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Kelly C, Jawahar J, Davey L, Everitt JI, Galanko JA, Anderson C, Avendano JE, McCann JR, Sartor RB, Valdivia RH, Rawls JF. Spontaneous episodic inflammation in the intestines of mice lacking HNF4A is driven by microbiota and associated with early life microbiota alterations. mBio 2023; 14:e0150423. [PMID: 37526424 PMCID: PMC10470520 DOI: 10.1128/mbio.01504-23] [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] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 06/22/2023] [Indexed: 08/02/2023] Open
Abstract
The inflammatory bowel diseases (IBD) occur in genetically susceptible individuals who mount inappropriate immune responses to their microbiota leading to chronic intestinal inflammation. Whereas IBD clinical presentation is well described, how interactions between microbiota and host genotype impact early subclinical stages of the disease remains unclear. The transcription factor hepatocyte nuclear factor 4 alpha (HNF4A) has been associated with human IBD, and deletion of Hnf4a in intestinal epithelial cells (IECs) in mice (Hnf4aΔIEC) leads to spontaneous colonic inflammation by 6-12 mo of age. Here, we tested if pathology in Hnf4aΔIEC mice begins earlier in life and if microbiota contribute to that process. Longitudinal analysis revealed that Hnf4aΔIEC mice reared in specific pathogen-free (SPF) conditions develop episodic elevated fecal lipocalin 2 (Lcn2) and loose stools beginning by 4-5 wk of age. Lifetime cumulative Lcn2 levels correlated with histopathological features of colitis at 12 mo. Antibiotic and gnotobiotic tests showed that these phenotypes in Hnf4aΔIEC mice were dependent on microbiota. Fecal 16S rRNA gene sequencing in SPF Hnf4aΔIEC and control mice disclosed that genotype significantly contributed to differences in microbiota composition by 12 mo, and longitudinal analysis of the Hnf4aΔIEC mice with the highest lifetime cumulative Lcn2 revealed that microbial community differences emerged early in life when elevated fecal Lcn2 was first detected. These microbiota differences included enrichment of a novel phylogroup of Akkermansia muciniphila in Hnf4aΔIEC mice. We conclude that HNF4A functions in IEC to shape composition of the gut microbiota and protect against episodic inflammation induced by microbiota throughout the lifespan. IMPORTANCE The inflammatory bowel diseases (IBD), characterized by chronic inflammation of the intestine, affect millions of people around the world. Although significant advances have been made in the clinical management of IBD, the early subclinical stages of IBD are not well defined and are difficult to study in humans. This work explores the subclinical stages of disease in mice lacking the IBD-associated transcription factor HNF4A in the intestinal epithelium. Whereas these mice do not develop overt disease until late in adulthood, we find that they display episodic intestinal inflammation, loose stools, and microbiota changes beginning in very early life stages. Using germ-free and antibiotic-treatment experiments, we reveal that intestinal inflammation in these mice was dependent on the presence of microbiota. These results suggest that interactions between host genotype and microbiota can drive early subclinical pathologies that precede the overt onset of IBD and describe a mouse model to explore those important processes.
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Affiliation(s)
- Cecelia Kelly
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA
| | - Jayanth Jawahar
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA
| | - Lauren Davey
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Jeffrey I. Everitt
- Department of Pathology, Research Animal Pathology Core, Duke University School of Medicine, Durham, North Carolina, USA
| | - Joseph A. Galanko
- Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Chelsea Anderson
- Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jonathan E. Avendano
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA
| | - Jessica R. McCann
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA
| | - R. Balfour Sartor
- Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Raphael H. Valdivia
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina, USA
| | - John F. Rawls
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA
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Ormandy A, Davey L, Inder S. Atypical papilloma arising within a benign epithelial inclusion in an axillary sentinel lymph node. Pathology 2023. [DOI: 10.1016/j.pathol.2022.12.229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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3
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Schwabkey ZI, Wiesnoski DH, Chang CC, Tsai WB, Pham D, Ahmed SS, Hayase T, Turrubiates MRO, El-Himri RK, Sanchez CA, Hayase E, Oquendo ACF, Miyama T, Halsey TM, Heckel BE, Brown AN, Jin Y, Raybaud M, Prasad R, Flores I, McDaniel L, Chapa V, Lorenzi PL, Warmoes MO, Tan L, Swennes AG, Fowler S, Conner M, McHugh K, Graf T, Jensen VB, Peterson CB, Do KA, Zhang L, Shi Y, Wang Y, Galloway-Pena JR, Okhuysen PC, Daniel-MacDougall CR, Shono Y, da Silva MB, Peled JU, van den Brink MR, Ajami N, Wargo JA, Reddy P, Valdivia RH, Davey L, Rondon G, Srour SA, Mehta RS, Alousi AM, Shpall EJ, Champlin RE, Shelburne SA, Molldrem JJ, Jamal MA, Karmouch JL, Jenq RR. Diet-derived metabolites and mucus link the gut microbiome to fever after cytotoxic cancer treatment. Sci Transl Med 2022; 14:eabo3445. [PMID: 36383683 PMCID: PMC10028729 DOI: 10.1126/scitranslmed.abo3445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Not all patients with cancer and severe neutropenia develop fever, and the fecal microbiome may play a role. In a single-center study of patients undergoing hematopoietic cell transplant (n = 119), the fecal microbiome was characterized at onset of severe neutropenia. A total of 63 patients (53%) developed a subsequent fever, and their fecal microbiome displayed increased relative abundances of Akkermansia muciniphila, a species of mucin-degrading bacteria (P = 0.006, corrected for multiple comparisons). Two therapies that induce neutropenia, irradiation and melphalan, similarly expanded A. muciniphila and additionally thinned the colonic mucus layer in mice. Caloric restriction of unirradiated mice also expanded A. muciniphila and thinned the colonic mucus layer. Antibiotic treatment to eradicate A. muciniphila before caloric restriction preserved colonic mucus, whereas A. muciniphila reintroduction restored mucus thinning. Caloric restriction of unirradiated mice raised colonic luminal pH and reduced acetate, propionate, and butyrate. Culturing A. muciniphila in vitro with propionate reduced utilization of mucin as well as of fucose. Treating irradiated mice with an antibiotic targeting A. muciniphila or propionate preserved the mucus layer, suppressed translocation of flagellin, reduced inflammatory cytokines in the colon, and improved thermoregulation. These results suggest that diet, metabolites, and colonic mucus link the microbiome to neutropenic fever and may guide future microbiome-based preventive strategies.
