1
|
Ramos RJ, Zhu C, Joseph DF, Thaker S, Lacomb JF, Markarian K, Lee HJ, Petrov JC, Monzur F, Buscaglia JM, Chawla A, Small-Harary L, Gathungu G, Morganstern JA, Yang J, Li J, Pamer EG, Robertson CE, Frank DN, Cross JR, Li E. Metagenomic and bile acid metabolomic analysis of fecal microbiota transplantation for recurrent Clostridiodes difficile and/or inflammatory bowel diseases. Med Res Arch 2022; 10:10.18103/mra.v10i10.3318. [PMID: 36618438 PMCID: PMC9817289 DOI: 10.18103/mra.v10i10.3318] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
BACKGROUND Fecal microbiota transplantation (FMT) is an effective treatment of recurrent Clostridioides difficile infections (rCDI), but has more limited efficacy in treating either ulcerative colitis (UC) or Crohn's disease (CD), two major forms of inflammatory bowel diseases (IBD). We hypothesize that FMT recipients with rCDI and/or IBD have baseline fecal bile acid (BA) compositions that differ significantly from that of their healthy donors and that FMT will normalize the BA compositions. AIM To study the effect of single colonoscopic FMT on microbial composition and function in four recipient groups: 1.) rCDI patients without IBD (rCDI-IBD); 2.) rCDI with IBD (rCDI+IBD); 3.) UC patients without rCDI (UC-rCDI); 4.) CD patients without rCDI (CD-rCDI). METHODS We performed 16S rRNA gene sequence, shotgun DNA sequence and quantitative bile acid metabolomic analyses on stools collected from 55 pairs of subjects and donors enrolled in two prospective single arm FMT clinical trials (Clinical Trials.gov ID NCT03268213, 479696, UC no rCDI ≥ 2x IND 1564 and NCT03267238, IND 16795). Fitted linear mixed models were used to examine the effects of four recipient groups, FMT status (Donor, pre-FMT, 1-week post-FMT, 3-months post-FMT) and first order Group*FMT interactions on microbial diversity and composition, bile acid metabolites and bile acid metabolizing enzyme gene abundance. RESULTS The pre-FMT stools collected from rCDI ± IBD recipients had reduced α-diversity compared to the healthy donor stools and was restored post-FMT. The α-diversity in the pre-FMT stools collected from UC-rCDI or CD-rCDI recipients did not differ significantly from donor stools. FMT normalized some recipient/donor ratios of genus level taxa abundance in the four groups. Fecal secondary BA levels, including some of the secondary BA epimers that exhibit in vitro immunomodulatory activities, were lower in rCDI±IBD and CD-rCDI but not UC-rCDI recipients compared to donors. FMT restored secondary BA levels. Metagenomic baiE gene and some of the eight bile salt hydrolase (BSH) phylotype abundances were significantly correlated with fecal BA levels. CONCLUSION Restoration of multiple secondary BA levels, including BA epimers implicated in immunoregulation, are associated with restoration of fecal baiE gene counts, suggesting that the 7-α-dehydroxylation step is rate-limiting.
