In the first blog post of this two-part series, we introduced the human microbiome, the increasing amount of research focused on understanding its complexity, and how commercial ventures have already risen in an attempt to translate this understanding into therapeutic interventions for a wide variety of disorders. To further explore the translational side of the microbiome, this post will discuss some of the initial commercial ventures being made that, if nothing else, are likely to evolve the drug-discovery landscape definition into a broader concept encompassing “drugs” that could range from an entire bacterial ecology (in convenient pill formulation!) to a single bacteria genetically engineered to produce beneficial molecules on demand.

The variety of strategies targeting the microbiome is indicative of the level of potential many believe research in this area holds. The traditional sense of drug development, developing small molecules (or one disease, one target), is still a primary strategy being employed. However, with the microbiome that strategy now comes with the twist that the target is potentially the trillions of organisms making up this environment, not one molecule. Development of these agents, therefore, are focusing more on how the agent first interacts with the microbiome to generate desired changes that, theoretically, will in turn generate a desired outcome for the disease. Alternative strategies attempting to modulate the microbiome back to a homeostatic state are also being developed, with a particular bias towards GI conditions such as ulcerative colitis or to combat Clostridium difficile infections. Fecal microbiota transplantation, taking stool samples from healthy individuals and donating them to persons affected, may be the original and most oft discussed example, with some evidence supporting its potential in diseases such as ulcerative colitis, but conflicting evidence also exists.

Additional preliminary efforts to modulate the human microbiome are already impacting the consumer healthcare space. Although research does not yet broadly support their use, probiotic tablets, gummies in the familiar mode of chewable vitamins, and even infant formula designed to promote a stable microbiotic ecosystem are available from both large and small manufacturers. Despite the development of many microbiome-based therapeutics being in infancy themselves, some major pharmaceutical players (aka big pharma) have also begun investing in the relatively untapped potential of the microbiome with the intention to target diseases as mild as lactose intolerance all the way to life-altering or life-threatening as various immune disorders and even various cancers. These strategies will largely rely on the initiation (or planned initiation) of partnerships, some pretty unique; for example, AbbVie partnered with Synlogic, a “synthetic biotic” maker that combines the revolutionary field of synthetic biology with the potential power of the microbiome to genetically engineer bacteria that can produce therapeutic molecules as needed to potentially treat diseases such as ulcerative colitis or Crohn’s disease. Other companies such as Janssen, in addition to partnerships, have recently gone as far as creating an entire research platform within the company itself, sending a strong signal of commitment towards this area.

Big pharma interest aside, the majority of innovators in this space are clearly smaller start-ups and early-stage biotechnology companies, eager to obtain financing to get their flagellas in motion (see Table 1). This appetite for funding and affirmation by several venture capital firms is underscored by potential valuations that are likely to surpass one billion dollars, if the current market capitalization (at time of writing) of the first publicly traded microbiome-focused company, Seres Therapeutics, is any indication. However, like other areas that have seen early venture interest (e.g., CRISPR, CAR-T), persuasive clinical trial data is not yet available, making it difficult to truly evaluate the quality of the science underlying these investments – few microbiome-based interventions have progressed even to Phase II clinical trials, and given the current failure rate of investigational drugs, the outlook is difficult.

Academic research will continue to help fuel the march towards microbiome-based interventions as well, with one analyst writing here already a true believer in their potential. She appears to be in good company, with investments from the National Microbiome Institute and other foundations totaling over $400 million for research and some of the top research organizations in the United States participating in this effort. Her collaborating partner is more hesitant to promote a full-scale investment thesis in this area but does believe the current biotech landscape is overdue for a truly innovative breakthrough class of therapies to make it to the clinic. Whether now is the ideal time to invest in microbiome research can certainly be debated; the technology is still largely in its infancy, but with myriad approaches being tested, and significant unmet need present in many diseases, strong arguments can be made for both sides. Companies investing in this area or forming partnerships will be falling in with both pharmaceutical giants and innovators, joining the likes of GlaxoSmithKline, AbbVie, and Johnson & Johnson, as well as a slew of venture capital groups. The payoff for being first-to-market with a successful microbiome-based therapy could be as large as that of blockbuster drugs of the past, especially when launching into an uncrowded space.

Although both analysts agree microbiome-based therapies are likely several years in the future, the overgrowth of interest in this topic by pharmaceutical companies both large and small, a healthy set of start-ups, and an exponential increase of academic research indicate that this area may not be a quick fad. The microbiome is not likely to be a panacea, but the potential impacts on human health are significant, and this will be an interesting and important space to watch in the coming years.

Company Disease Area Intervention Approximate Value / Research Investment Link
Vedanta Biosciences Immune & Inflammatory Diseases Consortia of ‘healthy’ bacteria to modulate the microbiome, likely oral $339 M deal with J&J

$50 M venture capital infusion
Evelo Biosciences Oncology Small molecule therapies designed to activate the innate immune system or disrupting tumors $35 M venture capital from Flagship Ventures
Moleculera Labs Neuropsychiatric Disorders Diagnostic tests for disorder-linked microbial dysbiosis $1.6 M venture capital from i2E (2015)

$2.96 M venture capital, undisclosed (2013)

$1.84 M venture capital from i2E (2013)
Ritter Pharmaceuticals Lactose Intolerance Oral small molecule, galacto-oligosaccharide $13.7 M market cap (NASDAQ: RTTR, July 8, 2016))


Janssen Human Microbiome Institute Inflammatory Bowel Disease, general research Live microbial therapeutic product


Enterome Crohn’s Disease, Ulcerative Colitis, Inflammatory Bowel Disease Small molecules + proprietary screening tests €14.5 M Series C funding from multiple investors (including Seventure, Lundbeckfond Ventures, and Nestle Health Sciences, 2016)

Partnerships with Takeda, Abbvie, and Janssen Biotech (Site is in English)
Second Gemone IBD, Metabolic Disease including Obesity and Type 2 Diabetes Small molecules $42.6 Series B funding (co-led by Pfizer Venture Investments and Roche Venture Fund, 2016)

$59 M combined total investment
MicroBiome Therapeutics Metabolic Disease including Type 2 Diabetes, “Other Disorders” including IBD, UC, IBS, autoimmune diseases Prebiotics (oral small molecules) Seeking Series B financing (2015)
Seres Therapeutics C. difficile infections, UC, CD, IBD Bacterial ecology in an oral capsule $1.2 B market cap (NASDAQ:MCRB, July 8, 2016)


Synlogic Urea cycle disorder, phenylketonuria, metabolic diseases Synthetic biotics – genetically altered bacteria $40 M Series B funding (2016)

$30 M Series A funding (2013)

Table 1: Select microbiome-focused organizations and investment milestones.

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