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Affiliation(s)
- Zaker I. Schwabkey
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Diana H. Wiesnoski
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chia-Chi Chang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Wen-Bin Tsai
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dung Pham
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Saira S. Ahmed
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tomo Hayase
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Rawan K. El-Himri
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Christopher A. Sanchez
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Eiko Hayase
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Annette C. Frenk Oquendo
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Takahiko Miyama
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Taylor M. Halsey
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Brooke E. Heckel
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alexandria N. Brown
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yimei Jin
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mathilde Raybaud
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rishika Prasad
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ivonne Flores
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lauren McDaniel
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Valerie Chapa
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Philip L. Lorenzi
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Marc O. Warmoes
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lin Tan
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alton G. Swennes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Stephanie Fowler
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Margaret Conner
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kevin McHugh
- CPRIT Scholar in Cancer Research, Austin, TX 78701, USA
- Department of Bioengineering, Rice University, Houston, TX 77251, USA
| | - Tyler Graf
- Department of Bioengineering, Rice University, Houston, TX 77251, USA
| | - Vanessa B. Jensen
- Department of Veterinary Medicine and Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Christine B. Peterson
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kim-Anh Do
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Liangliang Zhang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yushu Shi
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yinghong Wang
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jessica R. Galloway-Pena
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, College Station, TX 77843, USA
| | - Pablo C. Okhuysen
- Department of Infectious Diseases, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Yusuke Shono
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Marina Burgos da Silva
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jonathan U. Peled
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Weill Cornell Medical College, New York, NY 10021, USA
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Marcel R.M. van den Brink
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Weill Cornell Medical College, New York, NY 10021, USA
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Nadim Ajami
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jennifer A. Wargo
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Pavan Reddy
- Department of Hematology and Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Raphael H. Valdivia
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710 USA
| | - Lauren Davey
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710 USA
| | - Gabriela Rondon
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Samer A. Srour
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rohtesh S. Mehta
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Amin M. Alousi
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Elizabeth J. Shpall
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Richard E. Champlin
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Samuel A. Shelburne
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Infectious Diseases, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jeffrey J. Molldrem
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Hematopoietic Biology and Malignancy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mohamed A. Jamal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jennifer L. Karmouch
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Robert R. Jenq
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- CPRIT Scholar in Cancer Research, Austin, TX 78701, USA
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Corresponding author.
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4
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Hayase E, Hayase T, Jamal MA, Miyama T, Chang CC, Ortega MR, Ahmed SS, Karmouch JL, Sanchez CA, Brown AN, El-Himri RK, Flores II, McDaniel LK, Pham D, Halsey T, Frenk AC, Chapa VA, Heckel BE, Jin Y, Tsai WB, Prasad R, Tan L, Veillon L, Ajami NJ, Wargo JA, Galloway-Peña J, Shelburne S, Chemaly RF, Davey L, Glowacki RWP, Liu C, Rondon G, Alousi AM, Molldrem JJ, Champlin RE, Shpall EJ, Valdivia RH, Martens EC, Lorenzi PL, Jenq RR. Mucus-degrading Bacteroides link carbapenems to aggravated graft-versus-host disease. Cell 2022; 185:3705-3719.e14. [PMID: 36179667 PMCID: PMC9542352 DOI: 10.1016/j.cell.2022.09.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 06/15/2022] [Accepted: 08/31/2022] [Indexed: 01/26/2023]
Abstract
The intestinal microbiota is an important modulator of graft-versus-host disease (GVHD), which often complicates allogeneic hematopoietic stem cell transplantation (allo-HSCT). Broad-spectrum antibiotics such as carbapenems increase the risk for intestinal GVHD, but mechanisms are not well understood. In this study, we found that treatment with meropenem, a commonly used carbapenem, aggravates colonic GVHD in mice via the expansion of Bacteroides thetaiotaomicron (BT). BT has a broad ability to degrade dietary polysaccharides and host mucin glycans. BT in meropenem-treated allogeneic mice demonstrated upregulated expression of enzymes involved in the degradation of mucin glycans. These mice also had thinning of the colonic mucus layer and decreased levels of xylose in colonic luminal contents. Interestingly, oral xylose supplementation significantly prevented thinning of the colonic mucus layer in meropenem-treated mice. Specific nutritional supplementation strategies, including xylose supplementation, may combat antibiotic-mediated microbiome injury to reduce the risk for intestinal GVHD in allo-HSCT patients.