Collapse
|
2
|
Li E, Zhang Y, Tian X, Wang X, Gathungu G, Wolber A, Shiekh SS, Sartor RB, Davidson NO, Ciorba MA, Zhu W, Nelson LM, Robertson CE, Frank DN. Influence of Crohn's disease related polymorphisms in innate immune function on ileal microbiome. PLoS One 2019; 14:e0213108. [PMID: 30818349 PMCID: PMC6395037 DOI: 10.1371/journal.pone.0213108] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 11/14/2018] [Accepted: 02/14/2019] [Indexed: 12/13/2022] Open
Abstract
We have previously identified NOD2 genotype and inflammatory bowel diseases (IBD) phenotype, as associated with shifts in the ileal microbiome ("dysbiosis") in a patient cohort. Here we report an integrative analysis of an expanded number of Crohn's disease (CD) related genetic defects in innate immune function (NOD2, ATG16L1, IRGM, CARD9, XBP1, ORMDL3) and composition of the ileal microbiome by combining the initial patient cohort (Batch 1, 2005-2010, n = 165) with a second consecutive patient cohort (Batch 2, 2010-2012, n = 118). These combined patient cohorts were composed of three non-overlapping phenotypes: 1.) 106 ileal CD subjects undergoing initial ileocolic resection for diseased ileum, 2.) 88 IBD colitis subjects without ileal disease (predominantly ulcerative colitis but also Crohn's colitis and indeterminate colitis, and 3.) 89 non-IBD subjects. Significant differences (FDR < 0.05) in microbiota were observed between macroscopically disease unaffected and affected regions of resected ileum in ileal CD patients. Accordingly, analysis of the effects of genetic and clinical factors were restricted to disease unaffected regions of the ileum. Beta-diversity differed across the three disease categories by PERMANOVA (p < 0.001), whereas no significant differences in alpha diversity were noted. Using negative binomial models, we confirmed significant effects of IBD phenotype, C. difficile infection, and NOD2 genotype on ileal dysbiosis in the expanded analysis. The relative abundance of the Proteobacteria phylum was positively associated with ileal CD and colitis phenotypes, but negatively associated with NOD2R genotype. Additional associations with ORMDL3 and XBP1 were detected at the phylum/subphylum level. IBD medications, such as immunomodulators and anti-TNFα agents, may have a beneficial effect on reversing dysbiosis associated with the IBD phenotype. Exploratory analysis comparing microbial composition of the disease unaffected region of the resected ileum between 27 ileal CD patients who subsequently developed endoscopic recurrence within 6-12 months versus 34 patients who did not, suggested that microbial biomarkers in the resected specimen helped stratify patients with respect to risk of post-surgical recurrence.
Collapse
Affiliation(s)
- Ellen Li
- Department of Medicine, Stony Brook University, Stony Brook, NY, United States of America
| | - Yuanhao Zhang
- Department of Medicine, Stony Brook University, Stony Brook, NY, United States of America
| | - Xinyu Tian
- Department of Medicine, Stony Brook University, Stony Brook, NY, United States of America
| | - Xuefeng Wang
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, United States of America
| | - Grace Gathungu
- Department of Pediatrics, Stony Brook University, Stony Brook, NY, United States of America
| | - Ashley Wolber
- Department of Medicine, University of North Carolina, Chapel Hill, NC, United States of America
| | - Shehzad S. Shiekh
- Department of Medicine, University of North Carolina, Chapel Hill, NC, United States of America
| | - R. Balfour Sartor
- Department of Medicine, University of North Carolina, Chapel Hill, NC, United States of America
| | - Nicholas O. Davidson
- Department of Medicine, Washington University St. Louis, St. Louis, MO, United States of America
| | - Matthew A. Ciorba
- Department of Medicine, Washington University St. Louis, St. Louis, MO, United States of America
| | - Wei Zhu
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, United States of America
| | - Leah M. Nelson
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America
| | - Charles E. Robertson
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America
| | - Daniel N. Frank
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America
| |
Collapse
|
3
|
Gathungu G, Zhang Y, Tian X, Bonkowski E, Rowehl L, Krumsiek J, Nix B, Chalk C, Trapnell B, Zhu W, Newberry R, Denson L, Li E. Impaired granulocyte-macrophage colony-stimulating factor bioactivity accelerates surgical recurrence in ileal Crohn’s disease. World J Gastroenterol 2018; 24:623-630. [PMID: 29434451 PMCID: PMC5799863 DOI: 10.3748/wjg.v24.i5.623] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 12/05/2017] [Accepted: 12/12/2017] [Indexed: 02/06/2023] Open
Abstract
AIM To examine the relationship between elevated granulocyte-macrophage colony-stimulating factor (GM-CSF) auto-antibodies (Ab) level and time to surgical recurrence after initial surgery for Crohn’s disease (CD).
