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Cargill
National Institute of Standards & Technology
NIST
Agenda Day 1
Wednesday June 21st
Zachary Pitluk, PhD
VP Life Science BD
Paradigm4
Talk Title: Uniting Kingdoms - How to Manage Omics Data from Helicobacter to Humans using REVEAL: SingleCell
Abstract:
While the term meta-organism has been used to describe the obligate nature of prokaryotes for mammalian survival, the relationship has always been at flagella's length. With the increasingly central role that the human microbiome plays, efforts focused on truly integrating data to support joint discovery across kingdom boundaries. Challenges, like managing sparsity of data and the scale of the feature maps, can be solved using modern data modeling and management techniques, like those that are in Paradigm4's REVEAL platform.
Kristin Neumann, PhD
Co-Founder & CEO
MyMicrobiome
Talk Title: What the Bleep Do We Know about the Microbiome?
Abstract:
The microbiome is an exciting new area humanity is exploring. After the decoding of the human genome, we realized that our genome does not offer sufficient tools to make our body work properly. This is how the Human Microbiome Project was initiated. Now, 16 years later, the microbiome became mainstream. Products analysing, supporting and healing our microbiome are flooding the market, spreading the hope to improve everyone’s health.
What do we currently know about this amazing topic and how can applications be used in a meaningful way? In this talk we are going to summarize the current state of research and what can be done to support a healthy microbiome in our lives.
Alexander Senf, PhD
Senior Bioinformatics Engineer
Biomatics
Talk Title: Beyond Genomics: Multi-Omics and Microbiome Data and the Importance of FAIRness
Abstract:
An overview of omics data beyond genomic sequences and sequence variations, leading to the importance of data being FAIR. The microbiome is introduced, in terms of omics data, leading to a case study underlining the usefulness of FAIR data when analyzing data in this environment.
Syed Ana Jawaid
Bioinformatics Analyst
Biomatics
Talk Title:
Abstract:
Ken Finley, PhD
Principal Biotechnologist
Cargill
Talk Title: Galleon - Cargill’s Microbiome Intelligence Tool
Abstract:
Cargill’s Galleon™ Microbiome Intelligence is a simple, non-invasive analysis tool that allows producers to determine the gut microbiome health of their flocks. After sampling, poultry producers receive a report that includes a summary of their site samples, flock microbiome biomarker composition, predictions and insights about the microbiome constitution of their flock. A Cargill technical expert walks producers through the report in detail and provides recommendations on how to take action to support performance, health and preharvest food safety. Galleon™ simplifies a complex process to provide poultry producers with practical, actionable insights to help improve animal health, performance, food safety, and ultimately, a return on investment through non-invasive testing of the gut microbiome health of their flock. Cargill’s Galleon™ uses an AI-powered engine that allows producers to determine the gut microbiome fitness of their flock while also helping them understand how it correlates to numerous management parameters and practices.
Pedro Torres, PhD
Sr. Scientist, Computational Biology & Data Science
Persephone Biosciences
Talk Title:
My Baby Biome Study: A Data-Driven Approach to Infant Probiotic Development
Abstract:
The infant microbiome plays a crucial role in establishing a healthy host-microbiome relationship. Recent research has identified a critical window in early-life (the first 3 months) where gut microbial dysbiosis has the most impact on human immune development. Existing infant microbiome datasets lack comprehensive multi-omics analysis and sufficient racial and ethnic diversity for population-wide biomarker discovery. Persephone Biosciences addressed this gap through the My Baby Biome (MBB) study, enrolled ~700 infants up to the age of 3 months across the U.S, representative of US birth and feeding modes Using shotgun metagenomic sequencing and metabolomics, we identified three microbiome compositional clusters. A healthy cluster was distinguished by high Bifidobacterium levels and association with specific anti-inflammatory metabolites. Further exploration of MBB isolated strains and commercial strains in ex-vivo gut environments revealed their impact on microbial composition and function. These findings provide a data-driven approach to infant probiotic development.
