2024 Conference Agenda

Monday, March 25, 2024

7:30 AM

Registration/Continental Breakfast

8:15 AM

Chairperson's Opening Remarks

Mollie Roth, JD, Chairperson, The Annual Translational Microbiome Conference

8:30 AM

Unraveling Gut-Derived Molecules for Innovative IBD Therapeutics

In the pursuit of groundbreaking drug discovery, Pragma Bio employs a comprehensive and multidisciplinary approach integrating real-world data, artificial intelligence/machine learning (AI/ML), synthetic biology, and pharmacology. Pragma's in-house Discovery Pipeline encompasses three integrated stages: 1) In silico phenotypic correlations for BGC identification, 2) A synthetic biology-based platform for BGC-derived small molecule production and 3) Pharmacological lead generation using both in vitro and in vivo models. Our latest research demonstrates an analysis of 6,490 samples from 608 patients across seven cohorts, including healthy controls and IBD patients. In this study, we identified and ranked unique BGCs correlated with specific patient groups. Synthetic biology efforts led to the production of PB010, a gut-derived molecule with a distinct in vitro immunological phenotype. In vivopharmacodynamic studies revealed a reduction in disease-relevant immune cell subtypes, positioning PB010 as a unique therapeutic opportunity for inflammatory diseases. Beyond its significance in IBD, this research underscores the potential of harnessing microbiome-derived molecules for drug discovery, aligning with Pragma Bio's overarching mission to revolutionize healthcare through innovative and data-driven research.
Orly Levitan, Ph.D., VP of Partnerships and Business Development, PragmaBio

9:00 AM

Modulators that Improve the Microbiome and Promote Healthy Gut Aging

The signs of gut aging typically include dysbiosis of the microbiome, increased permeability in the intestines (known as "leaky gut"), low-grade systemic inflammation (called "inflammaging"), and digestive disorders. In addition, the gut-brain axis research has clearly shown a clear connection between metabolites produced by microbes in the gut on cognitive health. Probiotics and prebiotics can help address gut health and cognitive decline associated with aging. Our studies showed that middle-aged and older adults with mild cognitive impairment (MCI) have a different gut microbiome and that probiotics can specifically target those differences. Pre-clinical and in vitro studies evaluated the effectiveness of galacto-oligosaccharides (GOS) in reducing gut aging in mice. We found that GOS increased the abundance of specific bacteria and reduced intestinal permeability and inflammation. The same prebiotics were effective in reducing symptoms and altering the fecal microbiome in lactose-intolerant patients. Overall, our studies suggest that probiotic and prebiotic interventions targeting the gut microbiome can preserve and restore cognitive health, protect the aging brain via the gut-brain axis, and improve digestive issues.
M. Andrea Azacarate-Peril, Ph.D., Assoc. Prof., Depts. of Medicine & Nutrition, Dir., Microbiome Core Facility, Univ. of North Carolina at Chapel Hill School of Medicine

9:30 AM

Constructing Microbial Communities to Advance Live Biotherapeutic Product Discovery

The microbiome industry seeks to develop live biotherapeutic products (LBPs) that will be efficacious in broad patient populations. However, heterogeneity of native microbiomes can confound efficacy in a subset of patients. A key question in LBP development is: How can we find microbial therapeutics with efficacy that is robust to variation in the host microbiome? Concerto's kChip discovery platform not only reveals which microbes can be combined into ensembles for therapeutics, it also directly measures how robust each ensemble’s efficacy is to the presence of other microbes. Here, we present progress on Concerto's efforts to discover an LBP for recurrent vulvovaginal candidiasis, including a demonstration of how robustness can optimized during the discovery process using kChip.
Cheri Ackerman, Ph.D., Co-founder & Chief Scientific Officer, Concerto Biosciences

10:00 AM

AI Implementation for Microbiome Secondary Metabolites Discovery and Therapeutics

Natural products and their derivatives are an important source of therapeutics. The human microbiome is a large, mostly untapped source of small molecules. At Xbiome we are using artificial intelligence and bioinformatics techniques to improve our ability to identify natural products with therapeutic potential, with particular interest in their synergistic potential in anti-tumor therapy.
Antonio Gomes, Ph.D., Principal Scientist, XBiome

10:30 AM

Morning Refreshment Break, Exhibit-viewing and Poster Session

11:00 AM

Developing FDA-Approvable Live Biotherapeutic Products: Exploratory Analyses of Microbiome Restoration and Engraftment in the Phase 3 Trial of Fecal Microbiota, Live-JSLM (Rebyota™)

Ken Blount, Ph.D., Chief Scientific Officer, Rebiotix, A Ferring Company

11:30 AM

Measurement Assurance for Innovation in Microbiome Science

Appreciation for the role of microbes in our lives has been growing rapidly, but the measurement science needed to understand and fully utilize microbial systems has developed at a much slower pace than the industries dependent on them demand. In all applications involving complex microbial communities, the research is hampered by the lack of standards, protocols, and technical infrastructure to allow confidence in the data and comparability. NIST is developing standards to enable research investigations and commercial translation of microbiome science by providing measurement assurance tools: protocols, reference materials, validated measurements, and critically evaluated reference data.
Stephanie Servetas, Ph.D., Microbiologist, National Institute of Standards & Technology

