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Allegretti JR, Kelly CR, Grinspan A, Mullish BH, Hurtado J, Carrellas M, Marcus J, Marchesi JR, McDonald JAK, Gerardin Y, Silverstein M, Pechlivanis A, Barker GF, Miguens Blanco J, Alexander JL, Gallagher KI, Pettee W, Phelps E, Nemes S, Sagi SV, Bohm M, Kassam Z, Fischer M. Inflammatory Bowel Disease Outcomes Following Fecal Microbiota Transplantation for Recurrent C. difficile Infection. Inflamm Bowel Dis 2021; 27:1371-1378. [PMID: 33155639 PMCID: PMC8376126 DOI: 10.1093/ibd/izaa283] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [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: 08/02/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND Recurrent Clostridioides difficile infection (CDI) in patients with inflammatory bowel disease (IBD) is a clinical challenge. Fecal microbiota transplantation (FMT) has emerged as a recurrent CDI therapy. Anecdotal concerns exist regarding worsening of IBD activity; however, prospective data among IBD patients are limited. METHODS Secondary analysis from an open-label, prospective, multicenter cohort study among IBD patients with 2 or more CDI episodes was performed. Participants underwent a single FMT by colonoscopy (250 mL, healthy universal donor). Secondary IBD-related outcomes included rate of de novo IBD flares, worsening IBD, and IBD improvement-all based on Mayo or Harvey-Bradshaw index (HBI) scores. Stool samples were collected for microbiome and targeted metabolomic profiling. RESULTS Fifty patients enrolled in the study, among which 15 had Crohn's disease (mean HBI, 5.8 ± 3.4) and 35 had ulcerative colitis (mean partial Mayo score, 4.2 ± 2.1). Overall, 49 patients received treatment. Among the Crohn's disease cohort, 73.3% (11 of 15) had IBD improvement, and 4 (26.6%) had no disease activity change. Among the ulcerative colitis cohort, 62% (22 of 34) had IBD improvement, 29.4% (11 of 34) had no change, and 4% (1 of 34) experienced a de novo flare. Alpha diversity significantly increased post-FMT, and ulcerative colitis patients became more similar to the donor than Crohn's disease patients (P = 0.04). CONCLUSION This prospective trial assessing FMT in IBD-CDI patients suggests IBD outcomes are better than reported in retrospective studies.
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Affiliation(s)
- Jessica R Allegretti
- Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Colleen R Kelly
- Division of Gastroenterology, Alpert Medical School of Brown University, Providence, RI, USA
| | - Ari Grinspan
- The Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Benjamin H Mullish
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Jonathan Hurtado
- Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women’s Hospital, Boston, MA, USA
| | - Madeline Carrellas
- Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women’s Hospital, Boston, MA, USA
| | - Jenna Marcus
- Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women’s Hospital, Boston, MA, USA
| | - Julian R Marchesi
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
- School of Biosciences, Cardiff University, Cardiff, UK
| | - Julie A K McDonald
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | | | | | - Alexandros Pechlivanis
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
- Center for Interdisciplinary Research and Innovation, School of Chemistry, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Grace F Barker
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Jesus Miguens Blanco
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - James L Alexander
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Kate I Gallagher
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | | | - Emmalee Phelps
- Division of Gastroenterology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Sara Nemes
- Division of Gastroenterology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Sashidhar V Sagi
- Division of Gastroenterology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Matthew Bohm
- Division of Gastroenterology, Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Monika Fischer
- Division of Gastroenterology, Indiana University School of Medicine, Indianapolis, IN, USA
