Microbiome Restoration Research Articles

Microbiome Restoration by RBX2660 Does Not Preclude Recurrence of Multidrug-Resistant Urinary Tract Infection Following Subsequent Antibiotic Exposure: A Case Report.

A 62-year-old woman received RBX2660, an investigational microbiome restoration therapeutic, for recurrent multidrug-resistant (MDR) urinary tract infection (UTI). RBX2660 increased gut microbiome diversity but did not eliminate uropathogen carriage, and MDR UTI recurred after subsequent antibiotic exposure. Thus, restoration of microbiome diversity does not preclude disease recurrence by residual MDR pathogens.

669. Twelve-Month Durability of Microbiota-Based Therapy RBX2660 for Prevention of Recurrent Clostridium difficile Infection

BackgroundRecurrent Clostridium difficile infections (rCDI) are a public health threat with insufficient treatment options at present. Two Phase 2 clinical studies have reported the efficacy of RBX2660, a standardized, stabilized microbiota-based drug, in preventing rCDI. For one of these trials, we report herein the durability of clinical response (lack of CDI recurrence) and microbiome restoration to 12 months after RBX2660 treatment.MethodsData were drawn from an interim analysis of a multicenter, open-label Phase 2 study in which participants with multi-recurrent rCDI received up to 2 doses of RBX2660 delivered via enema 7 days apart; this analysis includes data to 12 months after treatment, with follow-up ongoing. Efficacy was defined as the absence of CDI recurrence to 56 days after the last dose; and durability is defined as a continued lack of reported recurrence. Participant stool samples collected prior to and at 1, 7, 30, 60 days and 6 and 12 months after treatment were sequenced using a shallow shotgun method, with only treatment responders reported herein. Operational taxonomic unit (OTU) data were used to calculate relative abundance at the class level and Microbiome Health Indices.ResultsThis study included 149 RBX2660-treated participants and 110 historical control patients, in the United States and Canada. As previously reported, the efficacy of RBX2660 in preventing rCDI (79.9%; 119/149) was higher than CDI-free rates in the historical control group (51.8%, 57/110; P < 0.001). Of 109 participants who had a 6-month follow-up, 97.2% (106/109) remained CDI-free, and no new CDI recurrences were reported at 12 months. Among treatment responders, the microbiome composition was restored after treatment to predominance by Bacteroidia- and Clostridia-class bacteria, and these compositions remained stable to 12 months after treatment among participants who provided samples.ConclusionRBX2660, a microbiota-based drug, was efficacious for preventing rCDI, with clinical and microbiome restoration durability to at least 12 months after treatment. The follow-up of efficacy, safety, and microbiome restoration are ongoing. Disclosures All authors: No reported disclosures.

LB5. A Long-Time Coming: Final 2-year Analysis of Efficacy, Durability, and Microbiome Changes in a Controlled Open-Label Trial of Investigational Microbiota-Based Drug RBX2660 for Recurrent Clostridioides difficile Infections

BackgroundRecurrent Clostridioides difficile infection (rCDI) is an urgent public health threat associated with significant mortality and medical cost. Microbiota therapy is gaining acceptance as a strategy to reduce rCDI recurrence. We present the final 24-month analysis of clinical safety, efficacy, and microbiome restoration from a Phase 2 open-label trial of RBX2660 for prevention of CDI recurrence.MethodsParticipants with multi-recurrent CDI received <2 doses of RBX2660 delivered via enema 7 days apart in this multicenter, open-label Phase 2 study. Efficacy was defined as the absence of CDI recurrence through 56 days after the last dose and was compared with 8-week recurrence-free rates for a historical control cohort that received standard-of-care antibiotic therapy. Fisher exact test compared the proportion of treatment participants who were CDI-free by age and sex. Durability was defined as continued absence of CDI episodes beyond 8 weeks. Safety and durability assessments occurred at 3, 6, 12, and 24 months. Participant stool samples were collected prior to and for up to 720 days after treatment, and microbiome changes were assessed by shallow shotgun sequencing.ResultsThe efficacy of RBX2660 to prevent rCDI at 8 weeks (78.9%; 112/142) was higher than the CDI-free rate in the historical control group (30.7%, 23/75; P < 0.0001). Age and sex did not impact efficacy. Among participants who achieved treatment success at 8 weeks and were evaluable for long-term durability (n = 95), 8 experienced a new CDI episode by the 24-month follow-up for an overall durability of 91.6%. The safety profile was consistent with previous reports for RBX2660. In total, 503 stool samples from 110 treatment responders were analyzed. Within 7 days of treatment, the relative abundance of Bacteroidia and Clostridia remained shifted higher than pre-treatment levels while Gammaproteobacteria and Bacilli declined sharply after treatment, and these changes persisted to at least 24 months.ConclusionRBX2660, a microbiota-based drug, was safe and efficacious for preventing rCDI with clinical durability to 24 months after treatment, independent of age or sex, and RBX2660 durability associated with durable microbiome shifts from pre-treatment to a healthier composition. DisclosuresRobert Orenstein, DO, Rebiotix Inc. (Advisor or Review Panel member), Sarah Mische, PhD, Rebiotix Inc. (Employee), Ken Blount, PhD, Rebiotix Inc. (Employee), Lindy Bancke, PharmD, Rebiotix Inc. (Employee), Xin Su, MD, MSci, Rebiotix Inc. (Employee), Dana Walsh, PhD, Rebiotix Inc. (Employee), Adam Harvey, PhD, Rebiotix Inc. (Employee), Carlos Gonzalez, MS, Rebiotix Inc. (Consultant), Dale N. Gerding, MD, Rebiotix Inc. (Board Member).

