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Global Engage 6th Microbiome R&D and Business Collaboration Forum Summary: Days 1 & 2

Leaders in the microbiome industry met in San Diego (USA) for two days, on October 29th and 30th, 2018, to dive into the advancements in research and product development that have occurred to date. Microbiome Insights was an exhibitor at this event—The 6th Microbiome R&D and Business Collaboration Forum–one of the largest annual microbiome-related gatherings in the US, with 300 attendees coming from North America and Europe.

The conference talks were divided into three tracks: microbiome therapeutics, skin microbiome, and probiotics. Here, we present highlights from each of the tracks in this two-day event:

Day 1

Probiotics

Jennifer Spinler of Baylor College of Medicine spoke on “Targeting Antibiotic-Associated Digestive Diseases Using Next-Generation Probiotics”. She started by outlining the need for new therapies to prevent antibiotic-associated diarrhea. Clostridium difficile infection is one of the leading reasons for antibiotic administration, and a 2017 Cochrane Review showed probiotics can prevent Clostridium difficile-associated diarrhea in adults and children. Spinler’s approach is to explore a probiotic strategy for preventing Clostridium difficile infection in the first place by looking at how host bacteria are normally able to protect against C. difficile. She focused on Lactobacillus reuteri, which has anti-inflammatory effects and activity against Gram positive and Gram negative bacteria. She found that L. reuteri alone didn’t prevent the growth of C. difficile, but L. reuteri plus glycerol knocked down C. diff growth in the system—with an accompanying shift in the overall microbial community.

Brunella Gonzalez Cautela of Lallemand gave a talk on “Probio’Stick and the brain-gut axis: Focus on recent clinical findings”. She noted that the etiology of depression is obscure, but one contributor under consideration is immune-mediated inflammation. She thus posed the question: can probiotics be used for depression? A pilot study by the company, in collaboration with researchers from Queen’s University, focused on patients who were depressed but never treated before. In addition to completing a survey, the subjects were tested for inflammatory markers in the blood, serotonin levels, and fecal microbiome composition. Those who received ProbioStick for 8 weeks showed significant improvement in mood-related symptoms compared to those who received a placebo.

Microbiome

Kathy McCoy of University of Calgary presented on “Impact of the gut microbiome in shaping innate immunity: Defining Mechanisms”, going over several examples of using gnotobiotics to define mechanisms underlying microbiome and host interactions. In one example, researchers studied microbial impact on T Cells in a non-obese diabetic mouse model of type 1 diabetes. They looked at the ability of the bacteria to bring the integrase-specific T cells to the gut, and found that microbial antigens had a dramatic protective effect against colitis.

Jessica Schneider of Takeda Pharmaceuticals spoke about the company’s growing microbiome drug portfolio, and how gastrointestinal indications are paving the way for future indications (gut-brain axis and others). She explained the company’s interest in commensal bacterial co-occurrence networks in various disease states, and deriving effective therapeutics from these. Takeda is driven by the hypothesized mechanism of disease: either bugs as drugs, or (in the case of their collaboration with Enterome), drugs for/from bugs. She listed approaches in the industry, in increasing order of R&D complexity: fecal microbiota transplantation, bacteriophage engineering, bacterial consortia, engineered bacteria, single strain commensal bacteria, and small molecules.

Morten Isaksen of Bio-Me spoke on “Positioning microbiome analysis for use in precision medicine”. The company has developed a platform that does precision microbiome profiling (species/strain level) and direct quantification reads in less than a day. Isaksen described a demonstration study on diet: subjects consumed their normal diet for 4 weeks, then changed their diet in some way for the next 4 weeks—for example, consuming more fiber or changing sugar consumption. Bio-Me carried out daily sampling of fecal microbiota and found, interestingly, that after an initial microbiome change (after 3-5 days) there tended to be a rebound to pre-intervention levels of bacteria. Follow-up work will try to uncover the cause of this phenomenon.

Skin microbiome

Kausar Malik of Amway Corporation presented “The Cinco de Mayo Study: A one-year longitudinal study of the facial skin microbiome in normal healthy adults”—a project done in collaboration with the Microbiome Insights team. Malik described how bacterial species on the skin vary depending on the environment (e.g. moist or dry); the study aimed to find out the stability of the skin microbiome in a large population of healthy individuals over time, in order to begin identifying biomarkers of skin aging. In addition to skin swabs, they looked at red spots, wrinkles, brown spots, skin elasticity, barrier function, and surface pH. They found no significant change in alpha diversity over time, although some individuals showed a change in microbiome diversity on the cheek. Corynebacterium increased with age, and was also correlated with higher redness (in line with other published work).

Day 2

Microbiome

Eric Pamer of Memorial Sloan Kettering Cancer Center gave a keynote address on “Microbiota-mediated defense against intestinal infection”. His research focused on patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT): these patients receive antibiotics, chemotherapy, and radiation, and mortality is high in the case of bloodstream infection caused by vancomycin-resistant enterococcus (VRE). Given that the microbiome normally eliminates persistent VRE, the question is whether there’s a way to eliminate VRE in allo-HSCT patients. Pamer and colleagues showed that with a fecal transplant in these patients they re-established almost all the normal microbiome components—but which bugs were causing clearance of VRE? The researchers used particular bacteria and did a dilution test to examine the clearance of VRE. Blautia producta were the only bacteria that caused complete inhibition. When they looked into what Blautia producta expresses that none of the others do, they found it encodes a lantibiotic operon; these lantibiotics can also be expressed by anaerobes living in the colon.