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Affiliation(s)
- Eiko Hayase
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Tomo Hayase
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Mohamed A Jamal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Takahiko Miyama
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Chia-Chi Chang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Miriam R Ortega
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Saira S Ahmed
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Jennifer L Karmouch
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Christopher A Sanchez
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Alexandria N Brown
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Rawan K El-Himri
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Ivonne I Flores
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Lauren K McDaniel
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Dung Pham
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Taylor Halsey
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Annette C Frenk
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Valerie A Chapa
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Brooke E Heckel
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Yimei Jin
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Wen-Bin Tsai
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Rishika Prasad
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Lin Tan
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77230, USA; Metabolomics Core Facility, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Lucas Veillon
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77230, USA; Metabolomics Core Facility, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Nadim J Ajami
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Jennifer A Wargo
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Jessica Galloway-Peña
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Veterinary Pathobiology, Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX 77843, USA
| | - Samuel Shelburne
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Roy F Chemaly
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lauren Davey
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA
| | - Robert W P Glowacki
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Chen Liu
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Gabriela Rondon
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Amin M Alousi
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jeffrey J Molldrem
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Richard E Champlin
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Elizabeth J Shpall
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Raphael H Valdivia
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA
| | - Eric C Martens
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Philip L Lorenzi
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77230, USA; Metabolomics Core Facility, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Robert R Jenq
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; CPRIT Scholar in Cancer Research, Houston, TX, USA.
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5
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Becken B, Davey L, Middleton DR, Mueller KD, Sharma A, Holmes ZC, Dallow E, Remick B, Barton GM, David LA, McCann JR, Armstrong SC, Malkus P, Valdivia RH. Genotypic and Phenotypic Diversity among Human Isolates of Akkermansia muciniphila. mBio 2021; 12:e00478-21. [PMID: 34006653 PMCID: PMC8262928 DOI: 10.1128/mbio.00478-21] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 04/05/2021] [Indexed: 12/12/2022] Open
Abstract
The mucophilic anaerobic bacterium Akkermansia muciniphila is a prominent member of the gastrointestinal (GI) microbiota and the only known species of the Verrucomicrobia phylum in the mammalian gut. A high prevalence of A. muciniphila in adult humans is associated with leanness and a lower risk for the development of obesity and diabetes. Four distinct A. muciniphila phylogenetic groups have been described, but little is known about their relative abundance in humans or how they impact human metabolic health. In this study, we isolated and characterized 71 new A. muciniphila strains from a cohort of children and adolescents undergoing treatment for obesity. Based on genomic and phenotypic analysis of these strains, we found several phylogroup-specific phenotypes that may impact the colonization of the GI tract or modulate host functions, such as oxygen tolerance, adherence to epithelial cells, iron and sulfur metabolism, and bacterial aggregation. In antibiotic-treated mice, phylogroups AmIV and AmII outcompeted AmI strains. In children and adolescents, AmI strains were most prominent, but we observed high variance in A. muciniphila abundance and single phylogroup dominance, with phylogroup switching occurring in a small subset of patients. Overall, these results highlight that the ecological principles determining which A. muciniphila phylogroup predominates in humans are complex and that A. muciniphila strain genetic and phenotypic diversity may represent an important variable that should be taken into account when making inferences as to this microbe's impact on its host's health.IMPORTANCE The abundance of Akkermansia muciniphila in the gastrointestinal (GI) tract is linked to multiple positive health outcomes. There are four known A. muciniphila phylogroups, yet the prevalence of these phylogroups and how they vary in their ability to influence human health is largely unknown. In this study, we performed a genomic and phenotypic analysis of 71 A. muciniphila strains and identified phylogroup-specific traits such as oxygen tolerance, adherence, and sulfur acquisition that likely influence colonization of the GI tract and differentially impact metabolic and immunological health. In humans, we observed that single Akkermansia phylogroups predominate at a given time but that the phylotype can switch in an individual. This collection of strains provides the foundation for the functional characterization of A. muciniphila phylogroup-specific effects on the multitude of host outcomes associated with Akkermansia colonization, including protection from obesity, diabetes, colitis, and neurological diseases, as well as enhanced responses to cancer immunotherapies.
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Affiliation(s)
- Bradford Becken
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
- Department of Pediatrics, Duke University Hospital, Durham, North Carolina, USA
| | - Lauren Davey
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Dustin R Middleton
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Katherine D Mueller
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Agastya Sharma
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Zachary C Holmes
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Eric Dallow
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Brenna Remick
- Division of Immunology & Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Gregory M Barton
- Division of Immunology & Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Lawrence A David
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Jessica R McCann
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Sarah C Armstrong
- Department of Pediatrics, Duke University Hospital, Durham, North Carolina, USA
| | - Per Malkus
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Raphael H Valdivia
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
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6
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Davey L, Davidson V, Charlton S, Hunnisett A. 16 Preliminary investigation into the effects of McTimoney chiropractic treatment and combined with pulsed electromagnetic field therapy on mechanical nociceptive thresholds of horses. J Equine Vet Sci 2021. [DOI: 10.1016/j.jevs.2021.103479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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7
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Davey L, Valdivia RH. Bacterial genetics and molecular pathogenesis in the age of high throughput DNA sequencing. Curr Opin Microbiol 2020; 54:59-66. [PMID: 32044689 PMCID: PMC8765803 DOI: 10.1016/j.mib.2020.01.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 01/12/2020] [Indexed: 12/17/2022]
Abstract
When Stanley Falkow introduced Molecular Koch's Postulates (Falkow, 1988) as a conceptual framework to identify microbial factors that contributed to disease, he reaffirmed the prominent role that the basic principles of genetic analysis should play in defining genotype-phenotype associations in microbial pathogens. In classical bacterial genetics the nature of mutations is inferred through cis-trans complementation and by indirectly mapping their relative position and physical distance through recombination frequencies - all of which were made possible by the genetic tools of the day: natural transformations, conjugation and transduction. Unfortunately, many of these genetic tools are not always available to study pathogenic bacteria. The recombinant DNA revolution in the 1980s launched the field of molecular pathogenesis as genes could be treated as physical units that could be cut, spliced and transplanted from one microbe to another and thus not only 'prove' that an individual gene complemented a virulence defect in a mutant strain but also could impart pathogenic properties to otherwise benign microbes. The recombinant DNA revolution also enabled the generation of newer versions of genetic tools to generate mutations and engineer microbial genomes. The last decade has ushered in next generation sequencing technologies as a new powerful tool for bacterial genetics. The routine and inexpensive sequencing of microbial genomes has increased the number and phylogenetic scope of microbes that are amenable to functional characterization and experimentation. In this review, we highlight some salient advances in this rapidly evolving area.
