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.

[VIDEO] Rethinking germs: Healthy living with our microbes, parts 1-3

In this series of videos, Microbiome Insights co-founder Dr. Brett Finlay, along with Dr. Jennifer Gardy, answers questions about the microbiome and its role in human health and development—making a case for rethinking what it means to live a healthy lifestyle.

Rethinking germs: Healthy living with our microbes Part 1 Q&A

https://www.youtube.com/watch?v=OzOHeyq53FU

Topics addressed in Part 1 of the Q&A session include:

  • How clean should we be? Finlay says we don’t need antibacterial soaps, nor do we need to sterilize our homes. In general, just keeping the numbers of microbes in your home down is enough. In certain cases, more cleaning is necessary: when getting rid of mold or when cooking raw meat, for example.
  • How do we receive our first dose of microbes? From our mothers during birth. This initial microbial community has effects on early life development.
  • Is coffee bad for the microbiome? And how does diet affect the microbiome?
  • How is inflammation related to health and aging? Finlay gives an example of how Parkinson’s disease may actually originate in the gut.

Rethinking germs: Healthy living with our microbes Part 2 Q&A

https://www.youtube.com/watch?v=ldIuwecaKGU&t=32s

In Part 2 Finlay discusses:

  • How do early life microbes influence allergies and asthma? He explains that they shape the immune system; he describes some early results of research into timing of exposure to common allergens like peanuts.
  • Should we let kids be dirty? Finlay talks about the importance of kids’ exposure to the world and its microbial environments, a topic that’s detailed in the book he co-authored, “Let Them Eat Dirt”.
  • Probiotics and prebiotics—what are they and what do we know?
  • How important is diet for maintaining a healthy microbiome? Hint—the white sugar and white flour diet is not ideal.
  • What will be the focus of personalized medicine in future?
  • What threat do antibiotics pose?

Rethinking germs: Healthy living with our microbes Part 3 Final Thoughts

https://www.youtube.com/watch?v=jZ6rGcR1x9g

Finlay gives a final bit of advice on taking care of our microbiomes: it’s really important to make sure our hygiene practices and products like antibacterial soaps are used appropriately: for example, in cases where infection control is required or when dealing with vulnerable groups like seniors.

He advises not be alarmed by the microbial world—but rather, to recognise and respect the organisms living on and in you because they are part of what makes you who you are.

Denise Kelly representing Seventure on what makes a successful microbiome company

A growing number of start-up microbiome companies—from new players in the established probiotics industry, to university spin-outs focused on novel microbiome-based therapeutics—are looking for support and funding. In this competitive environment, how can a new company make the cut?

For the past several years Professor Denise Kelly has worked with Seventure Partners, a leading European Investor—which has the first venture fund, Health for Life, dedicated to investing in microbiome-focused start-ups, led by Seventure’s CEO, Isabelle de Cremoux. Kelly has participated in panels at both the Translational Microbiome Conference (Boston, USA) and the Global Engage Microbiome Futures event (New York, USA) and recently gave keynote lectures at the IHMC meeting in Killarney and the NeuroCon-X meeting in Prince Edward Island, Canada. Here, Microbiome Insights hears Prof. Kelly’s summary of what will set up a microbiome-based company for success.

Use strong science—and own it

Kelly says Seventure has looked at more than 400 companies in the microbiome sector. The first question she asks is whether the science behind the product or service is robust—a major factor for the Seventure Life Science team. She notes, “We are really fortunate that a lot of interest comes from tier one academics and the findings are published in high-impact journals”—so the science has been peer-reviewed and often validated by independent research, adding to its credibility.

Moreover, Kelly says the strongest scientific ‘package’ combines wetlab work with human studies that address potential mechanisms of action in humans. And she notes that companies generally need to have more than 16S data on hand: “We know so much about strain level impact; shotgun sequencing gets you a lot more information. But even then, the industry is moving towards a multi-omics approach—for example, including metatranscriptomics  and metabolomics, so we know ‘who’ occupies an ecosystem but also what they are doing.”

The next question about the science is whether it’s unique: Do competitors have something similar? Having a strong patent portfolio is crucial as it gives the company a distinct competitive advantage.

Build your revenue stream

Among all the possible life sciences areas in which VCs can invest, microbiome science is still in its early days—meaning they are likely to proceed with caution. Kelly says, “Investing in the ‘discovery’ phase is inherently risky; investors want to see that others have invested in the ideas as well.” She says the solution is to use as many resources as possible to build a company’s revenue space, including building multiple product opportunities and diversifying target disease indications—and importantly, building partnerships and licensing opportunities. Very competitive companies are also winning sizeable non-dilutive grants.