670. VRE Clearance in Patients with Recurrent Clostridium difficile Infection Following Treatment with Microbiota-Based Drug RBX2660

BackgroundVancomycin-resistant Enterococcus (VRE) infection is frequently associated with immunocompromised and critically ill patients. VRE carriers are at increased risk for infection due to VRE colonization and they pose a risk as a transmission source. VRE infection and Clostridium difficile infection (CDI) share common risk factors, including disruption of the intestinal microbiome. Thus, therapeutic approaches that decolonize VRE would be valuable. Herein, we report on stool VRE clearance in a cohort analysis from a Phase 2 open-label study of RBX2660, standardized microbiota-based drug, for recurrent CDI.MethodsThis prospective, multicenter, open-label Phase 2 study enrolled subjects with recurrent CDI. Participants received up to 2 doses of RBX2660 delivered via enema with doses 7 days apart. Patients were requested to voluntarily submit stool samples at baseline and at 7, 30 and 60 days, 6, 12, and 24 months after the last administration of RBX2660. Stool samples were tested for VRE using bile esculin azide agar with 6 µg/mL vancomycin and gram staining. Vancomycin resistance was confirmed via blood agar and etest.ResultsStool samples were available for 143 patients. Twenty-one patients were VRE-positive at the first test (baseline or 7 day). Of the 19 VRE-positive patients that provided additional samples at later timepoints, 18 (94.7%) converted to negative as of the last available follow-up (30 or 60 days and 6, 12, or 24 months). The remaining patient remained positive at all follow-ups.ConclusionThis cohort analysis of VRE-positive patients within an rCDI population provides additional support that microbiota-based formulations, such as RBX2660, may have additional benefit beyond reducing the recurrence of CDI. Additional study is needed to confirm the role of microbiome restoration on VRE clearance.Disclosures All authors: No reported disclosures

ES15.05 The Role of Microbiome Restoration in Chemotherapy and Immunotherapy

ES15.05 The Role of Microbiome Restoration in Chemotherapy and Immunotherapy

Sepsis in the era of data-driven medicine: personalizing risks, diagnoses, treatments and prognoses.

Sepsis is a series of clinical syndromes caused by the immunological response to infection. The clinical evidence for sepsis could typically attribute to bacterial infection or bacterial endotoxins, but infections due to viruses, fungi or parasites could also lead to sepsis. Regardless of the etiology, rapid clinical deterioration, prolonged stay in intensive care units and high risk for mortality correlate with the incidence of sepsis. Despite its prevalence and morbidity, improvement in sepsis outcomes has remained limited. In this comprehensive review, we summarize the current landscape of risk estimation, diagnosis, treatment and prognosis strategies in the setting of sepsis and discuss future challenges. We argue that the advent of modern technologies such as in-depth molecular profiling, biomedical big data and machine intelligence methods will augment the treatment and prevention of sepsis. The volume, variety, veracity and velocity of heterogeneous data generated as part of healthcare delivery and recent advances in biotechnology-driven therapeutics and companion diagnostics may provide a new wave of approaches to identify the most at-risk sepsis patients and reduce the symptom burden in patients within shorter turnaround times. Developing novel therapies by leveraging modern drug discovery strategies including computational drug repositioning, cell and gene-therapy, clustered regularly interspaced short palindromic repeats -based genetic editing systems, immunotherapy, microbiome restoration, nanomaterial-based therapy and phage therapy may help to develop treatments to target sepsis. We also provide empirical evidence for potential new sepsis targets including FER and STARD3NL. Implementing data-driven methods that use real-time collection and analysis of clinical variables to trace, track and treat sepsis-related adverse outcomes will be key. Understanding the root and route of sepsis and its comorbid conditions that complicate treatment outcomes and lead to organ dysfunction may help to facilitate identification of most at-risk patients and prevent further deterioration. To conclude, leveraging the advances in precision medicine, biomedical data science and translational bioinformatics approaches may help to develop better strategies to diagnose and treat sepsis in the next decade.