12:00 PM


1:00 PM

Leveraging the Vaginal Microbiome to Unlock Precision Female Health

The vaginal microbiome is a critical component of female health. More than 30% of people with vaginas suffer from imbalances in the microbiome (e.g. bacterial vaginosis, yeast infections, and recurrent UTIs) that drastically affect our quality of life. Additionally, research has uncovered groundbreaking links between the vaginal microbiome and infertility, HIV risk, preterm birth, gynecologic cancers, and more. Evvy’s longitudinal, metagenomic testing is unlocking personalized definitions of health and disease in the vagina — and providing women with education and insights about their vaginal health along the way. This talk will highlight opportunities to leverage the vaginal microbiome to positively impact women’s health outcomes across the board.
Pita Navarro, Co-founder & Chief Science Officer, Evvy

1:30 PM

The Defining Biomarkers for Spontaneous Preterm Birth

Conventional wet lab methods for finding immunoregulators are slow due to multi-omic data complexity. Linear analysis often overlooks intricate biological interactions, Turing Biosciences will discuss a patent pending AI-driven biological discovery platform that quickly discerns critical immunoregulators from real data, emphasizing practical interactions to innovate and streamline discovery.
Eric Luellen, MsC, MPH, Founder & Chief Technology Officer, Turing Biosciences

2:00 PM

A Microbiome-derived Sugar Protects Against Metabolic and Inflammatory Diseases

It is now clear that human health is intimately tied to the gut microbiota, and there has been significant enthusiasm over the past two decades to harness these host–microbiota interactions as novel therapeutics for medically recalcitrant diseases. While there has been some progress in identifying specific commensal bacteria that modulate disease, there are few examples of the microbiome-derived products that mediate these effects. This talk will describe a discovery platform we developed to identify commensal microbes that protect against disease. Using our approach, we have purified and characterized a commensal-derived sugar that protects against metabolic and inflammatory diseases through its ability to modulate innate immunity. Our findings lay the foundation for using this microbiome-derived product as a clinically relevant therapy.
Neil Surana, MD, Ph.D., Assist. Prof., Dept. of Pediatrics (Infectious Diseases), Molecular Genetics & Microbiology, & Immunology, Duke University

2:30 PM

Presentation to be Announced

3:00 PM

Refreshment Break, Exhibit-viewing, Poster Session

3:30 PM

Live Biotherapeutics Drug Development & Manufacturing: CMC Challenges

Appreciating that clinical LBP manufacturing is not an easy journey, many challenges are encountered along the path because of the nature of the living organisms we are interested in. In this presentation, Mr. Ellis will describe the challenges encountered and the solutions Biose bring to help their clients to take lab organism to a real GMP product accepted for use in the clinic by the FDA.
Richard Ellis, Head of Business Development, Biose Industrie

4:00 PM

Causal Inference and Feature Aggregation for High-dimensional Microbiome Data

Inferences for causal effects in the presence of both high-dimensional sequencing outcomes and confounders are “double-challenging.” The first is addressed by extending the classical definition of average causal effect (ATE), deploying biologically relevant aggregating metrics such as ecological distances. To overcome the second obstacle of high-dimensional confounders, especially when p>>n, recent development focuses on data-adaptive approaches such as machine learning (ML) with regularizations and cross-fitting. However, the induced regularization bias may propagate to invalidate the naive estimation of causal effects, especially when the imposed sparsity assumption is violated. In this talk, I will introduce a feature aggregation framework that bypasses the regularization and deploys the efficient influence function (EIF) at multiple levels to characterize the causal effect, which has been applied to decipher the timely issue of the “gut-brain axis” among the human microbiome, cognitive, and psychosocial measurements.
Jinyuan Liu, Ph.D., Assistant Professor of Biostatistics and Psychiatry & Behavioral Sciences, Vanderbilt University

4:30 PM

The Role of the Microbiome in Kidney Stone Disease: a Story of Oxalate, Drugs, and Vitamins

Kidney stone disease affects upwards of 10% of the North American population. While it has historically been a disease afflicting middle-aged men, in recent years rates have rapidly risen in women and children. Calcium oxalate is the most common stone composition, and they are often idiopathic in nature. Human health is intimately linked to the gut microbiota, but previous studies of microbiota involvement in kidney stone disease have been limited to potential oxalate degrading abilities by gut bacteria and the association with antibiotic exposure. We sought to provide a unified assessment of the bacterial contribution to kidney stone disease, not just in the gut, but also the urinary tract and oral cavity. We will present our findings from several clinical studies and complementary mechanistic work, which together illustrate a xenobiotic-induced bioenergetic network collapse in stone formers that ultimately modulates host calcium and vitamin homeostasis leading to stone formation.
Kait Al, Ph.D., Postdoctoral Research Fellow, Lawson Health Research Institute, University of Western Ontario

5:00 PM

Cocktail Reception

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