Get your regulatory ducks in a row

The science may look exciting now, but what’s the plan for bringing it to market? Many potential therapeutics in the microbiome area—for example, ‘bugs as drugs’—will face unique regulatory challenges. Kelly recommends connecting with regulatory advisors early on so the company can plan for the realities of getting past the hurdles. And even in cases where the regulatory path for a particular indication is relatively well-established, those at the helm of the company need to understand the complexities of the manufacturing process and how regulatory requirements need to be factored in.

Build relationships strategically

Kelly emphasizes that no successful company is built in a bubble: it needs supporters in order to build success. Companies need relationships with key people in academia and elsewhere—and not just a list of names to put up on the web page, but people who really care about what it’s doing and who are willing to jump in with advice and support.

Kelly says it’s especially important to engage with key opinion leaders (KOLs) with knowledge about the specific indication on which the product is focused. A company that demonstrates authentic engagement with these individuals has a better chance of leading the way in the therapeutic space.

Know when to keep your cards close

As a company is building, it’s important to strategize about how much to reveal—at what times, and to whom. She says, “Approach investors, such as Seventure, when you have a clear vision of your commercial opportunity. Although we invest in early stage start-ups, we appreciate companies that have a strong science package as well as a robust business plan that clearly sells the path to clinic and ultimately, to the marketplace.”

Having all these pieces in place won’t guarantee success—but Kelly says they will certainly make investors take a closer look. “The microbiome industry is moving very fast and the number of new start-ups continues to grow exponentially. At Seventure, we continue to build our portfolio and very recently our CEO, Isabelle de Cremoux, announced the first close of a new AVF fund with Adisseo, dedicated to innovation in Animal Health and Nutrition.”

Without a doubt, the microbiome industry as a whole is truly disruptive and represents a complete paradigm shift in human and animal healthcare. Says Kelly: “We are confronted with numerous modalities, ranging from nutritional products through to microbiome-based drug therapies which can modulate microbiome community function and structure, significantly impacting health status but also disease risk and disease progression. Personalized approaches to medical care are also envisaged, as predictive microbiome biomarkers are being sought—and these could provide more accurate diagnostic and prognostic patient read-outs, leading to more predictable and enhanced drug efficacy. The next five years will be very exciting for many, many reasons. Our knowledge base will continue to grow, but most importantly, we also start to see completion of phase II/III human clinical trials.”

Microbiome Movement Skin Health & Dermatology Conference Summary: Days 1 & 2

Microbiome Insights was a proud founding partner of the Microbiome Skin Health and Dermatology conference, a part of the Hanson Wade Microbiome Movement Series—held September 10th to 12th, 2018. The aim of this event was to explore ways of understanding the mechanisms underlying microbial interactions with skin health, and to discuss standardization of metagenomics research and how to develop effective products. Over 100 leaders in the skin microbiome field were on site at this exciting event.

We’re pleased to present a summary of the highlights from both the pre-conference workshop and the two-day main event.

Pre-conference workshop

The September 10th workshop, called “Harnessing the gut-skin-brain axis in health and disease”, was led by Lionel Breton, L’Oreal Advanced Research, Scientific Director. Breton spoke about what we know today regarding the connections between the skin microbiota, gut microbiota, and neurological disorders. Scientists are puzzling through these links, on the path to developing commercially viable therapeutics for skin health and brain health.

Day 1 summary

The first day of the conference began with opening remarks by Larry Weiss of Persona Biome: he acknowledged that the skin microbiome represents an exciting therapeutic frontier in dermatology, but encouraged the audience to be cautious and exercise humility—because after all, “we still don’t know what we don’t know”.

Richard Gallo of UCSD then spoke about “Targeted Design of Microbial Biotherapy for Skin Disease”. Gallo began with an overview of how microbes relate to human health in general: he argued that researchers need to look at the ‘hologenome’, as it takes into account that human functions are based on genes that are expressed via microbes and the environment.

Gallo turned specifically to the microbial life surrounding hair follicles on the skin. He noted that human follicles greatly increase the surface area of the skin; when the microbes in follicles were analyzed using 16S DNA sequencing, it appeared that most of the microbial DNA did not exist on the surface, but rather, it existed deep down in the follicle. A very small percentage of the microbes were further down, penetrating the fat and tissues under the follicle. The composition of the microbes in the fat was similar to that found on the surface.