Tu1880 – Durable Freedom from Clostridium Difficile Infection Recurrence and Microbiome Restoration During Six-Month Follow-Up For a Phase 1 Clinical Trial of Rbx7455?An Investigational Room Temperature-Stable, Oral Microbiotabased Therapeutic

Tu1880 – Durable Freedom from Clostridium Difficile Infection Recurrence and Microbiome Restoration During Six-Month Follow-Up For a Phase 1 Clinical Trial of Rbx7455?An Investigational Room Temperature-Stable, Oral Microbiotabased Therapeutic

Restoration of Bacterial Microbiome Composition and Diversity Among Treatment Responders in a Phase 2 Trial of RBX2660: An Investigational Microbiome Restoration Therapeutic.

BackgroundRBX2660 is an investigational microbiota restoration therapy in phase 3 clinical development for preventing recurrent Clostridioides difficile infections (CDIs). In a randomized, double-blinded placebo-controlled phase 2B trial, RBX2660 was effective at preventing CDI recurrence. The current study was performed to characterize the fecal bacterial microbiome before and after treatment among RBX2660- or placebo-treated responders in that trial.MethodsSamples were sequenced using 16S methods, and the resulting relative abundance data were fit to a Dirichlet-multinomial distribution to determine group mean relative taxonomic abundance and overdispersion at the class level. Alpha diversity was determined for all samples. Biostatistical tools, including effect size and repeated-measures analysis, were applied to evaluate the statistical significance of observed changes.ResultsAt study entry, subjects’ microbiomes were dominated by Gammaproteobacteria and Bacilli, with low abundance of Bacteroidia and Clostridia. After treatment, Bacteroidia, Clostridia, and alpha diversity increased among RBX2660 responders, concomitant with a decrease of Gammaproteobacteria and Bacilli. The resulting compositions differed significantly from baseline compositions, and the changes among RBX2660 responders differed significantly from those in placebo responders, in whom Bacteroidia or Gammaproteobacteria abundance did not change as much. Repeated-measures analyses indicated more rapid and extensive microbiome remodeling among RBX2660 responders compared with placebo responders, and effect size analyses revealed that RBX2660 responders’ microbiomes became more similar to the RBX2660 composition, also compared with placebo responders.ConclusionsPrevention of recurrent CDI with RBX2660 was associated with restorative microbiome changes that may help resist C. difficile colonization and recurrence. RBX2660 was more effective than placebo at restoring participant microbiomes.

1966. Evaluating a Prototype Microbiome Health Index (MHI) as a Measure of Microbiome Restoration Using Data Derived From a Published Study of Fecal Microbiota Transplant (FMT) to Treat Recurrent Clostridium difficile Infections (rCDI)

BackgroundThere are efforts to develop FDA-approved microbiota-based drugs to restore the microbiome, notably for recurrent Clostridium difficile infections (rCDI). Given the lack of established biomarkers for microbiome restoration, we are evaluating unidimensional Microbiome Health Indices (MHI™). We previously presented a prototype MHI for clinical trials of RBX2660—a standardized microbiota restoration therapy in Phase 3 clinical development. Herein we assessed MHI for a published study of fecal microbiota transplant (FMT) for treating rCDI.MethodsThe prototype MHI is based on the associations of Bacteroidia and Clostridia with colonization resistance, and Gammaproteobacteria and Bacilli with dysbiosis, and Receiver Operating Characteristic analysis of pooled RBX2660 trial data indicated that rCDI participants before treatment (baseline) are distinguished from the healthier RBX2660 profile with an odds ratio of 121 (AUC = 0.99, sensitivity = 0.96, specificity = 0.99, cutpoint = 8.2). MHI data for the published FMT cohort were calculated using publicly available data derived from pre- and post-treatment fecal samples (Khanna S, et al. Microbiome 2017 5:55), and this study included patients with or without a co-diagnosis of inflammatory bowel disease (IBD).ResultsAt baseline, 92% of patients in the FMT cohort were below the MHI = 8.2 cutpoint, consistent with a rCDI diagnosis. Among FMT responders 7 days after treatment, 91% of patients had shifted to MHI>8.2, (P < 0.0001 compared with baseline). Likewise, a significant shift was observed from baseline to 30 days (P < 0.0001), with 83% having MHI > 8.2. There were insufficient patients to support a statistical comparison of IBD vs. no IBD, but MHIs trended lower at all time points among patients with IBD.ConclusionMHI parameters derived from RBX2660 trials were predictive of pre- and post-treatment states for a published cohort of FMT-treated rCDI patients, suggesting that this prototype MHI represents a useful dysbiosis measure beyond RBX2660 trials. Lower MHI among patients co-diagnosed with IBD suggests the potential utility of MHI beyond rCDI. Collectively our results continue to support the utility of MHI and its prospective evaluation in ongoing Phase 3 clinical trials.Disclosures K. Blount, Rebiotix, Inc.: Employee, Salary. C. Jones, Rebiotix, Inc.: Employee, Salary. E. Deych, Rebiotix, Inc.: Research Contractor, Consulting fee. B. Shannon, Rebiotix, Inc.: Research Contractor, Consulting fee.

