2020 WEBINAR SCHEDULE
Rapid High-throughput Cultivation of Diverse and Rare Bacteria from the Human Gut Microbiome
Date: September 9, 2020
Time: 1:00 PM CDT
Being able to parse the full complexity of communities in the Human Gut Microbiome requires not just knowing which strains are present but also determining what each constituent strain does and how they interact with each other, their host and environment. Today’s microbiology workflow leans heavily on labor-intensive, low-throughput tools such as Petri dishes and broth cultures, that are not capable of detecting these nuances because they lack the scale and level of throughput needed for this level of analysis. New cost-effective, high-throughput tools for microbial isolation and cultivation can facilitate this level of analysis of thousands of strains at once while simultaneously preserving them in living form for functional characterization.
A second requirement for this level of analysis is the need to assemble a robust isolate library that is representative of the microbial community from which they are derived. Rare and/or slow-growing species can be missed during cultivation using petri dishes. Although they may comprise only a small percentage of the overall mix of microbes, rare and/or slow-growing species can be key players in maintaining the overall equilibrium of a community and may even be keystone species.
Dr. Jewell will discuss one method of assembling such a robust isolate community as compared to standard low-throughput tools and how being able to scale the generation of diverse isolate libraries that includes rare species is critical to accelerate microbiome-level insights for research and product development.
Dr. Jewell received her Ph.D. at University of California, Davis, in Microbiology and did her postdoctoral research at San Francisco State University and at Lawrence Berkeley National Laboratory, where she worked on development of in vitro diagnostic platforms for infectious disease. She currently leads development of the Prospector platform for high-throughput microbial cultivation and isolation from the human gut microbiome at GALT.
Viral Metagenomics and the Use of Standards: From Biology to Clinical Applications
Date: August 19, 2020
Time: 1:00 PM CDT
Viruses can infect bacteria as well as a myriad of eukaryotic cells. Virus membership and function within the human microbiome are being revealed with the advent of metagenomics, and knowledge on these communities will continue to expand with the application of new sequencing technologies and analysis tools. This information is readily translating into clinical applications, which include, but are not limited to, the rapid sequence identification of pathogenic viruses and phage therapy. However, without appropriate standards and controls, researchers are unable to make meaningful cross-study comparisons or assess biases that can be introduced at different stages of a viral metagenomics pipeline. As the field of viral metagenomics translates into clinical and other applications, the implementation of viral standards and controls is of increasing importance.
- Implementation of viral standards and controls can help determine biases that could be potentially introduced at different stages of a viral metagenomics pipeline.
- Identification of biases in a viral metagenomics study provides the opportunity to troubleshoot and benchmark reagents and analysis tools.
- Viral standards may evolve to mimic simple and more complex viral communities in diverse environments.
Dr. Tasha M. Santiago-Rodriguez is currently a Microbiome Bioinformatician at Diversigen in Houston, Texas. She received a PhD from the University of Puerto Rico in Public Health Water Microbiology, characterizing bacteriophages as indicators of water quality. Dr. Santiago-Rodriguez conducted postdoctoral research at the University of California, San Diego, focusing on virome research related to methicillin-resistant Staphylococcus aureus (MRSA) infections, urinary tract infections, and antibiotic use.
Dr. Santiago-Rodriguez was also a recipient of a postdoctoral fellowship from the Howard Hughes Medical Institute to conduct research on ancient microbiomes and viromes. She later joined the American Type Culture Collection (ATCC) Center for Translational Microbiology to develop standards and controls for microbiome research.
Optimizing Yield and Viability of Live Biotherapeutic Products (LBPs) While Minimizing Risk in Development
Date: July 29, 2020
Time: 1:00 PM CDT
Live Biotherapeutic Products (LBPs) have unique requirements unlike other biologics or small molecules. Understanding these differences is a critical part of mitigating risks in process development and manufacturing programs. Most LBPs have unique characteristics and processing requirements. Deep experience with LBPs and their unique challenges is essential to LBP development success, especially when looking ahead toward the late-stage activities on the critical path to commercial launch. This includes the ability to navigate hurdles such as the nascent regulatory pathway, highly nuanced processing, manufacturing and supportive analytics requirements as well as specialized facility and procedural controls required to handle them safely and effectively.