Peter Spanogiannopoulos of UCSF was next up, with “The metabolism of fluoropyrimidine anticancer drugs by the human gut microbiome”. He cited work showing that Proteobacteria can inactivate 5FU—and noted that, fortunately, there is a lot about Proteobacteria in literature. He and his colleagues in the Turnbaugh lab are looking to answer the question: can probiotics rescue toxicity? One day they hope to sequence someone’s microbiome before administering anticancer drugs, in order to assess the pharmacokinetics.

Pierre Belichard of Enterome spoke on “Building the leading microbiome-derived immunotherapy company”. He explained that Enterome, a spin-out of MetaGenoPolis in France, is focused on determining function of the microbiome in cancer and inflammatory bowel disease. They are developing everything except ‘live biotics’—and their multiple programs are currently in various stages: for instance, glioblastoma and solid tumors (phase 1); Crohn’s disease (phase 2). They work on epitope mimicry to trigger an anti-tumor T-cell response, ‘waking up’ existing dormant T-cells in the gut lining to activate the biggest group of T cells in the human body. Their work in animal models has established this and they are now carrying it through in clinical trials with humans.

The next event in the microbiome track was a panel discussion led by Microbiome Insights CEO Malcolm Kendall: “Where the money is going and where the money will be made: The unique perspective of venture capitalists”. On the panel were Asish Xavier of J&J Innovation and Denise Kelly of Seventure. In response to an audience question, the panelists emphasized that they look carefully at every company that comes through the door; sometimes they ask for more information or progress and a company comes back later having secured a better position. Kendall asked the panelists the key things they look for in a company, and Kelly responded that the number one factor is top-notch science: validated and preferably peer-reviewed. Then comes intellectual property: who else is competing, and what makes the company different? Third is the business team and the research team. Xavier agreed, adding that the science may be very interesting but the key is whether it is translatable.

Timing is another factor: Xavier says he has seen companies take 20 years to bring something to market. He said timing is critical for a company—so sometimes he explores whether they can build a small product to bring to market while working on a larger one.

Kendall asked the panelists how they think microbiome science is progressing. Xavier acknowledged a lot of good science emerging—with an exponential number of publications—but not all of the ideas can be translated into a drug. The science only has potential as a company if you can get to phase 3 and beyond. Most times the drugs will be advanced by a bigger company because of regulatory challenges so the start-ups will have to partner at some point in their existence. Kelly agreed, and noted that over the past five years we have seen a massive capitalization of the scientific progress.

For more on the conference talks, see #MicrobiomeProbioticsForum on Twitter.

Dr. Julian Davies speaks at celebration marking the opening of Microbiome Insights’ new lab facility

The Microbiome Insights team gathered with nearly 100 clients, friends, and supporters on May 28th for a champagne reception to celebrate the company’s continued growth and the opening of its new laboratory facility in the award-winning Pharmaceutical Sciences Building at the University of British Columbia (UBC). The event was topped off by remarks by the esteemed Dr. Julian Davies, UBC Professor Emeritus and chair of the External Scientific Board of the NIH Human Microbiome Project from 2009-2012.

In his speech, Davies gave a brief history of how the Human Microbiome Project came to be. He traced microbiome research up to the present day, saying: “Microbiome science is really getting going and I think it’s great that UBC has its own microbiome company. We should support them as strongly as possible.”

Company co-founders Drs. Brett Finlay and Bill Mohn were in attendance at the reception, along with Microbiome Insights clients, advisors, investors, granting agencies, and strategic collaborators.

CEO Malcolm Kendall said, “The microbiome is a really important area of science that is an important part of human, animal, plant and environmental health.” He emphasized that the company is not merely a service provider — but that the team members have a wealth of knowledge and are actively moving the science forward. “As we gain more understanding in this area we hope to be able to use microbiome derived products, tools, and services to enhance health and potentially cure or treat diseases,” he said.

Kendall also announced that Microbiome Insights hopes to foster the growing microbiome research community at UBC as a founding sponsor of the first annual UBC Microbiome Conference, to be held November 8 to 10, 2018.

The company hosted a microbiome poster competition alongside the reception, with winners receiving free sequencing services. Kevin Zhong, a postdoc at UBC’s Suttle Lab, received the top prize (50 free samples of amplicon sequencing); Peter Rahfeld and Spence Macdonald from Withers Lab received 2nd place (30 free samples of amplicon sequencing) and 3rd place (20 free samples of amplicon sequencing), respectively. The people’s choice award (a cash prize of $250) went to Peter Dobranowski of BCCHR.