METHODS We reviewed 412 charts from a clinical database at tertiary academic hospital. Patients included in the study had ileal or ileocolonic CD and surgical resection of small bowel or ileocecal region for management of disease. Serum samples were analyzed for serological assays including GM-CSF cytokine, GM-CSF Ab, ASCA IgG and IgA, and genetic markers including SNPs rs2066843, rs2066844, rs2066845, rs2076756 and rs2066847 in NOD2, rs2241880 in ATG16L1, and rs13361189 in IRGM. Cox proportional-hazards models were used to assess the predictors of surgical recurrence.
RESULTS Ninety six percent of patients underwent initial ileocecal resection (ICR) or ileal resection (IR) and subsequently 40% of patients required a second ICR/IR for CD. GM-CSF Ab level was elevated at a median of 3.81 mcg/mL. Factors predicting faster time to a second surgery included elevated GM-CSF Ab [hazard ratio (HR) 3.52, 95%CI: 1.45-8.53, P = 0.005] and elevated GM-CSF cytokine (HR = 2.48, 95%CI: 1.31-4.70, P = 0.005). Factors predicting longer duration between first and second surgery included use of Immunomodulators (HR = 0.49, 95%CI: 0.31-0.77, P = 0.002), the interaction effect of low GM-CSF Ab levels and smoking (HR = 0.60, 95%CI: 0.45-0.81, P = 0.001) and the interaction effect of low GM-CSF cytokine levels and ATG16L1 (HR = 0.65, 95%CI: 0.49-0.88, P = 0.006).
CONCLUSION GM-CSF bioavailability plays a critical role in maintaining intestinal homeostasis. Decreased bioavailability coupled with the genetic risk markers and/or smoking results in aggressive CD behavior.
Collapse
Affiliation(s)
- Grace Gathungu
- Department of Pediatrics, Division of Pediatric Gastroenterology, Stony Brook University, Stony Brook, NY 11794, United States
| | - Yuanhao Zhang
- Department of Medicine, Division of Gastroenterology, Stony Brook University, Stony Brook, NY 11794, United States
| | - Xinyu Tian
- Department of Medicine, Division of Gastroenterology, Stony Brook University, Stony Brook, NY 11794, United States
| | - Erin Bonkowski
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229-3026, United States
| | - Leahana Rowehl
- Department of Medicine, Division of Gastroenterology, Stony Brook University, Stony Brook, NY 11794, United States
| | - Julia Krumsiek
- Department of Pediatrics, Division of Pediatric Gastroenterology, Stony Brook University, Stony Brook, NY 11794, United States
| | - Billy Nix
- Department of Medicine, Washington University St. Louis, St. Louis, MO 63110, United States
| | - Claudia Chalk
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229-3026, United States
| | - Bruce Trapnell
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229-3026, United States
| | - Wei Zhu
- Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, United states
| | - Rodney Newberry
- Department of Medicine, Washington University St. Louis, St. Louis, MO 63110, United States
| | - Lee Denson
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229-3026, United States
| | - Ellen Li
- Department of Medicine, Division of Gastroenterology, Stony Brook University, Stony Brook, NY 11794, United States
| |
Collapse
|
4
|
Son JS, Zheng LJ, Rowehl LM, Tian X, Zhang Y, Zhu W, Litcher-Kelly L, Gadow KD, Gathungu G, Robertson CE, Ir D, Frank DN, Li E. Comparison of Fecal Microbiota in Children with Autism Spectrum Disorders and Neurotypical Siblings in the Simons Simplex Collection. PLoS One 2015; 10:e0137725. [PMID: 26427004 PMCID: PMC4591364 DOI: 10.1371/journal.pone.0137725] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 08/21/2015] [Indexed: 12/31/2022] Open
Abstract