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Shao DD, Straussberg R, Ahmed H, Khan A, Tian S, Hill RS, Smith RS, Majmundar AJ, Ameziane N, Neil JE, Yang E, Al Tenaiji A, Jamuar SS, Schlaeger TM, Al-Saffar M, Hovel I, Al-Shamsi A, Basel-Salmon L, Amir AZ, Rento LM, Lim JY, Ganesan I, Shril S, Evrony G, Barkovich AJ, Bauer P, Hildebrandt F, Dong M, Borck G, Beetz C, Al-Gazali L, Eyaid W, Walsh CA. A recurrent, homozygous EMC10 frameshift variant is associated with a syndrome of developmental delay with variable seizures and dysmorphic features. Genet Med 2021; 23:1158-1162. [PMID: 33531666 PMCID: PMC8187145 DOI: 10.1038/s41436-021-01097-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 08/07/2020] [Revised: 12/28/2020] [Accepted: 01/04/2021] [Indexed: 01/10/2023] Open
Abstract
PURPOSE The endoplasmic reticulum membrane complex (EMC) is a highly conserved, multifunctional 10-protein complex related to membrane protein biology. In seven families, we identified 13 individuals with highly overlapping phenotypes who harbor a single identical homozygous frameshift variant in EMC10. METHODS Using exome, genome, and Sanger sequencing, a recurrent frameshift EMC10 variant was identified in affected individuals in an international cohort of consanguineous families. Multiple families were independently identified and connected via Matchmaker Exchange and internal databases. We assessed the effect of the frameshift variant on EMC10 RNA and protein expression and evaluated EMC10 expression in normal human brain tissue using immunohistochemistry. RESULTS A homozygous variant EMC10 c.287delG (Refseq NM_206538.3, p.Gly96Alafs*9) segregated with affected individuals in each family, who exhibited a phenotypic spectrum of intellectual disability (ID) and global developmental delay (GDD), variable seizures and variable dysmorphic features (elongated face, curly hair, cubitus valgus, and arachnodactyly). The variant arose on two founder haplotypes and results in significantly reduced EMC10 RNA expression and an unstable truncated EMC10 protein. CONCLUSION We propose that a homozygous loss-of-function variant in EMC10 causes a novel syndromic neurodevelopmental phenotype. Remarkably, the recurrent variant is likely the result of a hypermutable site and arose on distinct founder haplotypes.
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Affiliation(s)
- Diane D Shao
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Rachel Straussberg
- Neurogenetics Clinic, Neurology Unit, Schneider Children Medical Center, Petah Tikvah, Israel
- Sackler School of Medicine, Tel Aviv University, Ramat Aviv, Israel
| | - Hind Ahmed
- Genetics Division, Department of Pediatrics, King Abdullah International Medical Research Centre, King Saud bin Abdulaziz University for Health Science, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia
| | - Amjad Khan
- Genetics Division, Department of Pediatrics, King Abdullah International Medical Research Centre, King Saud bin Abdulaziz University for Health Science, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia
| | - Songhai Tian
- Department of Urology, Boston Children's Hospital, and Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - R Sean Hill
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
| | - Richard S Smith
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Amar J Majmundar
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | | | - Jennifer E Neil
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
| | - Edward Yang
- Department of Radiology, Boston Children's Hospital, Boston, MA, USA
| | - Amal Al Tenaiji
- Medical Institute of Medical Affairs, Sheikh Khalifa Medica City, Abu Dhabi, UAE
| | - Saumya S Jamuar
- Department of Pediatrics, KK Women's and Children's Hospital, Ramat Aviv, Israel
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Singapore
| | - Thorsten M Schlaeger
- Stem Cell Program, Boston Children's Hospital, Harvard Medical School, and Harvard Stem Cell Institute, Harvard University, Boston, MA, USA
| | - Muna Al-Saffar
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, United Arab Emirates University, Abu Dhabi, UAE
| | | | - Aisha Al-Shamsi
- Division of Genetics, Department of Pediatrics, Tawam Hospital, Al Ain, UAE
| | - Lina Basel-Salmon
- Sackler School of Medicine, Tel Aviv University, Ramat Aviv, Israel
- Raphael Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital and Pediatric Genetics Clinic, Schneider Children's Medical Center, and Felsenstein Medical Research Center, Petah Tikvah, Israel
| | - Achiya Z Amir
- Sackler School of Medicine, Tel Aviv University, Ramat Aviv, Israel
- Pediatric Gastroenterology, Hepatology and Nutrition Clinic, Dana-Dwek Children's Hospital, Tel Aviv Medical Center, Ramat Aviv, Israel
| | - Lariza M Rento
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
| | - Jiin Ying Lim