See here for some photos from the event:

Dr. Julian Davies speaks with Microbiome Insights CEO Malcolm Kendall and guests; PHOTO CREDIT: Amer Abu-Khajil

 

 

Drinks table awaiting guest arrival; PHOTO CREDIT: Amer Abu-Khajil

 

 

Microbiome Insights co-founder Dr. Bill Mohn speaks with attendees; PHOTO CREDIT: Amer Abu-Khajil

 

 

Poster competition held in conjunction with the reception; PHOTO CREDIT: Amer Abu-Khajil

 

 

Remarks by Dr. Julian Davies; PHOTO CREDIT: Amer Abu-Khajil

 

 

Microbiome Insights co-founders, employees, and advisors; PHOTO CREDIT: Amer Abu-Khajil

 

4th Annual Translational Microbiome Conference: Day One Summary

The Microbiome Insights team is pleased to be exhibiting at the 4th Annual Translational Microbiome Conference in Boston! The first day of the main program was filled with talks that covered an excellent breadth of topics having to do with the microbiome field.

Beyond sequencing

A highlight of the morning was a lecture by Peter Christey (Co-Founder and CEO of General Automation Lab Technologies, or GALT) on “Going Beyond Sequencing – New Research Tools in the Era of the Microbiome”. Christey explained that next-generation sequencing provides an amazing window into the microbiome, but it does have its limitations. Comparing cultures with culture-independent techniques on the same sample shows that adding a small cultivation step in the process allows observation of many more OTUs per sample. Christey argued that for the best insights, a mix of old and new techniques is necessary—both next-generation sequencing and wet lab techniques.

Precision medicine

Morten L. Isaksen (CEO of Bio-Me AS) then spoke about “A Microbiome-based Approach to Precision Medicine and Personalized Nutrition”. Isaksen described GutCheck—a gut health test that can be combined with data from biobanks that are available. The company links a person’s profile with several medical databases to gain insights on how the microbiome relates to drug consumption and other factors.

Main track: Skin microbiome & cancer immunotherapies

From there, the sessions separated into two tracks: a main track and a consumer track. In the main track, audience members heard from Travis Whitfill (Co-Founder and CSO of Azitra, Inc) on “Translational Challenges in the Skin Microbiome”. Whitfill emphasized the need to eliminate the idea of ‘good’ bacteria and ‘bad’ bacteria, arguing the importance of knowing bacterial strain characteristics.

Vancheswaran Gopalakrishnan ( Translational Scientist, Computational & Analytics Support, & MD at Anderson Cancer Center, The University of Texas Health Science Center at Houston) spoke about a hot area: “Impact of Microbiome on Immunotherapy Response”. Gopalakrishnan is working with Seres Therapeutics to identify whether fecal microbiota transplantation, compared to probiotics or lifestyle changes, is the best way of shifting the microbiome into a state associated with a favorable response to cancer immunotherapies. This talk was followed by a panel with Gopalakrishnan and others on immunotherapies and the microbiome, moderated by Take Ogawa (Director, Business Development, Second Genome). Panelists discussed the need to find out what is happening mechanistically in the individuals who respond favorably to immunotherapies. Bernat Olle (CEO, Vedanta Biosciences) outlined the need for harmonizing the observations on which microbe communities might drive the response.

Gut microbiome modulation

Continuing after the lunch break, the talks in the main track turned to microbiome modulation. Mark Smith (CEO, Finch Therapeutics) presented on “Reverse Translation for Therapeutic Development in the Human Microbiome”. He described the dual approach of delivering entire microbial communities to individuals in order to have immediate efficacy, and then working to modulate the microbiome over time.

Next, Assaf Oron (CBO, BiomX) spoke about “A Novel Therapeutic Approach To IBD Through Microbiome Modulation”. Oron explained some individuals with IBD have bacteria residing in the body that bring about flare-ups. So when they come into the clinic they are asked to take a fecal sample; the company tests the pro-inflammatory bacteria and then introduce a phage to eradicate them. They take into account geography, microbiome, and clinical phenotype. At present, a topical gel containing a customized phage cocktail to modulate the skin microbiome is going through clinical trials.

Later in the day, David Kyle (CSO, Evolve Biosystems) spoke about going “From Dysbiosis to Recovery in the Infant Gut Microbiome”. He covered the differences observed in the microbiomes of infants today as compared to previous decades, and how the company is developing solutions to help human milk oligosaccharides (HMOs) be digested by bacteria in the infant digestive tract, thereby elevating the beneficial short-chain fatty acids acetate and lactate in the i

Events

6th Microbiome R&D and Business Collaboration Forum Europe

Microbiome Insights is headed to Europe! Look for us at Global Engage 6th Microbiome R&D and Business Collaboration Forum: Europe from May 20th to 22nd 2019 in Rotterdam, The Netherlands. Along with over 300 academic and industry leaders, CEO Malcolm Kendall will be in attendance to discuss innovative microbiome research and the challenges and opportunities associated with commercialization. Kendall will also be moderating a can’t-miss panel on venture capital investment related to the microbiome. This exciting event will for the first time span three whole days and is an excellent place to meet willing investors and collaborators, as well as the chance to hear from top researchers and product developers. With interactive sessions like roundtable discussions and ample networking time, the event promises to provide a valuable space to meet and forge new connections within the microbiome biotechnology industry.