Gut Microbiome Function Predicts Response to Anti-Integrin Biologic Therapy in Inflammatory Bowel Diseases

THE FECAL MICROBIOME AS A TOOL FOR MONITORING AND PREDICTING RESPONSE OUTCOMES IN USTEKINUMAB-TREATED, ANTITNFΑ REFRACTORY CROHN'S DISEASE PATIENTS: RESULTS FROM THE CERTIFI STUDY Matthew K. Doherty, Charles Koumpouras, Shannon Telesco, Calixte S. Monast, Carrie Brodmerkel, Patrick D. Schloss Background: We investigated the relationship between the fecal microbiome and clinical phenotypes in subjects with moderate to severe CD treated with ustekinumab (UST) to determine whether the fecal microbiome at baseline is predictive of disease severity and therapeutic response and to assess changes in the fecal microbiota due to therapy. Methods: CERTIFI was a phase 2b multicenter, double-blind, placebo-controlled trial to evaluate the efficacy of UST in subjects with moderate to severe CD who had not responded to antiTNFα therapy. The 16S rRNA gene from stool samples collected from roughly 350 patients at baseline and following treatment with UST or placebo (PBO) was sequenced using the Illumina MiSeq platform. Sequences were assigned to taxonomic groups using the mothur software package to determine the relative abundance of bacterial taxa. The relative abundances in addition to clinical metadata were used as input to a random forest (RF) machinelearning algorithm to predict disease severity and clinical response to treatment with UST. Results: Fecal microbiome richness at baseline significantly correlated with clinical parameters, including CDAI, stool frequency, and disease duration (Table 1). Changes in the community structure of the microbiome (beta diversity) were significantly associated with stool frequency, CRP, fecal lactoferrin, fecal calprotectin, corticosteroid use, disease duration, and tissue involvement (Table 1). Community structure and species diversity were significantly different between Week 6 clinical responders and non-responders to UST and between clinical remitters and non-remitters. The microbiome of responders and remitters also changed over time but did not change in non-responders. Faecalibacterium, among other taxa, was significantly more abundant in responders and remitters. Using RF, the differences in the baseline microbiome and clinical metadata were able to predict response to UST with AUC values of roughly 0.85. Conclusions: The ability to predict response to treatment using the microbiome has the potential to provide a quantitative clinical tool for guiding the treatment of CD patients. In addition our results point to specific microbes that might contribute to CD pathogenesis and maintaining CD remission. Microbes related to achieving remission could be investigated as co-therapies designed to increase the likelihood of response to anti-inflammatory therapeutics.

1045

Table 1. Relationship between the microbiome at week 0 and clinical variables (N=306 subjects)

ALTERED PHAGE DIVERSITY AND INCREASED GROWTH RATE OF ESCHERICHIA COLI ARE ASSOCIATED WITH FECAL TRANSPLANTATION FAILURE IN PATIENTS WITH CLOSTRIDIUM DIFFICILE INFECTION HeeKuk Park, Braden Millan, Naomi Hotte, Dina H. Kao, Karen Madsen

1059 GUT MICROBIOME FUNCTION PREDICTS RESPONSE TO ANTI-INTEGRIN BIOLOGIC THERAPY IN INFLAMMATORY BOWEL DISEASES Ashwin Ananthakrishnan, Chengwei Luo, Vijay Yajnik, Hamed Khalili, John Garber, Betsy Stevens, Thomas Cleland, Ramnik Xavier