- Department of Pediatrics, KK Women's and Children's Hospital, Ramat Aviv, Israel
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Singapore
| | - Indra Ganesan
- Department of Pediatrics, KK Women's and Children's Hospital, Ramat Aviv, Israel
| | - Shirlee Shril
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Gilad Evrony
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- New York University School of Medicine, Center for Human Genetics & Genomics, New York, NY, USA
| | - A James Barkovich
- Neuroradiology, University of California at San Francisco, San Francisco, CA, USA
| | | | - Friedhelm Hildebrandt
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Min Dong
- Department of Urology, Boston Children's Hospital, and Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Guntram Borck
- Center for Rare Diseases (ZSE Ulm), Ulm University Medical Center, Ulm, Germany
- genetikum, Neu-Ulm, Germany
| | | | - Lihadh Al-Gazali
- Department of Pediatrics, United Arab Emirates University, Al Ain, UAE
| | - Wafaa Eyaid
- Genetics Division, Department of Pediatrics, King Abdullah International Medical Research Centre, King Saud bin Abdulaziz University for Health Science, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia
| | - Christopher A Walsh
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA.
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA.
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Ziesack M, Gibson T, Oliver JKW, Shumaker AM, Hsu BB, Riglar DT, Giessen TW, DiBenedetto NV, Bry L, Way JC, Silver PA, Gerber GK. Engineered Interspecies Amino Acid Cross-Feeding Increases Population Evenness in a Synthetic Bacterial Consortium. mSystems 2019; 4:e00352-19. [PMID: 31409662 PMCID: PMC6697442 DOI: 10.1128/msystems.00352-19] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 07/23/2019] [Indexed: 01/15/2023] Open
Abstract
In nature, microbes interact antagonistically, neutrally, or beneficially. To shed light on the effects of positive interactions in microbial consortia, we introduced metabolic dependencies and metabolite overproduction into four bacterial species. While antagonistic interactions govern the wild-type consortium behavior, the genetic modifications alleviated antagonistic interactions and resulted in beneficial interactions. Engineered cross-feeding increased population evenness, a component of ecological diversity, in different environments, including in a more complex gnotobiotic mouse gut environment. Our findings suggest that metabolite cross-feeding could be used as a tool for intentionally shaping microbial consortia in complex environments.IMPORTANCE Microbial communities are ubiquitous in nature. Bacterial consortia live in and on our body and in our environment, and more recently, biotechnology is applying microbial consortia for bioproduction. As part of our body, bacterial consortia influence us in health and disease. Microbial consortium function is determined by its composition, which in turn is driven by the interactions between species. Further understanding of microbial interactions will help us in deciphering how consortia function in complex environments and may enable us to modify microbial consortia for health and environmental benefits.
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Affiliation(s)
- Marika Ziesack
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, Massachusetts, USA
| | - Travis Gibson
- Massachusetts Host-Microbiome Center, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - John K W Oliver
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, Massachusetts, USA
| | - Andrew M Shumaker
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, Massachusetts, USA
| | - Bryan B Hsu
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - David T Riglar
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, Massachusetts, USA
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Tobias W Giessen
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Nicholas V DiBenedetto
- Massachusetts Host-Microbiome Center, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Lynn Bry
- Massachusetts Host-Microbiome Center, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jeffrey C Way
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, Massachusetts, USA
| | - Pamela A Silver
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, Massachusetts, USA
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Georg K Gerber
- Massachusetts Host-Microbiome Center, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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