteria inhabiting body surfaces, but these surfaces also are home to large populations of viruses. Many are bacteriophages, and their role in driving bacterial diversity is difficult to decipher without the use of in vitro ecosystems that can reproduce human microbial communities. RESULTS We used chemostat culture systems known to harbor diverse fecal bacteria to decipher whether these cultures also are home to phage communities. We found that there are vast viral communities inhabiting these ecosystems, with estimated concentrations similar to those found in human feces. The viral communities are composed entirely of bacteriophages and likely contain both temperate and lytic phages based on their similarities to other known phages. We examined the cultured phage communities at five separate time points over 24 days and found that they were highly individual-specific, suggesting that much of the subject-specificity found in human viromes also is captured by this culture-based system. A high proportion of the community membership is conserved over time, but the cultured communities maintain more similarity with other intra-subject cultures than they do to human feces. In four of the five subjects, estimated viral diversity between fecal and cultured communities was highly similar. CONCLUSIONS Because the diversity of phages in these cultured fecal communities have similarities to those found in humans, we believe these communities can serve as valuable ecosystems to help uncover the role of phages in human microbial communities.
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Affiliation(s)
- Tasha M Santiago-Rodriguez
- Department of Pathology, University of California, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA
| | - Melissa Ly
- Department of Pathology, University of California, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA
| | - Michelle C Daigneault
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Ian H L Brown
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Julie A K McDonald
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Natasha Bonilla
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Emma Allen Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - David T Pride
- Department of Pathology, University of California, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA.
- Department of Medicine, University of California, San Diego, CA, USA.
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Petrof EO, Gloor GB, Vanner SJ, Weese SJ, Carter D, Daigneault MC, Brown EM, Schroeter K, Allen-Vercoe E. Stool substitute transplant therapy for the eradication of Clostridium difficile infection: 'RePOOPulating' the gut. Microbiome 2013; 1:3. [PMID: 24467987 PMCID: PMC3869191 DOI: 10.1186/2049-2618-1-3] [Citation(s) in RCA: 503] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 07/18/2012] [Indexed: 05/03/2023]
Abstract
BACKGROUND Fecal bacteriotherapy ('stool transplant') can be effective in treating recurrent Clostridium difficile infection, but concerns of donor infection transmission and patient acceptance limit its use. Here we describe the use of a stool substitute preparation, made from purified intestinal bacterial cultures derived from a single healthy donor, to treat recurrent C. difficile infection that had failed repeated standard antibiotics. Thirty-three isolates were recovered from a healthy donor stool sample. Two patients who had failed at least three courses of metronidazole or vancomycin underwent colonoscopy and the mixture was infused throughout the right and mid colon. Pre-treatment and post-treatment stool samples were analyzed by 16 S rRNA gene sequencing using the Ion Torrent platform. RESULTS Both patients were infected with the hyper virulent C. difficile strain, ribotype 078. Following stool substitute treatment, each patient reverted to their normal bowel pattern within 2 to 3 days and remained symptom-free at 6 months. The analysis demonstrated that rRNA sequences found in the stool substitute were rare in the pre-treatment stool samples but constituted over 25% of the sequences up to 6 months after treatment. CONCLUSION This proof-of-principle study demonstrates that a stool substitute mixture comprising a multi-species community of bacteria is capable of curing antibiotic-resistant C. difficile colitis. This benefit correlates with major changes in stool microbial profile and these changes reflect isolates from the synthetic mixture. CLINICAL TRIAL REGISTRATION NUMBER CinicalTrials.gov NCT01372943.
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Affiliation(s)
- Elaine O Petrof
- Department of Medicine, GIDRU Wing, Kingston General Hospital, Queen’s University, 76 Stuart Street, Kingston, ON, K7L 2V7, Canada
| | - Gregory B Gloor
- Department of Biochemistry, University of Western Ontario, 1151 Richmond Street, London, ON, N6A 3K7, Canada
| | - Stephen J Vanner
- Department of Medicine, GIDRU Wing, Kingston General Hospital, Queen’s University, 76 Stuart Street, Kingston, ON, K7L 2V7, Canada
| | - Scott J Weese
- Department of Pathobiology, University of Guelph, Guelph, 50 Stone Road East, ON, N1G 2W1, Canada
| | - David Carter
- London Regional Genomics Centre, Robarts Research Institute, 100 Perth Drive, London, ON, N6A 5K8, Canada
| | - Michelle C Daigneault
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Eric M Brown
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Kathleen Schroeter
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
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Abstract
A locus that codes for a high-molecular-weight adhesin was previously isolated from Mannheimia haemolytica A1. In this study, we showed that this locus, named ahs, codes for two proteins (AhsA and AhsB) that exhibit characteristics of a trimeric autotransporter adhesin. Sequence analysis of AhsA showed the presence of 21 collagen-binding motifs in the protein. Collagen-binding assays showed that M. haemolytica A1 binds to collagen in a dose-dependent manner. This binding activity is trypsin sensitive and can be inhibited by anti-AhsA antibody. AhsB is the cognate transporter for AhsA. The C-terminal of AhsB showed highly conserved amino acids typical of trimeric autotransporters. Experimental data showed that the C-terminal 120 amino acids of AhsB could indeed form trimeric molecules. Western immunoblots showed the presence of anti-AhsA antibodies in the sera of calves that had been challenged with M. haemolytica A1, suggesting that AhsA is expressed and immunogenic in cattle.
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Affiliation(s)
- Michelle C Daigneault
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
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