The Human Microbiome: Advancing New Frontiers in a Rapidly Emerging Market

The Human Microbiome: Advancing New Frontiers in a Rapidly Emerging Market

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Pharmaceuticals

Published Date

1st Jan 2016

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136

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The field of Human Microbiome research and development is apparently one of the most popular hubs of the biotechnology industry. While the Human Microbiome Project, MetaHIT and other huge studies of human microbiota, have garnered a lot of attention over that past few years, the microbiome space has literally exploded in terms of both basic and applied biomedical research. In 2009, a PubMed search on the term ‘human microbiome’ yielded 579 citations, with a radical increase to 4,490 by 2014. Not only has the field seen massive investments from Venture Capital firms and Angel Investors, showing keen interest, but there has also been a flurry of deals and collaborations with the expected flux and knowledge exchange. Another milestone achieved was the first major microbiome IPO issued.

(Chapter 4)

This report focuses on biomedical aspects of research, development, and commercial endeavors in the human microbiome space. It includes essential background information, evolution of the field, advances in basic research, events in the emerging commercial market, deal activity, interviews with experts, and trends in microbiome research and commerce. Primary sources of information for this report include the scientific literature, discussions with experts, and an online survey of individuals working in this space.

History and Evolution

After pioneering several milestones in the field of genomics, Craig Venter led an expedition to collect samples of marine bacteria and sequence them en masse using Sanger shotgun sequencing technology. Venter and his team identified over 1,800 species, a groundbreaking feat that established metagenomics as a sustainable field for investigation and commercial involvement. The arrival of next-generation sequencing (NGS) technologies with the ensuing emphasis on short hypervariable regions of microbial 16S rRNAs enabled the Human Microbiome Project and other similar efforts to comprehensively characterize the human microbiome to encourage full participation in the field. Initial efforts in microbiome research and development helped to identify several enterotypes (classification of living organisms based on its bacteriological ecosystem in the gut microbiome); a solid foundation for subsequent work in personalized microbial medicine. Evidence shows that individual enterotypes seem to change in response to dietary alterations. Another observation is that a well-balanced microbiome can help to maintain weight, whereas disruption or dysbioses can lead to obesity. Several other correlations have been made between dysbiosis and disease. The current wave of increased commercial activity was born out of several studies showing that patients suffering from recalcitrant Clostridium difficile associated diarrhea could be treated with a fecal transplant from a ‘healthy’ matched donor. Antibiotic treatment temporarily alters the gut microbiome and allows the normally dormant commensal C. difficile to overgrow. This fecal microbiota restoration therapy helps to restore balance with success rates of up to 100%.

Advances in Research on the Human Microbiome Initially NGS sequencing of metagenomes was based on the Roche 454 pyrosequencing platform. 454 Life Sciences will no longer support the platform after 2016. The need for more time saving and cost effective alternatives shifted attention to mainly Illumina’s faster and cheaper short-fragment sequencing systems. Some researchers favor working with combinations of sequencing platforms depending on the application. Other researchers prefer Pacific Biosciences’ platform; the latest release P6-C4 provides impressively long reads averaging 10,000 - 15,000 bases. Data analysis remains a challenge in the microbiome space. Informatics workflows can be either gene-centric, preferred when addressing high complexity applications; or assembly-based, favored for lower diversity applications. Either choice requires further selections downstream from the branch point.

Quite a few substantial advances in data analysis have been made recently yet inconsistency among results of metagenomic analyses from different laboratories and technologies/platforms is a huge challenge. Protocols must be standardized and results made consistent across laboratories and technology platforms. In a collaborative effort, researchers from Human Longevity, Inc. (HLI) and the J. Craig Venter Institute (JCVI) recently published a paper calling for standardization of practices across laboratories. The paper highlighted inconsistencies in microbiome work from different library preparation methods and data analysis.