1775. Microbiome-Based Classifiers Accurately Differentiate Infectious Diarrhea From Functional Gastrointestinal Disorders and Provide Population-Scale Confidence Measures of Fecal Microbiota Restoration in Recurrent C. DifficileInfection

BackgroundFecal microbiota therapy is being actively pursued as treatment for recurrent C. difficile infection (rCDI), as well as for other GI disease indications associated with dysbiosis, for example, irritable bowel syndrome (IBS). RBX2660 is a microbiota-based drug designed to restore a healthier microbiome and has demonstrated clinical efficacy for preventing rCDI. Despite this and other treatment successes, our understanding of functional microbiota reconstitution at the population scale is still evolving, as is the ability to distinguish IBS from CDI recurrence. Herein we describe development of a Random Forest classifier for CDI diagnosis, and we evaluate microbiome restoration in participants of the Phase 2 trial of RBX2660.MethodsFecal 16S rDNA sequences from 2,129 subjects enrolled in diverse multi-center cohorts were analyzed (1,235 adults and 447 children with CDI, AAD, IBS, or controls). Technical variations due to different DNA extraction, primer region coverage, and sequencing platforms were addressed using closed-reference OTU picking with UCLUST. The RDP classifier and SILVA database assigned taxonomy for each OTU sequence. Stratified random sampling with 50 repeated tests of microbiota training sets was performed for supervised learning. Microbiota signatures of patients in the RBX2660 PUNCH CD2 trial were then assessed using classifiers built to predict CDI treatment outcomes and IBS misdiagnosis.ResultsRandom Forest built the best classifiers accurately predicting 97.7% of CDI cases, and confidently distinguished CDI from IBS patients based on their microbiome signatures (figure). RBX2660 treatment significantly restored microbiota community composition in rCDI cases compared with placebo controls.ConclusionRandom Forest classifiers built on a population-scale study of microbiota composition in patients with GI disease provide a highly accurate predictor of CDI cases versus potential IBS misdiagnosis in adults and children. RBX2660 significantly reduced disease classification scores in rCDI patients with a healthy-like microbiota reconstitution markedly accelerating after 30 days of treatment.This study was funded by 1UO1 AI24290-01 and Rebiotix, Inc. Disclosures C. Jones, Rebiotix, Inc.: Employee, Salary. K. Blount, Rebiotix, Inc.: Employee, Salary. T. Savidge, Rebiotix: Grant Investigator, Research grant.

1641. Treatment of Recurrent Clostridium difficile Infection With SER-109 Reduces Gastrointestinal Carriage of Antimicrobial Resistance Genes