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Affiliation(s)
- Lauren Davey
- Duke University School of Medicine, Molecular Genetics and Microbiology, 272 Jones Bldg DUMC 3580, Durham, NC 27710, United States
| | - Raphael H Valdivia
- Duke University School of Medicine, Molecular Genetics and Microbiology, 272 Jones Bldg DUMC 3580, Durham, NC 27710, United States.
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Agarwal A, Modliszewski J, Davey L, Reyes-Martinez M, Runyambo D, Corcoran D, Dressman H, George DJ, Valdivia R, Armstrong AJ, Zhang T. Investigating the role of the gastrointestinal microbiome in response to immune checkpoint inhibitors (ICIs) among patients (pts) with metastatic renal cell carcinoma (mRCC). J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.6_suppl.730] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
730 Background: ICIs are effective in mRCC, but one pertinent clinical need is to identify predictive biomarkers for response. The PD-1 receptor has been implicated in regulating gastrointestinal commensal bacteria, with varied immune interactions, thereby impacting response to ICIs. We evaluated bacterial taxa and ICI outcomes in mRCC pts. Methods: Fecal samples from 22 mRCC pts were collected at baseline, week (wk)-4 on ICI, and upon disease progression. Pts were grouped as responders (R, complete or partial response) or non-responders (NR, stable or progressive disease). Microbial DNA was isolated by next generation DNA sequencing. The V4 region of bacterial 16S ribosomal RNA was amplified from extracted DNA and analyzed for bacterial abundance, as well as alpha diversity indices (number of amplicon sequence variants [ASVs], Shannon’s Index, Faith’s Phylogenetic Diversity, and Pielou’s evenness) and beta diversity indices on ASVs (Bray-Curtis, Jaccard, and unweighted/weighted UniFrac dissimilarity measures). Results: Beta diversity analysis at baseline showed no difference in microbial composition between Rs and NRs. However, beta diversity analysis did show a significant change in composition from baseline to wk 4 in R vs NR pts (Bray Curtis p-value=0.03). Among mRCC pts with CR to ICIs, counts of bacteria in the phylum Verrucomicrobia had an upward trend from baseline to wk 4. All mRCC pts with CR (n=3) had Akkermansia at wk 4. However, Akkermansia colonization was not sufficient for response, present in 7/9 Rs and 6/11 NRs. Conclusions: Baseline microbiome differences between ICI Rs and NRs are not enough to predict outcomes. Diversity changes between baseline and wk-4 on treatment could be an early predictor of response. Factors other than presence of Akkermansia (tumor or host-specific, Akkermansia strain variation, or other bacteria in the microenvironment) may contribute to response. Further species and strain-level profiling of the microbiota, tumor-specific genomic alterations, host immune response, and increasing sample size of ICI-treated patients may improve detection of significant differences between Rs and NRs.
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Abstract
BACKGROUND Living with alopecia areata (AA) totalis and universalis (collectively referred to here as AA) involves unpredictable, sometimes rapid hair loss. There is currently no effective treatment and patients describe feelings of shock, loss, trauma and disrupted identity. Cultural meanings attached to hair and hair loss, including associations between hair and femininity, and hair loss and cancer may exacerbate distress. Consequently, wigs and make-up are frequently used as camouflage, but this can produce feelings of inauthenticity, shame and anxiety. OBJECTIVES This article explores how meanings associated with hair and hair loss influence experiences of living with AA. We also aim to identify how this understanding might inform practice by healthcare professionals to best support patients to cope with the condition. METHODS A total of 95 participants with AA completed an online qualitative survey about their experiences of living with the condition. Data were subjected to thematic analysis within a critical realist theoretical framework. RESULTS The following four themes were identified: (i) It's (not) only hair; (ii) A restricted life; (iii) Abandon hope all ye who lose their hair and (iv) Seeking support in 'a highly personal journey'. CONCLUSIONS Findings suggest that negative cultural meanings of hair and hair loss are pervasive and may drive social avoidance and camouflage behaviours in people with AA. Normalizing social interactions with healthcare practitioners, significant others and peers were cited as pivotal to positive adjustment. Support groups and online forums were highly valued particularly as few had been offered specialist psychological support. Future research should develop and evaluate psychological support in order to address the specific challenges of living with AA.