Commercial Activity

This report profiles the activities of 28 microbiome companies, most of which are engaged in developing therapeutics for various diseases. The most frequent target indication is C. difficile gastroenteritis; not surprisingly the gut microbiome is the research focus of the majority of the companies. Other diseases include inflammatory bowel disease, irritable bowel syndrome, acne, and diabetes. Particular programs are directed at larger therapeutic areas such as: neurodevelopmental disorders, autoimmune disease, metabolic disorders, and infectious disease. One company works to develop synthetic oral biotics to address the challenges of inborn errors of metabolism. Several companies are committed to developing more refined alternatives to FMT, including oral preparations and storage devices.

Diagnostics in development range from biomarkers to monitor mucosal healing in IBD, to oral preparations for sampling the gut. The report also describes 15 recent microbiome-related deals including four research partnerships between small companies and Big Pharma. These include an unidentified global Pharma company and Janssen Research and Development unit. The APC Microbiome Institute University of College Cork, Ireland is collaborating to support two small companies. The National Institute of Allergy and Infectious Diseases (NIAID) and Swiss Foods Company Nestlé are providing collaborative support to smaller companies.

In an online survey of 119 individuals active in the microbiome space, more than half of respondents work in academia compared to less than half who work in commerce. Nearly one-third are addressed as research / development manager, group leader or supervisor. Almost half stated their work involved analytical methods to detect or describe microbiomes in individuals or populations. About two-thirds work on the gut microbiome and by therapeutic area, another two-thirds focus on inflammation. The majority of respondents work on cancer.

None of the participants expect a change in the research focus of their company, and two-thirds expect an increase in the company’s microbiome efforts over the next 2 years. One-third of respondents opined that sufficient microbiome-related information has been obtained to warrant translational efforts, while less than one-third disagreed. Nearly one-third use microarrays to detect dysbiosis, while less than a third use short-read next-generation sequencing. Nearly half of respondents agree that the next decade will see an avalanche of new personalized biotherapeutics.

Trends and conclusions

Our interviews and survey results show that persons working in the microbiome field are highly optimistic about the relevance of their work to the future success of microbiome research and development. The market is growing tremendously and microbiome market potential is projected to rise from $294 million in 2019, to $658 million by 2023. Several research efforts are geared towards establishing cause over correlation regarding dysbiosis related disorders. Groups and consortia have called for a unified global microbiome effort possibly to promote consistency of results and standardized protocols. This is requisite to maintain the highest standards of quality control for human health.
Table of Contents


Executive Summary

History and Evolution

Advances in Research on the Human Microbiome

Commercial Activity

Trends and conclusions


CHAPTER 1

Introduction

Scope and Structure of the Report


CHAPTER 2

History and Evolution

Exhibit 2.1 PubMed citations for the search term ‘human microbiome’


CHAPTER 3

Advances in Research on the Human Microbiome

Culture

Systems Biology

Microbial Ecology

Synthetic Biology and Microbiome Engineering

Diet

The Virome

Diagnostics

Infectious Disease

The microbiome in health and disease

The Gut-Brain Axis

Multiple Sclerosis

Colorectal cancer

The Microbiome at the Extremes of Life


CHAPTER 4

Commercial Aspects of Microbiome Research and Development

Selected Companies Active in the Microbiome Space

Exhibit 4.1 Companies Active in the Microbiome Space

AdvancingBio Inc.

AOBiome LLC

Assembly Biosciences, Inc.:

AvidBiotics Corp.:

C3 Jian, Inc.

Diversigen, Inc.

Eligo Bioscience

Enterome Bioscience SA

Evelo Therapeutics

Evolve BioSystems Inc.

ExeGi Pharma LLC

Human Longevity, Inc.

Interface Diagnostics

Intrexon Corporation

MaaT Pharma

MetaboGen AB

Microbiome Therapeutics LLC

OpenBiome, Inc.

Pureflora, Inc.

Rebiotix Inc.