With more than 11 years of experience working with more than 135 species spanning 85 genera, Arranta Bio is acutely aware of pitfalls and critical success factors of capably manufacturing these complex LBPs. During this webinar, leaders from Arranta Bio will illustrate how microbiome innovators can use this experience, expertise and infrastructure to optimally develop a high-yielding high-viability LBP product while reducing time, risk and cost.
David Stevens is the Chief Operations Officer of Arranta Bio. In this role, Mr. Stevens is responsible for Arranta’s operations functions including laboratories, manufacturing, client program management and engineering.
Mr. Stevens brings over 20 years of broad international operations and commercial experience in the CRO and CDMO sectors. He was formerly the Senior Vice President & Head of AMRI’s Drug Product business unit where he had P&L responsibility for sales and operations. During his tenure, he led the division through a period of significant growth and capacity expansion. Before leading the division, Mr. Stevens held senior leadership roles at AMRI including Vice President, Sales & Marketing and General Manager of a sterile dosage form development and GMP manufacturing facility.
Mr. Stevens holds an MBA in strategy, finance and marketing from the University of Edinburgh and an undergraduate degree in Business from Edinburgh.
Dr. Aaron Cowley is the Chief Scientific Officer at Arranta Bio, having been a co-founder and the Chief Technical Officer of Captozyme, which served the microbiome CDMO market for 10 years since 2009 and merged with Arranta Bio in October 2019.
He is a renowned member of the biotech community and was the recipient of the prestigious Ruth L. Kirschstein National Research Service Award for his post-doctoral work at the University of Georgia. His further work has resulted in 15 peer-reviewed journal articles.
Prior to establishing Captozyme in 2009, Dr. Cowley was a Scientist II/Preclinical Manager at OxThera, Inc. in Alachua, Florida.
He holds a Bachelor’s Degree in Biochemistry from Benedictine College, a Ph.D in Inorganic Chemistry from the University of Kansas, and an MBA from the University of Florida.
Attracting Big Pharma to the Microbiome Field
Date: July 8, 2020
Time: 1:00 PM CDT
Unlike other therapeutic areas, the microbiome therapeutics field is not dominated by Big Pharma. Instead, we see many innovative SMEs dominating, all focused on driving the development of a single or a small pipeline of bio-therapeutics. This has resulted in an impressive range of innovative products in development, often targeting conditions for which conventional “small molecule” drug discovery projects have failed to adequately address. In 2018 we saw the first acquisition of a microbiome company by Big Pharma, with the purchase of Rebiotix by Ferring. However, most Big Pharma are perhaps more tentatively venturing into the microbiome field via collaborations (e.g. MSD and 4D Pharma, Takeda and Finch Therapeutics).
The discussion will begin by looking at the advantages and disadvantages of engaging with Big Pharma, and then move onto looking at what attracts Big Pharma and broadly at the options open in the microbiome field. More specifically, looking at: “Drugs from bugs” (bio-active molecules derived from bacteria), “Bugs as drugs” (therapeutic bacteria and phage with combinations of such from single strain to FMT), “Bugs for drugs” (the use of bacteria as adjuvant technology for enhancing “conventional” therapeutics). The discussion will conclude with hints and tips for those preparing to pitch their technology to one of the Big Pharma.
Alex Therein, Executive Director and Head of Investigational Biology at Merck’s Exploratory Science Center (ESC), and Andrew Wells, Head of the HGF Pharmaceutical Group and formerly in-house council at AstraZeneca (AZ), have direct experience of what Big Pharma look for in emerging technologies. Craig Thomson, Partner and member of the HGF Microbiome IP group (http://www.hgf.com/industry/microbiome/), will be chairing a discussion between these experienced individuals on the above topic.
Craig is a founding member of the HGF IP Microbiome Team, one of the largest IP teams of its type in Europe (http://www.hgf.com/industry/microbiome/). He has considerable experience in providing pragmatic, commercially focused advice to a wide-range of clients and in relation to biotechnological and pharmaceutical inventions. As well as patent drafting and prosecution, Craig advises on the development of company-wide IP strategies, preparing for or carrying out funding/acquisition due diligence, and advising on aggressive/defensive strategies in relation to third party IP.