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Affiliation(s)
- L Davey
- Centre for Appearance Research, University of the West of England, Bristol, U.K
| | - V Clarke
- Centre for Appearance Research, University of the West of England, Bristol, U.K
| | - E Jenkinson
- Centre for Appearance Research, University of the West of England, Bristol, U.K
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10
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Abstract
Disulfide bonds are a common posttranslational modification that contributes to the folding and stability of extracytoplasmic proteins. Almost all organisms, from eukaryotes to prokaryotes, have evolved enzymes to make and break these bonds. Accurate and efficient disulfide bond formation can be vital for protein function; therefore, the enzymes that catalyze disulfide bond formation are involved in multiple biological processes. Recent advances clearly show that oral bacteria also have the ability to from disulfide bonds, and this ability has an effect on a range of dental plaque-related phenotypes. In the gram-positive Streptococcus gordonii, the ability to form disulfide bonds affected autolysis, extracellular DNA release, biofilm formation, genetic competence, and bacteriocin production. In Actinomyces oris, disulfide bond formation is needed for pilus assembly, coaggregation, and biofilm formation. In other gram-positive bacteria, such as Enterococcus faecalis, disulfide bonds are formed in secreted bacteriocins and required for activity. In these oral bacteria, the enzymes that catalyze the disulfide bonds are quite diverse and share little sequence homology, but all contain a CXXC catalytic active site motif and a conserved C-terminal cis-proline, signature features of a thiol-disulfide oxidoreductase. Emerging evidence also indicates that gram-negative oral bacteria, such as Porphyromonas gingivalis and Tannerella forsythia, use disulfide bonds to stabilize their outer membrane porin proteins. Bioinformatic screens reveal that these gram-negative bacteria carry genes coding for thiol-disulfide oxidoreductases in their genomes. In conclusion, disulfide bond formation in oral bacteria is an emerging field, and the ability to form disulfide bonds plays an important role in dental plaque formation and fitness for the bacteria.
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Affiliation(s)
- S F Lee
- 1 Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada.,2 Canadian Center for Vaccinology, Dalhousie University and the IWK Health Centre, Halifax, NS, Canada.,3 Department of Pediatrics, Faculty of Medicine, Dalhousie University and the IWK Health Centre, Halifax, NS, Canada.,4 Department of Applied Oral Sciences, Faculty of Dentistry, Dalhousie University, Halifax, NS, Canada
| | - L Davey
- 1 Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada.,2 Canadian Center for Vaccinology, Dalhousie University and the IWK Health Centre, Halifax, NS, Canada.,Current address: Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
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Davey L, Halperin SA, Lee SF. Mutation of the Streptococcus gordonii Thiol-Disulfide Oxidoreductase SdbA Leads to Enhanced Biofilm Formation Mediated by the CiaRH Two-Component Signaling System. PLoS One 2016; 11:e0166656. [PMID: 27846284 PMCID: PMC5112981 DOI: 10.1371/journal.pone.0166656] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [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: 08/12/2016] [Accepted: 11/01/2016] [Indexed: 01/11/2023] Open
Abstract
Streptococcus gordonii is a commensal inhabitant of human oral biofilms. Previously, we identified an enzyme called SdbA that played an important role in biofilm formation by S. gordonii. SdbA is thiol-disulfide oxidoreductase that catalyzes disulfide bonds in secreted proteins. Surprisingly, inactivation of SdbA results in enhanced biofilm formation. In this study we investigated the basis for biofilm formation by the ΔsdbA mutant. The results revealed that biofilm formation was mediated by the interaction between the CiaRH and ComDE two-component signalling systems. Although it did not affect biofilm formation by the S. gordonii parent strain, CiaRH was upregulated in the ΔsdbA mutant and it was essential for the enhanced biofilm phenotype. The biofilm phenotype was reversed by inactivation of CiaRH or by the addition of competence stimulating peptide, the production of which is blocked by CiaRH activity. Competition assays showed that the enhanced biofilm phenotype also corresponded to increased oral colonization in mice. Thus, the interaction between SdbA, CiaRH and ComDE affects biofilm formation both in vitro and in vivo.
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Affiliation(s)
- Lauren Davey
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, B3H 1X5, Canada
- Canadian Center for Vaccinology, Dalhousie University and the IWK Health Centre, Halifax, NS, B3K 6R8, Canada
| | - Scott A. Halperin
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, B3H 1X5, Canada
- Canadian Center for Vaccinology, Dalhousie University and the IWK Health Centre, Halifax, NS, B3K 6R8, Canada
- Department of Pediatrics, Faculty of Medicine, Dalhousie University and the IWK Health Centre, Halifax, NS, B3K 6R8, Canada
| | - Song F. Lee
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, B3H 1X5, Canada
- Canadian Center for Vaccinology, Dalhousie University and the IWK Health Centre, Halifax, NS, B3K 6R8, Canada
- Department of Pediatrics, Faculty of Medicine, Dalhousie University and the IWK Health Centre, Halifax, NS, B3K 6R8, Canada
- Department of Applied Oral Sciences, Faculty of Dentistry, Dalhousie University, Halifax, NS, B3H 4R2, Canada
- * E-mail:
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Davey L, Halperin SA, Lee SF. Thiol-Disulfide Exchange in Gram-Positive Firmicutes. Trends Microbiol 2016; 24:902-915. [PMID: 27426970 DOI: 10.1016/j.tim.2016.06.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/08/2016] [Accepted: 06/28/2016] [Indexed: 11/17/2022]
Abstract
Extracytoplasmic thiol-disulfide oxidoreductases (TDORs) catalyze the oxidation, reduction, and isomerization of protein disulfide bonds. Although these processes have been characterized in Gram-negative bacteria, the majority of Gram-positive TDORs have only recently been discovered. Results from recent studies have revealed distinct trends in the types of TDOR used by different groups of Gram-positive bacteria, and in their biological functions. Actinobacteria TDORs can be essential for viability, while Firmicute TDORs influence various physiological processes, including protein stability, oxidative stress resistance, bacteriocin production, and virulence. In this review we discuss the diverse extracytoplasmic TDORs used by Gram-positive bacteria, with a focus on Gram-positive Firmicutes.