Seres Therapeutics

Symbiotic Health Inc.

Symbiotix Biotherapies, Inc.

Synlogic Therapeutics

Synthetic Biologics Inc

ViThera Pharmaceuticals Inc.

Xycrobe Therapeutics, Inc.

Deal Activity

Exhibit 4.2 Deals

4D Pharma – The Microbiota Company and GT Biologics

4D Pharma and The APC Microbiome Institute UCC Ireland

Ab-Biotics SA and Janssen Research and Development

Enterome and Abbvie

Enterome and Gustav Rouss

Evelo Therapeutics and University of Chicago

Intrexon Corporation and Oragenics Inc.

Intrexon Corporation and Synthetic Biologics, Inc.

Optibiotix and Venture Life

Second Genome and APC Microbiome Institute University College Cork

Second Genome and Evotec

Seres Health and Nestlé

Symbiotix and National Institute of Allergy and Infectious Diseases (NIAID)

Synlogic and a Global Pharmaceutical Partner

Vedanta Biosciences and Janssen Research and Development


CHAPTER 5

Market Dynamics

Exhibit 5.1 Respondents’ Subject Matter Category inMicrobiome R&D

Exhibit 5.2 Type of Organization Where Respondents Work

Exhibit 5.3 Further description of type of company where respondents work

Exhibit 5.4 Respondents’ Position/Designation at the Workplace

Exhibit 5.5 Type of Work Currently Performed by Respondents

Exhibit 5.6 Type of Work Respondents Will Likely Perform in the Next Year

Exhibit 5.7 Respondents’ Current Research Focus by Body Site/Niche

Exhibit 5.8 Respondents’ Current Research Focus by Therapeutic Area

Exhibit 5.9 Respondents’ Current Research Focus by Disease Condition

Exhibit 5.10 Respondents’ Current or Future Research Focus by Product

Exhibit 5.11 Respondents’ Expectation of Change in Their Organization’s Microbiome Involvement in the Next Two Years

Exhibit 5.12 Respondents’ Opinion Regarding Academic Participation in Developing New Concepts for Rx and/or Dx of Dysbiosis

Exhibit 5.13 Respondents’ Level Agreement with Statement: Current Methods are Adequate for Quantitative Characterization

of the Microbiome for Personalized Medicine

Exhibit 5.14 Respondents’ Level Agreement with Statement: Sufficient Information about the Composition and Function of Human Microbiomes

has been Gathered to Justify Translational R&D

Exhibit 5.15 Respondents’ Current Research Work on Detecting Dysbiosis Uses the Following Techniques

Exhibit 5.16 Respondents’ Opinion on the Potential of Microbiome R&D to Provide Major Contributions to Healthcare

Exhibit 5.17 Respondents’ Level of Agreement with the Statement: "Recent Findings Relating the Microbiome to Health and Disease

Will Enable an Important New Generation of Therapies for a Number of Chronic Diseases.”

Exhibit 5.18 Respondents’ Level of Agreement With the Statement: "Recent Findings Relating the Microbiome to Health and Disease

Will Provide an Important New Generation of Measures to Maintain Good Health."

Exhibit 5.19 Respondents’ Level of Agreement With the Statement: "It is Still Early Days for Translational Interventions Based on Microbiome R&D,

and More Years of Research are Necessary to Establish its Potential."

Exhibit 5.20 Respondents’ Level of Agreement With the Statement: "Sequencing Technologies Will Remain Dominant Over Microarrays

for Most Microbiome Diagnostic Applications."

Exhibit 5.21 Respondents’ Level of Agreement With the Statement: "Big Pharma Involvement in Microbiome-related R&D Will Increase Significantly

Over the Next Decade.”

Exhibit 5.22 Respondents’ Level of Agreement With the Statement: "We Can Expect a Flood of New Rationally Designed and/or

Personalized Biotherapeutics to Emerge During the Next Decade."