The gut microbiome contains a diverse bacteriophage community that plays a largely unknown role in shaping microbial colonization and disease pathogenesis. Fecal microbial transplantation (FMT) is the most effective therapy for recurrent Clostridium difficile infection (RCDI) and has been shown to transfer phages along with gut microbes. Aim: The aim of this study was to examine the effects of FMT on microbial and phage composition in RCDI patients. Methods: Patients with RCDI (n=19) received FMT from 1 of 3 donors via colonoscopy. Stool samples were collected prior to and following FMT. DNA was extracted and indexed paired-end DNA libraries constructed using an Illumina Nextera® XT DNA kit, then sequenced on a MiSeq. Reads from individual samples were mapped to >5 kb assembled contigs using Metaphlan 2 for taxonomy, HUMAnN for gene function, and Bowtie2 with NCBI RefSeq database for prophage. To assess the metabolic state of the microbial community in RDCI patients, growth dynamics of E. coli were inferred from the metagenomic data by measuring the proportion of DNA copies near the origin to those near the terminus (peak-to-trough ratio (PTR)). Results: In RCDI patients prior to FMT, Escherichia and Klebsiella dominated. RCDI patients also harbored numerous phages within the Siphoviridae family, including Enterobacteria, Escherichia, Salmonella, Klebsiella and Lactobacillus phages. In contrast, the gut microbiome of donors consisted primarily of Bacteroides and Firmicutes; donors also had a much reduced phage population which consisted primarily of Streptococcus phages. Eleven patients were successfully treated with a single FMT (FMTS) while 8 patients required multiple FMTs (FMT-M). A successful FMT resulted in the appearance of donor phages in the RCDI recipients with a complete loss or sighnificant reduction of Siphoviridae phages and increased Bacteroidetes and Firmicutes. There were no significant differences in microbial composition or predicted gene function between the FMT-S and FMT-M groups; however, the patients requiring multiple FMT had increased abundances of Enterobacteria phages HK542, mEp237, and phiP27. This was associated with an increased inferred growth rate of Escherichia coli suggesting that E. coli and associated phages may be driving disease pathogenesis in some RCDI patients that fail to respond to FMT. Summary: Patients with recurrent C. difficile infection had decreased microbial diversity but increased numbers and diversity of phages compared with healthy individuals. A successful FMT altered both bacterial and phage composition to resemble the donor. Patients who required at least two FMT had significant differences in their phage population suggesting that the presence of particular phages may have a role in modulating response of patients to fecal transplantation.

Introduction: Inflammatory bowel diseases (IBD; Crohn's disease (CD), ulcerative colitis (UC)) are chronic, progressive diseases. Existing biomarkers perform poorly in predictive response to biologic therapy. No prior data exists regarding longitudinal trajectory of changes in the gut microbiome composition and function with gut-selective anti-integrin therapy with vedolizumab in IBD. Methods: This prospective cohort enrolled patients with refractory CD or UC initiating therapy with vedolizumab. Disease activity was assessed prospectively using validated clinical indices and primary outcome was remission at week 14. Shotgun metagenomic sequencing was performed on stool samples at baseline, weeks 14, 30, and 54. Microbial taxonomic and functional pathway abundances at baseline and longitudinally was compared among those attaining remission and those not. A neural network algorithm was developed to predict clinical remission. Results: This study included 85 patients with IBD (43 UC, 42 CD). At week 14, 31 patients achieved clinical remission. Community alpha-diversity at baseline was significantly higher in CD patients who achieved remission at week 14 (Figure). Two species, Roseburia inulinivorans and a Burkholderiales species were significantly more abundant at baseline among CD patients achieving week 14 remission compared to those not (q=0.0914 and 0.0614 respectively) (Figure). In contrast to these few changes in microbial composition, there were significantly greater association with microbial function; 13 pathways including branched chain amino acid synthesis were significantly enriched in baseline samples from the CD patients achieving remission compared to those who did not. A neural network algorithm incorporating microbiome and clinical data provided the highest classifying power (AUC=0.872). Conclusion: Early clinical remission could be predicted by microbial functional composition at baseline with a weaker influence at the level of the species or genus.

S-191

AGA Abstracts

AGA Abstracts

1058

AGA Abstracts Baseline alpha-diversity among inflammatory bowel disease patients, stratified by remission at week 14

Effect of Lactobacillus case strain on exacerbated colitis in Tcrα KO mice exposed to rWAS

1061 ENDOSPORE-FORMING BACTERIA ARE ASSOCIATED WITH MAINTENANCE OF REMISSION FOLLOWING INTESTINAL RESECTION IN CROHN'S DISEASE Michael Laffin, Troy Perry, HeeKuk Park, Patrick M. Gillevet, Masoumeh Sikaroodi, Gilaad Kaplan, Richard N. Fedorak, Karen Kroeker, Levinus A. Dieleman, Bryan Dicken, Karen Madsen

Differences in relative abundance of taxa significant different at baseline between those in remission at week 14 and non-remitters