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Affiliation(s)
- Lauren Davey
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, B3H 1X5 Canada; Canadian Center for Vaccinology, Dalhousie University and the IWK Health Centre, Halifax, NS, B3K 6R8 Canada
| | - Scott A Halperin
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, B3H 1X5 Canada; Canadian Center for Vaccinology, Dalhousie University and the IWK Health Centre, Halifax, NS, B3K 6R8 Canada; Department of Pediatrics, Faculty of Medicine, Dalhousie University and the IWK Health Centre, Halifax, NS, B3K 6R8 Canada
| | - Song F Lee
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, B3H 1X5 Canada; Canadian Center for Vaccinology, Dalhousie University and the IWK Health Centre, Halifax, NS, B3K 6R8 Canada; Department of Pediatrics, Faculty of Medicine, Dalhousie University and the IWK Health Centre, Halifax, NS, B3K 6R8 Canada; Department of Applied Oral Sciences, Faculty of Dentistry, Dalhousie University, Halifax, NS, B3H 4R2 Canada.
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13
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Davey L, Cohen A, LeBlanc J, Halperin SA, Lee SF. The disulfide oxidoreductase SdbA is active in Streptococcus gordonii using a single C-terminal cysteine of the CXXC motif. Mol Microbiol 2015; 99:236-53. [PMID: 26395460 DOI: 10.1111/mmi.13227] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2015] [Indexed: 12/31/2022]
Abstract
Recently, we identified a novel disulfide oxidoreductase, SdbA, in the oral bacterium Streptococcus gordonii. Disulfide oxidoreductases form disulfide bonds in nascent proteins using a CXXC catalytic motif. Typically, the N-terminal cysteine interacts with substrates, whereas the C-terminal cysteine is buried and only reacts with the first cysteine of the motif. In this study, we investigated the SdbA C(86) P(87) D(88) C(89) catalytic motif. In vitro, SdbA single cysteine variants at the N or C-terminal position (SdbAC86P and SdbAC89A ) were active but displayed different susceptibility to oxidation, and N-terminal cysteine was prone to sulfenylation. In S. gordonii, mutants with a single N-terminal cysteine were inactive and formed unstable disulfide adducts with other proteins. Activity was partially restored by inactivation of pyruvate oxidase, a hydrogen peroxide generator. Presence of the C-terminal cysteine alone (in the SdbAC86P variant) could complement the ΔsdbA mutant and restore disulfide bond formation in recombinant and natural protein substrates. These results provide evidence that certain disulfide oxidoreductases can catalyze disulfide bond formation using a single cysteine of the CXXC motif, including the buried C-terminal cysteine.
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Affiliation(s)
- Lauren Davey
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, B3H 1X5, Canada.,Canadian Center for Vaccinology (CCfV), Dalhousie University and the Izaak Walton Killam (IWK) Health Centre, Halifax, NS, Canada
| | - Alejandro Cohen
- Proteomics and Mass Spectrometry Core Facility, Life Sciences Research Institute, Dalhousie University, Halifax, NS, Canada
| | - Jason LeBlanc
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, B3H 1X5, Canada.,Department of Pathology, Dalhousie University, Halifax, NS, Canada.,Department of Pathology and Laboratory Medicine, Nova Scotia Health Authority (NSHA), Halifax, NS, Canada
| | - Scott A Halperin
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, B3H 1X5, Canada.,Canadian Center for Vaccinology (CCfV), Dalhousie University and the Izaak Walton Killam (IWK) Health Centre, Halifax, NS, Canada.,Department of Pediatrics, Faculty of Medicine, Dalhousie University and the IWK Health Centre, Halifax, NS, Canada
| | - Song F Lee
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, B3H 1X5, Canada.,Canadian Center for Vaccinology (CCfV), Dalhousie University and the Izaak Walton Killam (IWK) Health Centre, Halifax, NS, Canada.,Department of Pediatrics, Faculty of Medicine, Dalhousie University and the IWK Health Centre, Halifax, NS, Canada.,Department of Applied Oral Sciences, Faculty of Dentistry, Dalhousie University, Halifax, NS, Canada
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14
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Davey L, Halperin SA, Lee SF. Immunoblotting conditions for small peptides from streptococci. J Microbiol Methods 2015; 114:40-2. [PMID: 25937086 DOI: 10.1016/j.mimet.2015.04.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 04/29/2015] [Accepted: 04/30/2015] [Indexed: 11/19/2022]
Abstract
Streptococci secrete small peptides with important biological functions. These peptides are not amenable to standard immunoblotting, and are often detected indirectly using activity assays, or by alternative approaches that may be expensive and laborious. Here we describe an immunoblotting method that enables reproducible detection of these small streptococcal peptides.