CHAPTER 6

Observations and Conclusions

Microbiome Market Potential

Synthetic Biology

Dysbiosis and Disease – Establishing Causality Over Correlation

Consistency of Results Across Laboratories

Future Directions



CHAPTER 7

Interview Transcripts

Lee Jones, Founder CEO, Rebiotix

Brian Varnum, PhD, Chief Development Officer C3 Jian

Yanjiao Zhou, MD, PhD, Research Scientist, The Jackson Laboratory for Genomic Medicine, Farmington CT

Dr Bernard Malfroy-Camine, President and CEO, ViThera Pharmaceuticals

Mark L. Heiman, Ph.D., FTOS, Vice President, Research and CSO, MicroBiome Therapeutics (formerly NuMe Health)

Larry Weiss, MD, Chief Medical Officer, AOBiome, LLC

Karen E. Nelson, PhD, President, J. Craig Venter Institute (JCVI), Head, Microbiome Program, Human Longevity Institute (HLI)

Sara Malcus, PhD, CEO, MetaboGen AB
Tables and Figures
Exhibit 5.1 Respondents’ Subject Matter Category in Microbiome R&D


Exhibit 5.2 Type of Organization Where Respondents Work


Exhibit 5.3 Further description of type of company where respondents work


Exhibit 5.4 Respondents’ Position/Designation at the Workplace


Exhibit 5.5 Type of Work Currently Performed by Respondents


Exhibit 5.6 Type of Work Respondents Will Likely Perform in the Next Year


Exhibit 5.7 Respondents’ Current Research Focus by Body Site/Niche


Exhibit 5.8 Respondents’ Current Research Focus by Therapeutic Areas


Exhibit 5.9 Respondents’ Current Research Focus by Disease Condition


Exhibit 5.10 Respondents’ Current or Future Research Focus by Product


Exhibit 5.11 Respondents’ Expectation of Change in Their Organization’s Microbiome Involvement in the Next Two Years


Exhibit 5.12 Respondents’ Opinion Regarding Academic Participation in Developing New Concepts for Rx and/or Dx of Dysbiosis


Exhibit 5.13 Respondents’ Level Agreement with Statement: Current Methods are Adequate for Quantitative Characterization

of the Microbiome for Personalized Medicine


Exhibit 5.14 Respondents’ Level Agreement with Statement: Sufficient Information about the Composition and Function of

Human Microbiomes has been Gathered to Justify Translational R&D


Exhibit 5.15 Respondents’ Current Research Work on Detecting Dysbiosis Uses the Following Techniques


Exhibit 5.16 Respondents’ Opinion on the Potential of Microbiome R&D to Provide Major Contributions to Healthcare


Exhibit 5.17 Respondents’ Level of Agreement with the Statement: "Recent Findings Relating the Microbiome to Health and Disease

Will Enable an Important New Generation of Therapies for a Number of Chronic Diseases.”


Exhibit 5.18 Respondents’ Level of Agreement With the Statement: "Recent Findings Relating the Microbiome to Health and Disease

Will Provide an Important New Generation of Measures to Maintain Good Health."


Exhibit 5.19 Respondents’ Level of Agreement With the Statement: "It is Still Early Days for Translational Interventions Based on

Microbiome R&D, and More Years of Research are Necessary to Establish its Potential."


Exhibit 5.20 Respondents’ Level of Agreement With the Statement: "Sequencing Technologies Will Remain Dominant Over Microarrays

for Most Microbiome Diagnostic Applications."


Exhibit 5.21 Respondents’ Level of Agreement With the Statement: "Big Pharma Involvement in Microbiome-related R&D Will Increase

Significantly Over the Next Decade.”


Exhibit 5.22 Respondents’ Level of Agreement With the Statement: "We Can Expect a Flood of New Rationally Designed and/or

Personalized Biotherapeutics to Emerge During the Next Decade."

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