After having worked on matters in the field for more than 15 years, a particular focus of Craig’s practice relates to therapeutic microbiome innovations. Craig has worked on projects in relation to OTC products, faecal transplant therapies, bacterial and bacteriophage therapies (single strain and consortia), formulation technologies, bioinformatics analysis of microbiome, production and purification processes, synthetic biology and a wide range of diagnostics (for example, those for detecting or quantifying bacterial infection and those that use bacteriophage).
Having worked closely with multi-national corporations, Craig is aware of the particular challenges associated with efficiently prosecuting large multi-national patent portfolios, whilst keeping them relevant to the business. Craig has also found this experience of value when advising SMEs on collaborations with such large entities. Craig is a European, UK and Irish patent attorney, and has a BSc in Physiology and Pharmacology from the University of Dundee, and an MSc in Intellectual Property from the University of London. Prior to qualifying in London as a patent Attorney, he was a Patent Examiner at the UKIPO.
Andrew’s patent practice is principally in the pharmaceutical and chemical fields. He has extensive experience in securing patent protection for pharmaceuticals and specialises in drafting and prosecuting patent applications covering new chemical entities, salts, polymorphs, formulations (including advanced drug delivery technologies), manufacturing processes, medical uses, and medical devices.
Outside of the pharmaceutical field, Andrew’s practice encompasses polymer chemistry, petroleum additives, catalytic compositions, separation chemistry and biosensors. He acts for a diverse range of clients, including international corporations, universities, start-up companies and associate patent attorney firms based outside of the UK.
Andrew has a first class Bachelor of Pharmacy degree and a PhD in the development and evaluation of biodegradable carriers for nucleic acid vaccines, both from the University of Nottingham.
He commenced his patent career in private practice before joining the in-house patent department of a major multi-national pharmaceutical company in June 2004. As an in-house attorney, Andrew was responsible for the patent portfolios relating to a number of high priority drug development projects, as well as conducting due diligence evaluations to support in-licensing activities. Andrew returned to private practice in November 2008 when he joined the Manchester office of HGF as a partner.
Andrew draws on both his private practice and in-house experience to provide commercially-focused advice to his clients in relation to all patent matters, including patent portfolio management, enforcing patent rights, challenging third party patent rights, providing infringement and validity opinions, and conducting due diligence evaluations to support licensing and acquisition deals. Andrew also has considerable experience in representing clients in opposition and appeal proceedings at the European Patent Office.
Alex Therien is currently Executive Director and Head of Investigational Biology at Merck’s Exploratory Science Center (ESC) in Cambridge, MA. He was previously in the Department of Infectious Diseases where he played a key role in the development and licensing of the antitoxin antibody bezlotoxumab, indicated for prevention of recurrent C. difficile infections. He was also briefly Vice President and Head of Biology at Inception IBD / Ventus Therapeutics.
Alex has 19 years of drug discovery experience across a variety of therapeutic areas and has led research projects spanning the entire spectrum of the drug discovery/development process. His interest in the microbiome stems from his work on C. difficile which included the discovery of a key role played by the recovering gut microbiota in long-term protection by bezlotoxumab. His team at ESC continues to study the microbiome in the hope of identifying novel targets and therapeutics for far-ranging disease areas including oncology, neuroscience and infectious diseases.
Microbiome on the Cloud: A Case Study and Demo of the New Sigma-Aldrich® Bioinformatics Database and Software for 16S Analysis
Date: June 17, 2020
Time: 1:00 PM CDT
Translating Microbiome research from the lab bench to patients is a current challenge in the field due to the lack of reproducibility, caused by variables that can be introduced from sample collection upstream to statistical software used downstream. There is a growing need for robust tools and protocols that will enable safe adoption of microbiome studies while developing intervention or prevention strategies such as manipulations of diet and microbiome-based therapeutics.
MilliporeSigma offers a variety of Microbiome products for detection and standardization as well as a multi-omic service package, including the new Sigma-Aldrich® cloud-based platform for bioinformatics analysis. In this webinar, we will demo the ease of use and flexibility of the Sigma-Aldrich® 16S software to analyze large sample data sets and generate publication ready figures. We include unlimited data access and storage as well as in depth consultation with the experts in R&D and Bioinformatics at the start and finish of a project.
