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Determination of Strategic Priorities for a Microbiome Company Through Analysis of Technical Capabilities and Current Market Landscapes

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Determination of Strategic Priorities for a Microbiome Company Through Analysis of Technical Capabilities and Current Market Landscapes DETERMINATION OF STRATEGIC PRIORITIES FOR A MICROBIOME COMPANY THROUGH ANALYSIS OF TECHNICAL CAPABILITIES AND CURRENT MARKET LANDSCAPES by BRANDON EDWARD ANDREW Submitted in fulfillment of the requirements for the degree of Master of Science Thesis Advisors: Dr. Christopher Cullis, Dr. Emmitt Jolly, Dr. Neema Mayhugh Department of Biology CASE WESTERN RESERVE UNIVERSITY May 2020 CASE WESTERN RESERVE UNIVERSITY SCHOOL OF GRADUATE STUDIES We hereby approve the thesis/dissertation of Brandon Edward Andrew candidate for the degree of Master of Science. Committee Member Christopher Cullis Committee Member Emmitt Jolly Committee Member Neema Mayhugh Date of Defense April 2, 2020 *We also certify that written approval has been obtained for any proprietary material contained therein. 2 Table of Contents I. Technical and Scientific Background I.I Human Microbiome and Large-Scale Research Initiatives…………………..…….1 I.II Some notes on the design of current studies in microbiome-related research……………………………………………………………………….………..6 I.III Metagenomics and Sequencing Methods for Microbiome Characterization……………………………………………………………...….……..7 I.IV 16S and 18S rRNA Sequencing ………………………..………………………...9 I.V Whole Genome Sequencing: Coverage, Read Length, and Depth……………….12 I.VI Gut Microbiome and the Fungal Connection: Dr. Ghannoum’s Research ……...15 I.VII Crohn’s Disease, Ulcerative Colitis, and Irritable Bowel Disease ……………..20 II. Business Development Strategy and Commercialization Roadmap II.I Biohm’s Current Business Model ……………………………..……………………22 II.II Medical Foods Overview………………………………….…..…………………....23 II.III Medical Food FDA Regulations and Approval Process …………..………………25 II.IV Medical Food Market Size, Competitors, and Strategic Considerations….…….....27 II.V Direct-to-Consumer Test Kits Overview: Market and Competitor Case Studies…..30 II.VI Direct-to-Consumer Kit Regulations………………………..…………………..…32 II.VII Direct-to-Consumer Kits Strategic Considerations…………..………………..….33 II.VIII Therapeutic Pipeline Strategic Considerations ………………………………….36 II.IX Therapeutic Pipeline FDA Regulations……………………….………………...…38 II.X Intellectual Property Relevant to Biohm………………………..………………..…38 III. Strategic Conclusions for Biohm’s Business Development ……………..…....…40 3 List of Figures 1. Number of microbiome-related publications since 2000………………………………….7 2.Organisms sequenced and Phylogenetic Context from Human Microbiome Project……..9 3.Microbiome research funding related to HMP vs. non-HMP from 2007-2016………….11 4.Schematic detailing metagenomics analysis workflows and pipelines…………………..15 5.Gene map for E. coli 16S ribosomal subunit with variable/hypervariable regions……...16 6.Sample workflow for a whole genome shotgun sequencing experiment from sample prep through data preparation for bioinformatic analysis……………………………………..19 7.Taxonomic distribution and abundance of fungi in biofilms and image of fungal invasion of colon sample…………………………………………………………………………..23 8.Formation of biofilms in colon tissue by C. tropicalis, E. coli, C. albicans, and S. marcescens……………………………………………………………………………….25 9.Imaging of colon tissue demonstrating pathological differences in ulcerative colitis and Crohn’s disease………………………………………………………………………..…28 4 List of Tables 1.Largest medical food manufacturers with indication pipelines………………………..35 2.Companies developing a data-driven platform supplemented by at-home test kits…...41 3.Therapeutic pipelines and indications for microbiome pharmaceutical companies…..43 4.Relevant patents for Biohm and Mahmoud Ghannoum………………………………45 5 Acknowledgements Marissa – You have always been my light in the dark and the foundation from which I can grow. Thank you for listening to everything that comes out of my head during this process. Thank you for your eternal patience and unquestioned love. I would not be able to be who I am without you to be my guide star. Mom and Dad – I am who I am, and I am on the journey I am because of the model you provided. Thank you for teaching me radical independence and authenticity. Dr. Jolly – You gave me an opportunity to believe in myself when I couldn’t do that for myself. Thank you for being an incredible mentor and teaching me the value of “thinking about and doing science.” Your faith in me won’t go unrewarded. Neema – You chose to mentor me and advise me and let me grow in your incredible shadow. I appreciate how our relationship has blossomed and how you have given me the space to be authentic in my work. I look forward to the future in our work. Dr. Cullis – Thank you for guiding me through the racecourse of this program. I have always