BackgroundA healthy gut microbiome is associated with colonization resistance against C. difficile and other pathogens, including bacteria carrying antibiotic resistance genes (AbRG). Designed to facilitate microbiome restoration and reduce the risk of recurrent C. difficile infection (rCDI), SER-109, an investigational microbiome therapeutic, is an ecology of bacterial spores purified from stool from healthy screened donors. We evaluated the impact of engraftment of SER-109 dose species on the abundance of AbRG in rCDI subjects.MethodsWe generated whole metagenomic shotgun (WMS) data for a subset of study subjects with available stool samples receiving SER-109 (n = 66) or placebo (n = 25) from 2 clinical trials (a dose-ranging Phase 1b study and a fixed-dose Phase 2 trial). WMS data from stool was analyzed to (1) quantify the abundance of AbRG (Comprehensive Antibiotic Resistance Database CARD v.1.1.8) and (2) define subjects with significant engraftment of SER-109 dose species. For each subject and antibiotic drug class, we calculated the change in abundance of AbRG between samples collected at baseline (after antibiotic therapy for an episode of C. difficile infection) and following treatment with SER-109 or placebo. We evaluated the effect of SER-109 engraftment on AbRG abundance, independent of dose.ResultsIn subjects with significant high-confidence engraftment of SER-109 organisms (n = 30) we observed significantly greater reduction in AbRG relative to placebo at week 1 post treatment. These AbRG were associated with multiple classes of antibiotics including, but not limited to, cephalosporins (P = 0.035), and fluoroquinolones (P = 0.035) (Figure 1). Furthermore, the reduction of AbRG was correlated with the increased abundance of SER-109 dose species, and with a reduction in Proteobacteria (e.g., Enterobactericeae) (Figure 2).Figure 1.(a) Cephalosporin antibiotics(b) Fluoroquinolone antibioticsFigure 2.ConclusionRestoration of the gut microbiome with SER-109 in subjects with a history of rCDI is associated with a reduction in abundance of antibiotic resistance genes. These observations suggest that microbiome therapeutics could play a role in more rapidly decolonizing drug-resistant bacteria.Disclosures C. Ford, Seres Therapeutics, Inc: Employee and Shareholder, Salary. M. Henn, Seres Therapeutics, Inc: Employee and Shareholder, Salary. J. Bryant, Seres Therapeutics, Inc: Employee and Shareholder, Salary. L. Diao, Seres Therapeutics, Inc: Employee and Shareholder, Salary. J. Wortman, Seres Therapeutics, Inc: Employee and Shareholder, Salary. A. Tomlinson, Seres Therapeutics, Inc: Employee and Shareholder, Salary. K. Litcofsky, Seres Therapeutics, Inc: Employee and Shareholder, Salary. P. Bernardo, Seres Therapeutics, Inc: Employee and Shareholder, Salary. B. McGovern, Seres Therapeutics, Inc: Employee and Shareholder, Salary. J. G. Aunins, Seres Therapeutics, Inc: Employee and Shareholder, Salary. D. N. Cook, Seres Therapeutics, Inc: Employee and Shareholder, Salary. M. Trucksis, Seres Therapeutics, Inc: Employee and Shareholder, Salary.

621. Treatment of Recurrent Clostridium difficile Infection with SER-109 Increases the Concentration of Secondary Bile Acids in a Dose-Dependent Manner

Background C. difficile recurs when dormant spores germinate in the dysbiotic gut, facilitated by an increase of 1° vs. 2° bile acids. SER-109, an ecology of bacterial spores purified from stool of healthy donors, is an investigational first-in-class microbiome therapeutic intended to facilitate microbiome restoration and reduce risk of recurrent C. difficile (rCDI). Rapid engraftment of spore-forming species is associated with (i) higher doses of SER-109 in our dose-ranging Phase 1b study (Ph1b) and (ii) reduced rCDI in our Phase 2 trial (Ph2). We explored whether higher doses of SER-109 were associated with an increase in 2° bile acids.MethodsWhole metagenomic shotgun (WMS) data were generated from stool, and species were identified using a proprietary build of MetaPhlAn. Evaluation of spore-forming species richness and bile acid concentrations identified effects of SER-109 treatment. A triple stage bioreactor model of the human gut and rCDI was used to evaluate the impact of microbial therapeutics.ResultsPh1b subjects who received a higher dose (>1.5 × 108 SporQ) had significantly higher spore-forming species richness than subjects who received a low dose (<1.5 × 108 SporQ) at Week 1 post-treatment (P = 0.017, Figure 1). Spore-forming species richness in patients receiving a low dose in Ph1b was comparable to that observed in non-recurrent patients in Ph2, who received the same mean dose (Figure 1). Ph1b subjects in the high dose group had a significantly higher concentration of 2° bile acids as compared with Ph1b low dose subjects and non-recurrent Ph2 subjects (P = 0.036, P < 0.001, respectively, Figure 2). A higher dose (3 × 108 SporQ × 3 days) suppressed recurrence in a gut model of rCDI; a single dose did not.ConclusionHigher doses of SER-109 are significantly associated with (i) higher spore-forming species richness, (ii) concentrations of secondary bile acids, and (iii) prevention of recurrence in an gut model of CDI. These results suggest that SER-109 in the Phase 2 trial was biologically active and catalyzed a functional change in the microbiome of a subset of subjects; a dose increase may optimize efficacy across a broad population. Seres has initiated a Phase 3 study of SER-109 to reduce rCDI, which includes an increase in dose titer and frequency. Figure 1:Figure 2:Disclosures M. Henn, Seres Therapeutics, Inc.: Employee and Shareholder, Salary. C. Ford, Seres Therapeutics, Inc.: Employee and Shareholder, Salary. E. O’Brien, Seres: Employee and Shareholder, Salary. J. Wortman, Seres Therapeutics, Inc.: Employee and Shareholder, Salary. L. Diao, Seres Therapeutics, Inc.: Employee and Shareholder, Salary. C. Desjardins, Seres Therapeutics, Inc.: Employee and Shareholder, Salary. A. Tomlinson, Seres Therapeutics, Inc.: Employee and Shareholder, Salary. K. Litcofsky, Seres Therapeutics, Inc.: Employee and Shareholder, Salary. M. Wilcox, Seres Therapeutics, Inc.: Consultant, Research Contractor, Scientific Advisor and Shareholder, Research support. A. Buckley, Seres Therapeutics, Inc.: Research Contractor, Research support. P. Bernardo, Seres Therapeutics, Inc.: Employee and Shareholder, Salary. B. McGovern, Seres Therapeutics, Inc.: Employee and Shareholder, Salary. J. G. Aunins, Seres Therapeutics, Inc.: Employee and Shareholder, Salary. D. N. Cook, Seres Therapeutics, Inc.: Employee and Shareholder, Salary. M. Trucksis, Seres Therapeutics, Inc.: Employee and Shareholder, Salary.