In order to assess potential associations between autism spectrum disorder (ASD) phenotype, functional GI disorders and fecal microbiota, we recruited simplex families, which had only a single ASD proband and neurotypical (NT) siblings, through the Simons Simplex Community at the Interactive Autism Network (SSC@IAN). Fecal samples and metadata related to functional GI disorders and diet were collected from ASD probands and NT siblings of ASD probands (age 7-14). Functional gastrointestinal disorders (FGID) were assessed using the parent-completed ROME III questionnaire for pediatric FGIDs, and problem behaviors were assessed using the Child Behavior Check List (CBCL). Targeted quantitative polymerase chain reaction (qPCR) assays were conducted on selected taxa implicated in ASD, including Sutterella spp., Bacteroidetes spp. and Prevotella spp. Illumina sequencing of the V1V2 and the V1V3 regions of the bacterial 16S rRNA genes from fecal DNA was performed to an average depth of 208,000 and 107,000 high-quality reads respectively. Twenty-five of 59 ASD children and 13 of 44 NT siblings met ROME III criteria for at least one FGID. Functional constipation was more prevalent in ASD (17 of 59) compared to NT siblings (6 of 44, P = 0.035). The mean CBCL scores in NT siblings with FGID, ASD children with FGID and ASD without FGID were comparably higher (58-62 vs. 44, P < 0.0001) when compared to NT children without FGID. There was no significant difference in macronutrient intake between ASD and NT siblings. There was no significant difference in ASD severity scores between ASD children with and without FGID. No significant difference in diversity or overall microbial composition was detected between ASD children with NT siblings. Exploratory analysis of the 16S rRNA sequencing data, however, identified several low abundance taxa binned at the genus level that were associated with ASD and/or first order ASD*FGID interactions (FDR <0.1).
Collapse
Affiliation(s)
- Joshua S. Son
- Department of Medicine, Stony Brook University, Stony Brook, NY, United States of America
| | - Ling J. Zheng
- Department of Medicine, Stony Brook University, Stony Brook, NY, United States of America
| | - Leahana M. Rowehl
- Department of Medicine, Stony Brook University, Stony Brook, NY, United States of America
| | - Xinyu Tian
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, United States of America
| | - Yuanhao Zhang
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, United States of America
| | - Wei Zhu
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, United States of America
| | - Leighann Litcher-Kelly
- Department of Psychiatry, Stony Brook University, Stony Brook, NY, United States of America
| | - Kenneth D. Gadow
- Department of Psychiatry, Stony Brook University, Stony Brook, NY, United States of America
| | - Grace Gathungu
- Department of Pediatrics, Stony Brook University, Stony Brook, NY, United States of America
| | - Charles E. Robertson
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America
| | - Diana Ir
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America
| | - Daniel N. Frank
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America
| | - Ellen Li
- Department of Medicine, Stony Brook University, Stony Brook, NY, United States of America
| |
Collapse
|
5
|
Zhang Y, Rowehl L, Krumsiek JM, Orner EP, Shaikh N, Tarr PI, Sodergren E, Weinstock GM, Boedeker EC, Xiong X, Parkinson J, Frank DN, Li E, Gathungu G. Correction: Identification of Candidate Adherent-Invasive E. coli Signature Transcripts by Genomic/Transcriptomic Analysis. PLoS One 2015. [PMID: 26218289 PMCID: PMC4517915 DOI: 10.1371/journal.pone.0134759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
6
|
Gathungu G, Kim HJ, Morell RJ. A novel nonsense mutation (Q57X) of GJB2 in a deaf individual who is a compound heterozygote for the 30delG allele. Hum Mutat 1999. [DOI: 10.1002/(sici)1098-1004(1999)13:3<259::aid-humu20>3.0.co;2-i] [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: 11/12/2022]
|
7
|
Gathungu G, Kim HJ, Morell RJ. A novel nonsense mutation (Q57X) of GJB2 in a deaf individual who is a compound heterozygote for the 30delG allele. Hum Mutat 1999. [DOI: 10.1002/(sici)1098-1004(1999)13:5<414::aid-humu16>3.0.co;2-8] [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: 11/10/2022]
|