2023 Conference Agenda

• Database and method changes
• Relativity vs. absolute measure
• Consumer relevance and acceptance
• Connect multi-omics data to generate new insight
• Regulatory/regulation challenges – how to talk about benefits

Gut Microbiome Index for Clinical Applications
The genomic revolution has transformed our ability to uncover how our microbiome contributes to our health and wellness, and the role of gut microbiome has been studied over a broad range of diseases (>300). The presentation will discuss progress towards better understanding of gut microbiome using Precision Taxonomy and our efforts in developing a Gut Microbiome Index (GMI) reflecting the state of gut health to enable preventive medicine and endpoint measurements for microbiome clinical trials.
Hasan Nur, Ph.D., MBA, Chief Executive Officer, EZ Biome

Pipeline Development and Characterization for Long-read Microbiome and Metagenome Profiling and Assembly
In the past several years, the ability to capture full-length 16S rRNA has enabled researchers to profile microbiomes with significantly higher resolution at the species and strain level. On a complex human fecal reference sample, we found full-length 16S to have high correlation to shotgun metagenome taxonomic abundances emphasizing that it’s possible to get metagenome taxonomic resolution at amplicon sequencing costs. For metagenome taxonomic profiling, recent work has demonstrated that a few tools displayed the highest precision and recall of the methods evaluated for long-read datasets. These methods performed best with highly accurate long reads in comparison to other long reads and short reads. To improve access to these tools, we developed workflows and demonstrated the performance by analyzing several datasets. With the development of new metagenome assembly algorithms, it’s now possible to reconstruct full metagenome-assembled genomes (MAGs) for species. We have developed a pipeline that automates major steps including a custom binning strategy tailored to long-read assemblies, quality filtering, and taxonomic identification.
Jeremy Wilkinson, Ph.D., Senior Staff Specialist, Microbial Genetics, PacBio

R-3750: an Oral Microbiome Immunotherapy for the Treatment of Ulcerative Colitis
Description - R-3750 is a synthetic biology-based cellular immunotherapy being developed for the treatment of ulcerative colitis. R-3750 delivers a key microbiome-associated immune regulatory molecule that controls host immune function. Preclinical models showed that R-3750 engages a specific receptor expressed on dendritic cells to reestablish colonic immune homeostasis by reducing inflammation, improving gut membrane barrier integrity, and reestablishing a normal microbiome composition. This talk will review the preclinical development of R-3750 leading to initiation of the Phase I clinical trial.
Christian Freguia, Ph.D., Senior VP Research, Rise Therapeutics

Microbiome Medicine: Payors, Providers, and Patients
Microbiome management incorporated into disease preventive screening diagnostics, patient education, and health accountability as a standard practice of care.
Cassandra Isley, Chief Executive Officer, Microbiome Alliance for Disease Prevention

Metagenomics Assays to Study Clinical Pharmacology: Measuring Safety, Pharmacometrics and QA in Microbiome-relevant Terms
Live biotherapeutic products (LBPs) consisting of defined bacterial consortia have been proposed as a novel class of therapeutics for the treatment of diseases such as Clostridioides difficile infection. However, applying drug discovery principles to the LBP development process requires new analytical methods and assays. One Codex will present novel approaches to adapt reference databases with study-specific genomic libraries and create sensitive, genome-specific marker panels, achieving compounding gains in metagenomics data interpretability. In the second part of our talk, Vedanta will present the application of these techniques in the clinic to evaluate LBP strain detection and colonization, and host microbiome recovery associated with LBP administration in humans. These results help define the relationships between drug dose, exposure and effect for microbiome-directed medicines based on defined bacterial consortia and offer a rational path forward for clinical development.
Aaron Del Duca, Lead, Business Development, One Codex
Rajita Menon, Ph.D., Associate Director, Modeling & Statistics, Vedanta Biosciences

Restoring Nitric Oxide: Prebiotic Nitrate and the Oral Microbiome
Nitric oxide is one of the most important signaling molecules produced in the human body. It is critical for oxygen delivery, immune surveillance, cardiovascular, metabolic, and mental health. Unfortunately, as we grow older, we lose the ability to make it. Dietary inorganic nitrate is our back-up system in restoring nitric oxide beginning with the bioconversion of nitrate to nitric oxide by the oral microbiome. Shifting the oral microbiome to a nitric oxide-favorable microbiota to enhance local and systemic nitric oxide bioavailability is emerging to be consequential in cardiovascular medicine and dentistry. This presentation will discuss the importance of addressing oral dysbiosis with prebiotic nitrate formulas, including the delivery with functional chewing gums, and the implications in oral-cardiovascular health outcomes.
Shawn Green, Ph.D., Founder & CEO, MyFitStrip

Luncheon

Direct-to-consumer Microbiome Testing Combined with Extensive Validated Surveys Allow for Determination of Key Health and Lifestyle Drivers of Microbial Communities in Household Dogs
While there are studies detailing the structure of the gut microbiome in domestic dogs, little has been done to determine drivers of alpha-diversity in the general population of pet dogs. To this end, the combination of D2C microbiome testing of pet dogs, customized canine-gut microbial database, and extensive validated surveys allow us to generate these insights. Therefore, this talk highlights the use of machine learning to both determine health and lifestyle drivers of gut microbial alpha-diversity and predict health outcomes using microbial features in pet dogs. These insights provide evidence for pet dogs as a model for examining drivers in human microbial diversity as pet dogs have a similar living environment as their owners and have controlled diet and lifestyle.
Roshonda Jones, Ph.D., Senior Bioinformatics Scientist, Nom Nom

Surmounting the Challenges of Bringing the Next Generation of Microbiome Supplements for Companion Animals to Market
Holly Ganz, Ph.D., Chief Science Officer, Co-Founder, Animal Biome

Modeling and Modulating the Subgingival Microbiome - Implications for Development of Periodontal Healthcare Products
It is currently accepted that periodontitis is a result of an imbalance in the composition and function of the subgingival microbial community (dysbiosis) rather than an assault from a handful of pathogenic species. Consequently, an emerging strategy for prevention and/or adjunctive treatment of periodontitis is to promote or restore a “normobiotic” microbiome compatible with health by using modulators such as prebiotics and probiotics--a research area that is vastly understudied. In this presentation, Dr. Al-Hebshi will discuss his group's in vitro model in which they, by optimizing medium composition and growth conditions, managed to grow dysbiotic and normobiotic subgingival microbiomes in parallel in high throughput format. He will also present SMDI, an index with high clinical diagnostic accuracy for measuring subgingival microbial dysbiosis that his team recently developed to serve as a quantitative tool in microbiome modulation studies. Together, the in vitro model and SMDI, can be used to identify targetable drivers of dysbiosis as well as to screen banks of potential modulators to identify those with promising activities before testing them further in animals and humans, and eventually developed into periodontal healthcare products.
Nezar Al-Hebshi, Ph.D., Co-director, Oral Microbiome Research Laboratory, Kornberg School of Dentistry, Temple University

Multi-omic, Behavioral, and Molecular Studies Implicate Fatty Acids in Autism
In this presentation, Dr. Taturu will present the results of a multi-year long project elucidating the relationship between the gut microbiome and autism spectrum disorder (ASD). This project employs a combination of newly developed natural language processing techniques, mouse behavioral assays, and molecular biology techniques (omics) to build a compelling case for the importance of medium chain fatty acids in Autism. Data suggest a major role for medium and long-chain fatty acid availability in the behavioral and gastrointestinal aspects of ASD.
Christine Taturu, Ph.D., Postdoctoral Researcher, Oregon State University

End of Conference