Interaction of gut microbiota with dysregulation of bile acids in the pathogenesis of nonalcoholic fatty liver disease and potential therapeutic implications of probiotics

The intestinal microbiota is now recognised to play key roles in health due to its involvement in many aspects of human physiology. Disturbance in gut microbiota (dysbiosis) is thus associated with many diseases including nonalcoholic fatty liver disease (NAFLD) which includes nonalcoholic fatty liver and nonalcoholic steatohepatitis. The mechanisms for the effect of dysbiosis in NAFLD pathogenesis are not completely elucidated. Many explanations have been proposed to trigger dysbiosis, leading to NAFLD including inflammation, ethanol produced by the gut bacteria and lipotoxicity. Recently the roles of bile acids and nuclear receptors are highly regarded. It is well known that gut microbes produce enzymes that convert primary bile acids into secondary bile acids in the intestines. Several studies have demonstrated that disturbance of the intestinal microbiota leads to decreased synthesis of secondary bile acids, which in turn decreases activation of nuclear receptors such as farnesoid X receptor (FXR), pregnane X receptor, Takeda G-protein-coupled bile acid protein 5 and vitamin D receptor. These receptors are important in energy regulation and their dysregulation can cause NAFLD. Therefore, stimulation of nuclear receptors especially FXR has been extensively explored for the amelioration of NAFLD. However, paradoxical effects of nuclear receptor activation are a major problem for the clinical application of nuclear receptor stimuli. We further posit that microbiome restoration could be an alternative approach for the treatment of NAFLD. Several gut bacteria are now known to be involved in bile acid metabolism. It will be necessary to identify which one/ones is/are feasible. Careful selection of commensal bacteria for probiotics may lead to an effective therapy for NAFLD.

Clinical intervention using Bifidobacterium strains in celiac disease children reveals novel microbial modulators of TNF-α and short-chain fatty acids

Celiac disease (CD) is an immune-mediated systemic disease, caused by ingestion of gluten in genetically predisposed individuals. Gut microbiota dysbiosis might play a significant role in pathogenesis of chronic enteropathies and its modulation can be used as an intervention strategy in CD as well. In this study, we aimed to identify correlations between fecal microbiota, serum tumor necrosis factor alpha (TNF-α) and fecal short-chain fatty acids (SCFAs) in healthy children and children with CD after administration of probiotic Bifidobacterium breve BR03 and B632. A double-blind placebo-controlled study enrolled 40 children with CD (CD) and 16 healthy children (HC). CD children were randomly allocated into two groups, of which 20 belonged to the placebo (PL) group and 20 to the Probiotic (PR) group. The PR group received a probiotic formulation containing a mixture of 2 strains, B.breve BR03 (DSM 16604) and B.breve B632 (DSM 24706) in 1:1 ratio for 3 months. Subsequently, for statistical analysis, blood and fecal samples from CD children (on enrolment - T0 and after 3 months, at the end of intervention with probiotic/placebo - T1) and HC children were used. The HC group was sampled only once (T0). Verrucomicrobia, Parcubacteria and some yet unknown phyla of Bacteria and Archaea may be involved in the disease, indicated by a strong correlation to TNF-α. Likewise, Proteobacteria strongly correlated with fecal SCFAs concentration. The effect of probiotic administration has disclosed a negative correlation between Verrucomicrobia, some unknown phyla of Bacteria, Synergistetes, Euryarchaeota and some SCFAs, turning them into an important target in microbiome restoration process. Synergistetes and Euryarchaeota may have a role in the anti-inflammatory process in healthy human gut. Our results highlight new phyla, which may have an important relation to disease-related parameters, CD itself and health.

Retraction: Microbiome restoration diet improves digestion, cognition and physical and emotional wellbeing.