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Affiliation(s)
- Lauren Davey
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS B3H 1X5, Canada; Canadian Center for Vaccinology, Dalhousie University, IWK Health Centre, Halifax, NS B3K 6R8, Canada
| | - Scott A Halperin
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS B3H 1X5, Canada; Canadian Center for Vaccinology, Dalhousie University, IWK Health Centre, Halifax, NS B3K 6R8, Canada; Department of Pediatrics, Faculty of Medicine, Dalhousie University, IWK Health Centre, Halifax, NS B3K 6R8, Canada
| | - Song F Lee
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS B3H 1X5, Canada; Canadian Center for Vaccinology, Dalhousie University, IWK Health Centre, Halifax, NS B3K 6R8, Canada; Department of Pediatrics, Faculty of Medicine, Dalhousie University, IWK Health Centre, Halifax, NS B3K 6R8, Canada; Department of Applied Oral Sciences, Faculty of Dentistry, Dalhousie University, Halifax, NS B3H 4R2, Canada.
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15
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Zhu J, Kato H, Fu Y, Foreman C, Davey L, Van Arsdell G, Weisel R, Honjo O. A Pre-Clinical Animal Model of Mechanical Circulatory Support for Failing Single Ventricle Physiology: A Pilot Study. Can J Cardiol 2013. [DOI: 10.1016/j.cjca.2013.07.347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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16
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Abstract
Disulfide bonds are important for the stability of many extracellular proteins, including bacterial virulence factors. Formation of these bonds is catalyzed by thiol-disulfide oxidoreductases (TDORs). Little is known about their formation in Gram-positive bacteria, particularly among facultative anaerobic Firmicutes, such as streptococci. To investigate disulfide bond formation in Streptococcus gordonii, we identified five putative TDORs from the sequenced genome. Each of the putative TDOR genes was insertionally inactivated with an erythromycin resistance cassette, and the mutants were analyzed for autolysis, extracellular DNA release, biofilm formation, bacteriocin production, and genetic competence. This analysis revealed a single TDOR, SdbA, which exhibited a pleiotropic mutant phenotype. Using an in silico analysis approach, we identified the major autolysin AtlS as a natural substrate of SdbA and showed that SdbA is critical to the formation of a disulfide bond that is required for autolytic activity. Analysis by BLAST search revealed homologs to SdbA in other Gram-positive species. This study provides the first in vivo evidence of an oxidoreductase, SdbA, that affects multiple phenotypes in a Gram-positive bacterium. SdbA shows low sequence homology to previously identified oxidoreductases, suggesting that it may belong to a different class of enzymes. Our results demonstrate that SdbA is required for disulfide bond formation in S. gordonii and indicate that this enzyme may represent a novel type of oxidoreductase in Gram-positive bacteria.
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Affiliation(s)
- Lauren Davey
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia B3H 1X5, Canada; Canadian Center for Vaccinology, Dalhousie University and the Izaak Walton Killam Health Centre, Halifax, Nova Scotia B3K 6R8, Canada
| | - Crystal K W Ng
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia B3H 1X5, Canada; Canadian Center for Vaccinology, Dalhousie University and the Izaak Walton Killam Health Centre, Halifax, Nova Scotia B3K 6R8, Canada
| | - Scott A Halperin
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia B3H 1X5, Canada; Canadian Center for Vaccinology, Dalhousie University and the Izaak Walton Killam Health Centre, Halifax, Nova Scotia B3K 6R8, Canada; Department of Pediatrics, Faculty of Medicine, Dalhousie University and the Izaak Walton Killam Health Centre, Halifax, Nova Scotia B3K 6R8, Canada
| | - Song F Lee
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia B3H 1X5, Canada; Canadian Center for Vaccinology, Dalhousie University and the Izaak Walton Killam Health Centre, Halifax, Nova Scotia B3K 6R8, Canada; Department of Pediatrics, Faculty of Medicine, Dalhousie University and the Izaak Walton Killam Health Centre, Halifax, Nova Scotia B3K 6R8, Canada; Department of Applied Oral Sciences, Faculty of Dentistry, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada.
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Rodriguez E, Bober MB, Davey L, Zamora A, Li Puma AB, Chidekel A, Shaffer TH. Respiratory mechanics in an infant with perinatal lethal hypophosphatasia treated with human recombinant enzyme replacement therapy. Pediatr Pulmonol 2012; 47:917-22. [PMID: 22328548 DOI: 10.1002/ppul.22527] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 11/24/2011] [Indexed: 11/09/2022]
Abstract
Hypophosphatasia is a rare autosomal recessive disorder caused by deficient activity of tissue nonspecific alkaline phosphatase (TNSALP) and characterized by defective bone mineralization. In the perinatal lethal form, respiratory complications due to rachitic deformities of the thoracic cage and associated hypoplastic lungs are present. ENB-0040 is a bone-targeted human recombinant TNSALP fusion protein that aims to restore skeletal mineralization. The goal of this study was to characterize pulmonary and thoracic cage mechanics in an infant with the perinatal lethal form of hypophosphatasia under enzyme replacement therapy. Pulmonary function testing was performed on a preterm, 8-week-old patient with hypophosphatasia who was mechanically ventilated since birth because of severe chest wall insufficiency. The measurements consisted of respiratory impulse oscillation measurements (resistance and reactance), ventilatory mechanics (compliance and resistance), and thoracoabdominal motion (TAM) analysis. At baseline, chest wall compliance was 50% of normal, and the TAM indicated predominantly abdominal displacement. After 12 weeks of treatment, a consistent decrease in ventilator requirements and improvement in lung function and chest wall mechanics were observed and correlated with thoracic cage radiologic findings. Measurable changes in chest wall dynamics and respiratory mechanics using noninvasive technology were useful for respiratory management and therapeutic guidance of ENB-0040 treatment in this patient.