In this webinar, the presenters will do a deep dive into a case study of DNA extraction and sequencing that we’ve performed for one of our customers. We will demonstrate how we utilized Sigma-Aldrich® products and validated protocols to answer the customer’s key questions. We are offering every registrant a free of charge access to the Sigma-Aldrich® Microbiome platform for 16S analysis in 2020.
Andrew Schriefer is a Bioinformatic Data Scientist working for MilliporeSigma at the St. Louis, Missouri location.
Andrew is responsible for designing and validating the 16s-seq and WGS metagenomic analysis pipelines used in the Sigma-Aldrich metagenome webapp. Andrew also provides bioinformatic support to help optimize the microbiome Illumina sequencing workflows.
Before he joined MilliporeSigma, Andrew worked for Washington University in St. Louis as a bioinformatician assisting academic researchers with their Next Generation Sequencing projects.
Michal Daniely Ph.D. is the director of research and development for Merck KGaA, Darmstadt, Germany at the Jerusalem & Rehovot locations in Israel. Dr. Daniely is responsible for developing technologies and products for a wide range of research applications -- using core technologies such as: microbial fermentation, recombinant proteins design & expression, Next Generation Sequencing (NGS), Mass Spectrometry (MS), and antibodies development (monoclonal & polyclonal).
Over the past three years, Dr. Daniely has been deeply involved in shaping the company’s strategy within the microbiome research field -- aiming to develop products and technologies to support the growing need in this market.
Dr. Daniely earned her MSc & PhD in Human Genetics from the Sackler Medical School, Tel Aviv University, Israel. Prior to joining Merck KGaA, Darmstadt, Germany, she held various roles with medical device and pharma companies, where she managed the research & development activities.
De-risking Microbiome Research and Clinical Discoveries: Robust At-home Methods for Sample Collection, Storage and Transport
Date: May 20, 2020
Time: 1:00 PM CDT
Collection and storage of fecal material are the first steps in processing samples for evaluating microbiome composition and function via high-throughput shotgun sequencing. If samples are not handled and stored correctly, the risk of introducing unwanted variation into the analysis is high. Sample storage at -80°C immediately after sample collection is considered best-practice, or “gold standard”, in microbiome sample preservation. However, access to this storage condition is a major challenge, especially when sample collection occurs away from a research or clinical site. Changes affecting samples can occur rapidly, within days, yet many studies rely on cold chain or collection methods that do not rapidly freeze, or otherwise stabilize the sample. We sought to evaluate the changes in microbiome profile over short durations (1 to 7 days) using collection and storage conditions at room temperature, in an insulated foam container with ice packs, and using the OMNIgene®·GUT collection and stabilization device. Changes over time, and between start and end timepoints were compared to show that unstabilized fecal samples do not represent the originally collected sample. These changes have significant impact on the representation of the taxonomic and functional gene composition.
The presenters will discuss implications of unwanted variation for downstream data analysis, and how the OMNIgene·GUT collection device combined with high quality sequencing and analysis provided by Diversigen’s BoosterShot shallow shot gun approach can help generate more stable and reproducible results, and provide opportunities for home collection while mitigating the need for cold-chain transfer. This is true more so now than ever, allowing research and clinical discoveries to continue during these unprecedented times.
Jean Macklaim is a Bioinformatics Scientist at DNA Genotek, where she is developing and implementing bioinformatics and analytics approaches to sequence data. These R&D efforts are focused on deriving consistent, stable, and meaningful results from metagenomic, metatranscriptomic, and other omics data from a variety of human sample types including stool, oral, and urogenital.
She completed her Ph.D at Western University, Canada with a research focus on computational biology approaches for understanding microbiome function and composition. Her postdoctoral work contributed to developing compositional data analysis tools and methods for differential analysis in metatranscriptomic and high-throughput sequencing data for a number of human health, agriculture, in vitro, and environmental applications.
Christina Fragel is a Bioinformatics Scientist at DNA Genotek where she is developing and implementing bioinformatics and analytics approaches to sequence data. These R&D efforts are centered around statistical analysis and data visualization of the microbial composition in human-derived samples.
She received her Master’s degree in Bioinformatics from the University of Guelph, Ontario, Canada with a focus on machine learning techniques for assessing genetic diversity of invasive insect species.