Retraction: Microbiome restoration diet improves digestion, cognition and physical and emotional wellbeing.

Developing Microbiome Restoration Biomarkers for Clostridium difficile Infections: Evaluation and Plan of a Prototype Microbiome Rehabilitation IndexTM

Introduction: A healthy intestinal microbiome is important to human health, and microbiome disruption (dybiosis) is linked to many diseases, most notably recurrent Clostridium difficile infection (rCDI). This has spurred efforts to develop FDA-approved microbiome-based drugs to treat dysbiosis. Clinical efficacy for preventing rCDI has been demonstrated for some of these drugs, including RBX2660, a standardized microbiome-based therapeutic. However, quantitative biomarkers for microbiome restoration have not been established. Herein, we outline the challenges, preliminary data, and plan for developing a prototype Microbiome Rehabilitation IndexTM (MRITM) as a qualifiable biomarker. Methods: Gap analysis was conducted to map whether existing measures of microbiome data could meet FDA biomarker qualification criteria. As part of this analysis, reported microbiome data from rCDI clinical trials were assessed, including data from a double-blind, randomized, placebo-controlled Phase 2B trial of RBX2660, to determine if a clear relationship exists between microbiome changes and clinical outcome. Based on tentatively identified commonalities, a prototype MRITM was formulated and evaluated for capability to predict rCDI trial outcomes. Results: A key gap is standardization of data collection, reporting, and analysis tools. Sample extraction and 16S sequencing methods have progressed to the point that rapid and inexpensive protocols can be designed, but consensus tools for multidimensional data comparison are not established and would not be simple or rapid. A unidimensional parameter that captures key elements of multidimensional data could be an alternative. Toward that aim, rCDI patients who responded to RBX2660 treatment had increased Bacteroidia and Clostridia and decreased Bacilli and Gammaproteobacteria compared to baseline, changes that are consistent with reports for other rCDI therapies. Based on these data, a prototype MRITM was constructed that could differentiate untreated rCDI patients from healthy populations (Fig 1A) and quantify a significant change as early as 7 days after treatment (Fig 1B).Figure: (A) MRITM from enrolled rCDI patients before treatment (baseline, grey) in a Phase 2B trial of RBX2660 and MRITM of RBX2660 product consortium (RBX2660, blue). B) MRITM values for a healthy population as defined by the Human Microbiome Project (HMP) and for 7, 30, and 60 days after RBX2660 treatment. The asterisk (*) indicates values that are significantly different from the baseline MRITM (P<0.001), based on a Wilcoxon test.Conclusion: This prototype MRITM is a promising model for a unidimensional measure of microbiome restoration, but significant refinement will be needed and may include other taxa, differential weighting of taxa, and/or diversity metrics. This framework enables prospective hypothesis testing in future trials toward qualification of biomarkers for microbiome rehabilitation.

Gastrointestinal Tract Microbiome Dynamics Following Treatment with SER-109, an Investigational Oral Microbiome Therapeutic to Reduce the Recurrence of Clostridium difficile Infection (CDI)

BackgroundRecurrence of CDI occurs within a few weeks after treatment due to antibiotic-induced dysbiosis. SER-109, an investigational, first-in-class microbiome drug, was designed to sustain a clinical response through microbiome restoration with a purified ecology of spores. In an open-label Phase 1b (Ph1b) trial of SER-109 for prevention of recurrent CDI, 26 of 30 subjects did not recur following treatment. In a Phase 2 (Ph2) double-blind controlled trial of SER-109 (n = 59) vs. placebo (n = 30), no significant difference was observed in the proportions of subjects with recurrence (44.1% vs. 53.3%, respectively). Here we contrast gut microbiome changes among subjects in both trials to understand differences in clinical outcomes observed 8-weeks after dosing.MethodsWe used 16S v4 and high-resolution whole metagenomic shotgun (WMS) sequencing to characterize microbiome changes from stool samples collected at baseline and 1, 4, and 8 weeks post-treatment. Microbiome analyses focused on subjects diagnosed with recurrence via EIA toxin testing (high confidence recurrence; HCR).ResultsSignificantly greater richness of commensal spore-former species was observed in Ph2 subjects treated with SER-109 compared with PBO at weeks 1 and 4 post-treatment (Mann–Whitney P = 0.008, P = 0.044 respectively) consistent with drug engraftment. In addition, the number of spore-forming species at 1 week post-treatment was significantly greater in non-recurrent subjects vs. HCR subjects (Mann–Whitney P = 0.011). Furthermore, we identified 10 spore-former species that were significantly more prevalent in both SER-109 and non-recurrent subjects (Fig 1). In comparison to Ph1 subjects, SER-109 engraftment was significantly reduced and delayed among Ph2 subjects at all time points (Fig 2). Moreover, Ph1b subjects who received higher doses of SER-109 than that used in Ph2 had increased levels of engraftment.ConclusionIn patients with recurrent CDI and dysbiosis, a focused spore-based therapeutic approach leads to engraftment of SER-109 strains. In addition, microbiome signatures of engraftment were associated with a favorable clinical outcome. Although SER-109 was biologically active, a higher dose may improve the rate and degree of microbiome repair.Disclosures M. Henn, Seres Therapeutics: Employee and Shareholder, Salary and Stock Options; C. Ford, Seres Therapeutics: Employee and Shareholder, Salary and Stock Options; E. O’Brien, Seres Therapeutics: Employee and Shareholder, Salary and Stock Options; J. Wortman, Seres Therapeutics: Employee and Shareholder, Salary and Stock Options; S. Simmons, Seres Therapeutics: Employee and Shareholder, Salary and Stock options; L. Diao, Seres Therapeutics: Employee and Shareholder, Salary and Stock; K. Litcofsky, Seres Therapeutics: Employee and Shareholder, Salary and stock options; P. Bernardo, Seres Therapeutics: Employee and Shareholder, Salary and Stock options; J. Aunins, Seres Therapeutics, Inc.: Employee and Shareholder, Salary and Stock options; D. Cook, Seres Therapeutics: Employee and Shareholder, Salary and Stock Options; M. Trucksis, Seres Therapeutics Inc.: Employee and Shareholder, Salary and stock options