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Affiliation(s)
- Elena Rodriguez
- Nemours Research Lung Center, Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA.
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Kurissery SR, Kanavillil N, Leung KT, Chen A, Davey L, Schraft H. Electrochemical and microbiological characterization of paper mill biofilms. Biofouling 2010; 26:799-808. [PMID: 20835930 DOI: 10.1080/08927014.2010.519025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Biofilm samples collected from inside and outside the press and former sections of paper machines in a Northwestern Ontario paper mill for a period of 2 years were characterized microbiologically and electrochemically. Bacterial community profiling was done using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and selected bacterial isolates were identified using 16S rDNA analysis. The bacterial community showed the presence of Proteobacteria, Firmicutes, and Actinobacteria. Sphingomonas sp. was found to be the most common bacterial species, which showed the highest production of extracellular polymeric substances. Bacteria isolated from biofilms showed better adhesion properties than those from water samples. Cyclic voltammetry and electrochemical impedance spectroscopy studies showed that bacteria isolated from biofilms and feed water collected from inside the machine were more easily oxidized than those from outside, suggesting the need for a more rigorous biofilm abatement strategy for inside paper machines.
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Affiliation(s)
- S R Kurissery
- Department of Interdisciplinary Studies, Lakehead University, Orillia Campus, Orillia, ON, Canada
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Tian M, Kanavillil N, Davey L, Leung K, Schraft H, Chen A. Direct growth of biofilms on an electrode surface and its application in electrochemical biosensoring. J Electroanal Chem (Lausanne) 2007. [DOI: 10.1016/j.jelechem.2007.08.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Smith G, Mooney D, Davey L, Nebo L, Irwin ME, Senaratne MP. Efficiency and cost saving of 7 day per week exercise testing utilizing all electrocardiography technologists. Ann Noninvasive Electrocardiol 2006; 6:32-7. [PMID: 11174860 PMCID: PMC7027605 DOI: 10.1111/j.1542-474x.2001.tb00083.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND In most centers, exercise testing (ET) is performed by one or two trained technologists during the weekdays (0800 hours-1600 hours), leaving a void during evenings and weekends. This leads to unnecessary increased costs due to delays in management of patients. Electrocardiography technologists (ECGT) are often available for extended hours. This project was undertaken to improve the efficiency of the ET laboratory by using ECGT to perform ET during these extended hours. METHODS Clinical utility and cost saving of a 7 day per week ET for management of patients with suspected and/or known coronary artery disease utilizing ECGT was assessed after adequate training. Of 4099 patients undergoing ET between January 1995 and December 1997, 810 tests performed by ECGT were reviewed retrospectively. RESULTS Of the 810 patients (age mean 58.4 +/- 0.44 yrs; range 16-88; males: 508, females: 302), 806 (99.5%) underwent the Bruce protocol. The indications were: diagnostic, 61.3%, predischarge acute myocardial infarction (AMI), 17.7%, evaluation of angina, 19.6%, other, 1.4%. Only 8 (0.1%) patients had complications (prolonged chest pain, 6; nonsustained ventricular tachycardia, 2) with no AMIs or deaths. This strategy resulted in a savings of 158 bed days (Can189,600 dollars) on inpatients and 15 bed days (Can18,000 dollars) on those presenting to the emergency department. CONCLUSIONS This study demonstrates the feasibility and safety of utilizing ECGT for ET thus extending the hours of service. This resulted in efficient patient management, with a considerable cost-saving to the hospital.
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Affiliation(s)
- G Smith
- Division of Cardiac Sciences, Grey Nuns Hospital, 1100 Youville Drive West, Edmonton, Alberta, Canada, T6L 5X8
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Affiliation(s)
| | - J.M. Solomon
- DipPractitioner Research, is senior nurse, research and development
| | - S.F. Freeborn
- Director of pharmacy, Bolton Hospitals NHS Trust. Bolton
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Davey L, Naidoo D. Urinary screen for acetaminophen (paracetamol) in the presence of N-acetylcysteine. Clin Chem 1993; 39:2348-9. [PMID: 8222238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Faust D, Guilmette TJ, Hart K, Arkes HR, Fishburne FJ, Davey L. Neuropsychologists' training, experience, and judgment accuracy. Arch Clin Neuropsychol 1988. [DOI: 10.1093/arclin/3.2.145] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Faust D, Guilmette TJ, Hart K, Arkes HR, Fishburne FJ, Davey L. Neuropsychologists' training, experience, and judgment accuracy. Arch Clin Neuropsychol 1988; 3:145-63. [PMID: 14591267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023] Open
Abstract
It is often assumed that judgment accuracy improves as clinical training and experience increase, but the few studies on this topic within neuropsychology have yielded negative findings. In an extension of prior research, we obtained information on background training and experience from a nationally representative sample of clinical neuropsychologists and had each practitioner appraise one from among a series of 10 cases. Except for a possible tendency among more experienced practitioners to overdiagnose abnormality, no systematic relations were obtained between training, experience, and accuracy across a series of neuropsychologic judgments. Comparable results were obtained when analysis was limited to the top versus bottom 20% of the sample. This and other studies raise doubt that clinical neuropsychologists train and practice under conditions conducive to experiential learning. The potential benefits of further research on experience and judgment accuracy are discussed.
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