Eddie Adams, PhD
Chief Scientific Officer
Micronoma
Talk Title:
Using All Our Genomes: Multi-Species & Multi-Omic Liquid Biopsy Detection of Early-Stage Lung Cancer
Abstract:
Links between cancer and microbes date back four millennia (Sepich-Poore et al. 2021. Science). Recently, we found that microbial DNA is detectable in tumor tissues and patient blood from many human cancer types (Poore et al. 2020. Nature; Narunsky-Haziza et al. 2022. Cell). These intratumoral and bloodborne microbiomes were distinct between cancer types, between normal and malignant tissues, and present in cell-free plasma samples. However, the practical utility of cell-free microbial DNA (cf-mbDNA) as a bona fide liquid biopsy remains untested, including its ability to diagnose early-stage disease in treatment-naïve individuals, to distinguish histological subtypes, and to discriminate against non-cancer-but-diseased patients. Thus, we constructed an age and sex-matched cohort (“CODICES”) comprising >1000 individuals with lung cancer, lung disease, and no disease (healthy) to evaluate the utility of a cf-mbDNA-driven liquid biopsy diagnostic. We show that cf-mbDNA comprises a novel class of cancer-genome orthogonal biomarkers that complements host analytes.
Joseph Petrosino, PhD
Director, Alkek Center for Metagenomics & Microbiome Research & Professor
Baylor College of Medicine
Talk Title: Translational Microbiome Research in the Era of Personalized Medicine
Abstract:
The Alkek Center for Metagenomics and Microbiome Research is coordinating and leading research and development efforts in this area across the Texas Medical Center, and with collaborators from around the US and abroad. CMMR researchers are developing molecular and informatics tools and resources to advance diverse clinical and basic research projects pertaining to the organisms that comprise the microbiome, the genetic makeup of these bacteria, viruses and fungi, and how these commensal microorganisms interact with human cells and tissues during the course of life. In addition to germ free animal models, C. elegans and zebrafish, we are leveraging sophisticated 3D tissue culture systems to understand the reveal personalized interactions between the microbiome and host. These tools have helped us reveal causal microbiome interactions that may be critical for human health and development.
Kuan Ding, PhD
Chief Science Officer
Catalytic Data Science
Talk Title: In silico Hypothesis Generation and Testing for Microbiome Research
Abstract:
In recent years, the study of microbiomes and multiomics data has gained immense importance in unraveling complex biological systems. The integration of the various omics data sets, such as genomics, transcriptomics, metabolomics, and proteomics, with microbiome data has paved the way for a deeper understanding of the interplay between microbial communities and host health. However, extracting meaningful insights from the vast amounts of data generated by these technologies remains a significant challenge.
This presentation aims to highlight the power of Catalytic Data Science in advancing microbiome research with an approach to accelerate hypothesis generation with advanced, integrated multiomic data analysis. We showcase real-world applications of Catalytic Data Science in Crohn’s Disease, including an end to end workflow identifying candidate genes, pathway associations, and subsequent downstream analyses.
Catalytic Data Science has developed a comprehensive, cloud-based solution designed to empower life sciences researchers to streamline their data management, analysis and collaboration efforts. Catalytic Data Science combines machine learning, statistical modeling, and domain expertise with advanced analytics and visualizations to extract actionable insights from complex biological datasets.
Scott Peterson, PhD
VP Translational & Laboratory Science
Prescient Metabiomics
Talk Title:
Meta-analysis of Multi-functional Biomarkers for Predictive Modeling of Colorectal Adenoma and Carcinoma
Abstract:
We conducted a clinical meta-analysis of published deep metagenomic stool sequence datasets including 1,670 subjects from 9 countries, including 703 healthy controls, 161 precancerous colorectal adenoma (CRA), 48 advanced precancerous colorectal adenoma (CRAA) and 758 CRC cases confirmed by colonoscopy. We describe a novel automated machine learning workflow using a two-stage feature importance ranking and ensemble modeling method to identify and select highly predictive taxonomic and functional biomarkers. Machine learning modeling of selected features differentiated the metagenomic profiles of healthy patients from CRA, CRAA and CRC cases with an average area under the curve (AUC) for external holdout testing of 0.84 (sensitivity=0.82; specificity=0.71, accuracy=0.77) for CRC; an AUC of 0.97 (sensitivity=0.78; specificity=0.98, accuracy=0.97) for CRAA; and an AUC of 0.90 (sensitivity=0.74, specificity=0.89, accuracy=0.86) for CRA. Application of our ensemble approach for feature selection increased the predictive power and may generate greater generalizability.