Microbiome restoration diet improves digestion, cognition and physical and emotional wellbeing.

Manipulating gut bacteria in the microbiome, through the use of probiotics and prebiotics, has been found to have an influence on both physical and emotional wellbeing. This study uses a dietary manipulation ‘The Gut Makeover’ designed to elicit positive changes to the gut bacteria within the microbiome. 21 healthy participants undertook ‘The Gut Makeover’ for a four week period. Weight and various aspects of health were assessed pre and post intervention using the Functional Medicine Medical Symptoms Questionnaire (MSQ). Paired sample t-tests revealed a significant reduction in self-reported weight at the end of the intervention. Adverse medical symptoms related to digestion, cognition and physical and emotional wellbeing, were also significantly reduced during the course of the dietary intervention. The intervention, designed to manipulate gut bacteria, had a significant impact on digestion, reducing IBS type symptoms in this non-clinical population. There was also a striking reduction in negative symptoms related to cognition, memory and emotional wellbeing, including symptoms of anxiety and depression. Dietary gut microbiome manipulations may have the power to exert positive physical and psychological health benefits, of a similar nature to those reported in studies using pre and probiotics. The small sample size and lack of control over confounding variables means that it will be important to replicate these findings in larger-scale controlled, prospective, clinical trials. This dietary microbiome intervention has the potential to improve physical and emotional wellbeing in the general population but also to be investigated as a treatment option for individuals with conditions as diverse as IBS, anxiety, depression and Alzheimer’s disease.

Tu1924 - Does Rifaximin Prior to Fecal Microbiota Transplantation Improve Clinical Outcomes Compared to Microbiome Restoration Alone in Ulcerative Colitis? a Cohort Study Evaluating the Impact of Non-Absorbable Antibiotic Pretreatment

Tu1924 - Does Rifaximin Prior to Fecal Microbiota Transplantation Improve Clinical Outcomes Compared to Microbiome Restoration Alone in Ulcerative Colitis? a Cohort Study Evaluating the Impact of Non-Absorbable Antibiotic Pretreatment

Fecal microbiota transplantation for gastrointestinal disorders.

The importance of the gut microbiome in human health is being increasingly recognized. The purpose of this review is to examine the existing literature pertaining to alterations in the gut microbiome and the utility of microbiome restoration therapies in gastrointestinal disorders. Imbalance and maladaptation of the microbiome, termed dysbiosis, has been associated with several disease states such as irritable bowel syndrome, Clostridium difficile infection, inflammatory bowel diseases, nonalcoholic fatty liver disease, and obesity among others. The possibility of restoration of normal microbiota has become an attractive concept for diseases in which the normal microbiome is perturbed. The rationale of using fecal microbiota transplantation to treat disease has been validated by its successful use in treating recurrent Clostridium difficile infection, which occurs as a result of decreased microbial diversity in the gut, most often in the setting of recent antibiotic treatment. Similar strategies may be applicable to other disorders. Alterations in the gut microbiome are associated with several disorders, and microbiome restoration based therapies such as fecal microbiota transplantation may be an adjunct to conventional treatments but more investigation is needed.