appreciated your insight and encouragement. Emmaline – You have become my closest friend and confidant over the years. From Posner’s lab to Bioenterprise, I am so appreciative to be able to grow and evolve alongside you. You have given me courage and support in what feels like Sisyphean work. Thank you. To those not mentioned here, I appreciate you, too. Whether it was sharing a beer or trying to listen and understand what I do, thank you. You will never know how much you mean to me. 6 Determination of Strategic Priorities for a Microbiome Company Through Analysis of Technical Capabilities and Current Market Landscapes Abstract by: BRANDON EDWARD ANDREW The “mycobiome,” coined by the CWRU investigator Dr. Mahmoud Ghannoum, refers to the composition of both bacterial and fungal communities in the human gut microbiome and has been the focus of disease-state correlations investigated by his lab. Dr. Ghannoum started the company, Biohm, to sell direct-to-consumer at-home microbiome sequencing kits and probiotics that aim to balance the gut biofilm that contributes to the dysbiosis- associated conditions. Biohm has expressed an interest in developing new business strategies to leverage their intellectual and technical strengths. This thesis is composed of two parts: The first section is a scientific and technical investigation of the micro- and myco-biome, sequencing techniques and strategies (16S, ITS, WGS, and Shotgun Metagenomic Sequencing) that play a role in the characterization and identification of fungal and bacterial colonies in the gut. These strategies aim to overcome challenges in characterizing and quantifying microbiota composition. Next, this sequencing data can form a robust database of patient data that plays a role in disease identification, and this thesis identifies some of the bioinformatic analyses to achieve this goal. The section concludes with how insights derived from patient data can be used in the optimization of cohort design in clinical trials for various diseases. The second section investigates three different business models that Biohm has expressed interest in exploring for future development: (1) medical foods; (2) a therapeutic pipeline; and (3) a data-licensing and discovery platform for drug development. A detailed analysis of the market dynamics, competitive landscape, regulatory issues, and other nascent concerns was performed for each potential vertical as a foundation to develop future business strategy for Biohm. The thesis is concluded on a holistic analysis of the scientific and technical assets and business opportunities and strategies necessary for Biohm to successfully implement new business development. The final section serves as a final assessment of the holistic analysis and provides considerations regarding sustainable business growth for Biohm or any other microbiome-based biotech startup. 7 I. Technical and Scientific Background I.I Human Microbiome and Large-Scale Research Initiatives The human microbiome has been a focus of biologists for many years but has become increasingly focused upon within the last 10-15 years. Figure 1 below from a Silicon Valley Bank annual report1 shows that the number of microbiome publications went from about 500 collectively in 2010 to over 10,000 collectively by the year 2016. Several explanations for this exponential growth in research are explored here and include, but are not limited to: (1) large-scale, massively funded research initiatives such as the Human Microbiome Project (HMP), Integrative Human Microbiome Project (iHMP) and Metagenomics of the Human Intestinal Track (MetaHIT); (2) improvements in research tools and approaches like the accessibility of next generation sequencing, metagenomics, and bioinformatic tools; and (3) the increasing awareness of the connection between the microbiome and human diseases such as gastrointestinal diseases like Crohn’s Disease and IBD, as well as cognitive disorders like Autism Spectrum Disorder, depression, and anxiety. Figure 1: Number of microbiome-related publications since 2000. 1 Silicon Valley Bank. 2017 Annual Report. San Francisco, CA: SVB, 2017. Accessed February 15, 2020. 8 A microbiome refers to an entire ecosystem comprising all the microorganisms living together in a particular environment, as well their constitutive genes and interactions with the environment. This collection of organisms includes bacteria, fungi, viruses, phages, archaea, and other microbial eukaryotes.2 The human microbiome then is a localized ecosystem of microbiota that exist on or near a human, and there is significant diversity depending upon that existent location. The human microbiome has huge amounts of genetic diversity and material when compared to the native genome of its host.3 Interestingly, organisms in separate locations on a human may be stable over long periods of time and can be considered endemic, but they also may be transient and change over the
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