Stephanie Servetas, PhD
Microbiologist
National Institute of Standards & Technology (NIST)
Talk Title:
Measurement Assurance for Innovation in Microbiome Science
Abstract:
Appreciation for the role of microbes in our lives has been growing rapidly, but the measurement science needed to understand and fully harness microbial systems has developed at a much slower pace than the industries dependent on them demands. 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. At NIST, we are developing tools to enable measurement assurance of complex microbial systems for applications in clinical diagnostics, agriculture, and the environment.
Keith Robison, PhD
Principal Scientist
Ginkgo Bioworks
Talk Title:
Let's Do The Warp Drive Again! Can Sequencing Exhaustively Elucidate the Microbiome?
Abstract:
A bit over a decade ago, Warp Drive Bio formed to discover transformative natural product pharmaceuticals. In its six-year lifespan, WDB generated the largest industrial microbe database (about 145K genomes) for this purpose, yet multiple datapoints suggest it barely scratched the surface of the biochemical diversity of the Actinomycetes. Sequencing technology has improved immensely in the intervening time - if we tried again how much better could we expect to do? Are the new sequencing instruments up to the task? What are the gaps in DNA extraction and library prep technology that have resulted from the industry's focus on human not microbe genomes?
Vancheswaran Gopalakrishnan, PhD
Associate Director, Bioinformatics
AstraZeneca
Talk Title:
Abstract:
Casandra Hoffman
Director, Research Affinity Groups
University of Virginia
Talk Title:
Supporting Microbiome Research at Universities: UVA’s TransUniversity Microbiome Initiative
Abstract:
The infant microbiome plays a crucial role in establishing a healthy host-microbiome relationship. Recent research has identified a critical window in early-life (the first 3 months) where gut microbial dysbiosis has the most impact on human immune development. Existing infant microbiome datasets lack comprehensive multi-omics analysis and sufficient racial and ethnic diversity for population-wide biomarker discovery. Persephone Biosciences addressed this gap through the My Baby Biome (MBB) study, enrolled ~700 infants up to the age of 3 months across the U.S, representative of US birth and feeding modes Using shotgun metagenomic sequencing and metabolomics, we identified three microbiome compositional clusters. A healthy cluster was distinguished by high Bifidobacterium levels and association with specific anti-inflammatory metabolites. Further exploration of MBB isolated strains and commercial strains in ex-vivo gut environments revealed their impact on microbial composition and function. These findings provide a data-driven approach to infant probiotic development.
Agenda Day 2
Thursday, June 22nd
Simon Adar, PhD
CEO
Code Ocean
Talk Title:
Abstract:
Announcing The World’s First
Microbiome & Multi-Omics (M&M)
Virtual Conference
March 8-9, 2022
The amount of work happening today to understand biology has and will continue to exponentially increase. What comes along with that is exponential increases in data!
We will get to see major discoveries unfold over the next couple of years because of the microbiome and multi-omics research. We predict we will also see many associations and improvements in all aspects of life simply through the new understanding and how the microbiome is involved in multiple different systems.
Central to science and technology endeavors and understandings is and will be the ability to produce and consume FAIR data and processes and use the power of technology to exploit as much as possible.
Because of these immense current and future capabilities, 20/15 Visioneers will bring together the thought leaders who are making major impacts from a software, research, and product perspective. In the spirit of keeping things simple, highly interactive, and focused on knowledge sharing the live virtual conference will consist of the following:
Pivoting the typical conference approach while reducing the tracks and bringing the most interesting presentations for a better attendee experience.
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Daily Round Table summaries
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Key Notes
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Vendor Show Cases with individual Break-Out-Rooms (Augmented Reality), scheduled 2x each day
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Industry and academic speakers
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Free for attendees!
Conference Recording Links
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