The most common type of intestinal resection in CD patients is ileocolonic resection (ICR). However, disease recurs at the anastomosis in up to 80% of subjects. Evidence suggests that microbes and the fecal stream play a central role in disease recurrence. Aim: The aim of this study was to define the mucosal-associated microbiota at the time of ICR and 6 months post-operatively and to determine if microbial community structure at the time of surgery was predictive of future disease relapse. Methods: Ileal biopsies were obtained at surgery and after 6 months from CD patients undergoing ICR (n=45). Composition and function of mucosal associated microbiota was assessed by 16S rRNA sequencing and PICRUSt analysis. Endoscopic recurrence was assessed using the Rutgeerts score (Remission: 0-1; Recurrence ≥2). As a measurement of tissue disease activity, TNFα was measured in biopsies at the time of surgery using a MesoScale discovery platform. To identify microbial composition and metabolic pathways with differentiating abundance in the different groups, the LDA (Linear Discriminant Analysis) Effect Size (LEfSe) algorithm was used with the online interface Galaxy. Results: At 6 months, 30 patients were in endoscopic remission and 15 had recurrent disease. Demographic data and tissue TNFα levels at the time of surgery between the two groups was similar (Table). LEfSe analysis of mucosal biopsies taken at the time of surgery showed Clostridiales to predict maintenance of remission while Enterobacteriales predicted disease recurrence (p<0.05). An increase in Lachnospiraceae from surgery to 6 months post-ICR was associated with remission (p=0.05). At the time of resection a ratio >3:1 between anaerobic endospore-forming bacteria families to families capable of aerobic respiration within the Firmicutes phylum was shown to be predictive of maintenance of remission in an adjusted analysis (OR-9.2 95% CI 1.8-47.7 p<0.01). The favorable ratio was associated with increased α-diversity at follow-up endoscopy (p=0.04). In addition, recurrent subjects contained a greater proportion of reads associated with aerobic respiration while those samples collected from subjects in remission contained a higher proportion of reads associated with the germination of spores (p<0.05). Conclusion: Gut recolonization following ICR is facilitated by microbes which are capable of either aerobic respiration or endospore formation. The relative proportions of these species within the phylum Firmicutes at the time of surgery is predictive of subsequent microbial community restoration and disease recurrence. The identification of a novel niche driven approach to specific bacterial populations associated with maintenance of remission may enable the development of targeted therapies to alter gut ecology towards an endospore-rich profile and thus prevent post-operative recurrence of CD. Clinical and demographic characteristics of subjects by recurrence status

1060 CHRONIC PSYCHOLOGICAL STRESS DISRUPTED THE COMPOSITION OF THE MURINE COLONIC MICROBIOTA AND ACCELERATED A MURINE MODEL OF ULCERATIVE COLITIS Yohei Watanabe, Sohei Arase, Noriko Nagaoka, Hiromi Setoyama, Mitsuhisa Kawai, Satoshi Matsumoto Chronic psychological stress have reported to be associated with increased disease activity in inflammatory bowel disease (IBD), but the relationships among psychological stress, the gastrointestinal microbiota, and the severity of colitis is not yet fully understood. Here, we examined the impact of 12-week repeated water-avoidance stress (rWAS) on the microbiota of mouse model of ulcerative colits, T cell receptor alpha chain gene knockout mouse. Chronic exposure to rWAS exacerbated colitis, and altered the composition of the colonic microbiota including luminal bacteria and mucosa-associated commensal bacteria (MACB). The relative abundance of the toxin producing Clostridium was also increased, which was weakly positively associated with colitis severity score. This result suggested that expansion of specific populations of indigenous pathogens may be involved in the exacerbation of colitis. Interestingly, colitis was not exacerbated in mice with a relatively diverse microbiota even if their colonic microbiota contained an expanded toxin producing Clostridium population. Exposure to chronic stress also altered the concentration of free immunoglobulin A in colonic contents, which may be related to both the loss of bacterial diversity and the severity of the colitis exacerbation. In addition, the oral administration of a probiotic Lactobacillus casei strain was protective against the exacerbation of colitis, associated with preventing the loss of bacterial diversity in MACB. These results suggest that long-term exposure to psychological stress induces dysbiosis in the immunodeficient mice, and probiotic treatment may be useful for preservation of the bacterial diversity in MACB and alleviate gut inflammation induced by psychological stress.

Graphical abstract

AGA Abstracts

S-192