Gallo emphasized the capacity for systemic interactions linked to the skin microbiome, as the blood vessels on the skin can have extensive communication with, and impact on, the rest of the body. He gave the example of atopic dermatitis: not only do people with this condition have a higher abundance of Gram-positive bacteria (S. aureus) than other people, but Gallo’s work showed that they also have an immune abnormality that inhibited the development of antimicrobial peptides to fight the disease. The presence of S. aureus drives a Th2 immune response, which further decreases the antimicrobial peptides and amplifies the disease. So what appears to be a skin disease is actually a complex condition with systemic influences.

Next up was a talk by Curtis Huttenhower of the Harvard TH Chan School of Public Health, a member of the Microbiome Insights Scientific Advisory Board. He presented on “Structure, Function and Diversity of the Healthy Human Microbiome”. Huttenhower began by explaining the phases of the Human Microbiome Project (HMP): while HMP 1 had the goal of identifying the baseline microbiota of a healthy cohort of individuals, HMP 2 included more multi-omics analyses, and had a longitudinal focus, aiming to uncover interactions in disease. HMP1-II was a recent follow-up on the HMP 2 data; it involved 300 people (half men, half women). Huttenhower noted that the field has seen great advancements since the kick-off of HMP 1, and argued that we are getting to the point where scientists can do meta-analyses to see which methods are more reproducible and reliable.

Specifically related to the skin microbiome, Huttenhower said we have a long way to go—not only in characterizing the ‘healthy’ skin microbiome, but also in defining its biochemistry. Novel functionality is associated with certain strains. Ongoing work is looking at how the skin microbiome may be acquired in the first place, by examining mother-infant pairs. Initial analyses indicate the strains of most bugs on the infant do not originate from the mother.

Julia Oh of The Jackson Laboratory spoke next, on “The Human Skin Microbiome: From Metagenomes to Therapeutics”. Oh emphasized the differences in composition of the skin microbiome, depending on body site: oily sites, for example, are very different from dry sites.

She advised that when looking at therapeutics, skin microbiome researchers should consider factors like site specificity, diversity of the microbiome, and stability of the community. For instance, in those with atopic dermatitis, the skin microbiome looks different depending on whether you measure it at baseline, during a disease flare (when relative abundance of S. aureus increases), and post-flare.

Oh offered some general criteria for what organisms to focus on in the development of new skin therapeutics:

  1. An organism that grows well on the skin—that is, on a graph of time versus growth, an organism that has a U-shaped trajectory (rather than flat).
  2. An organism that is beneficial to the immune system. Their group looked at T cells and measured the rate of MAIT activation with 4000 different species.
  3. An organism that is innate. Most skin sites are stable over time, so the challenge is integrating a foreign species into a community. Previous experiments show it’s difficult to get something to colonize on the skin.

The set of talks was rounded out by Microbiome Insights CEO Malcolm Kendall, on the topic: “From Swab to Data: Considerations for Designing Skin Microbiome Studies.” He emphasized looking at skin microbiome studies from many angles: study design (including the power), collection, stabilization, transport, sequencing, and analysis.

He noted the in-house work of Microbiome Insights that investigated the total DNA as well as the microbial content while using swabs versus tape for a skin microbiome sample. Results showed little difference in total DNA content across systems, but higher microbial content (less host content) on premoistened swabs. Of course, this approach is useful for skin surface microbiome but may not be the best method to look at the follicle microbiome.

Kendall says he has noticed a lot of debate surrounding the variable region that will provide the most fruitful information for skin microbiome analysis using 16S. Microbiome Insights has done some internal R&D work to address this issue: the outcome of which is a new ‘V4_skin’ primer that provides better species-level identification of skin taxa while maintaining low error.

An intriguing panel discussion was held later that morning: “Where will the Skin Microbiome Need Standardization to Advance Science & Future Products?” It was led by Huttenhower, joined by Amanda Nelson of PennState.

Participants emphasized the problem of contamination, since skin microbiome samples have a low microbial biomass; researchers need to include positive and negative controls for ‘human’ and body site. The panelists covered the relative advantages of different collection techniques, sequencing techniques, and culture libraries. For bacteria and skin fungi, libraries are improving, but viruses change so quickly that they won’t be covered in reference libraries. Integrating different data (using multi-omics analyses) will lead to better insights.

In the afternoon of day one, participants heard from Huiying Li of UCLA, on “The Human Skin Microbiome in Health and Disease”. Li spoke about acne in particular: they found individuals with acne and those with healthy skin had significant differences in the facial microbiome at the strain level; there are genes that are differentially expressed.

Later, Pieter Dorrestein of UCSD moved the topic to metabolomics—he spoke about “Microbial Metabolites of the Skin Microbiome – Identifying Skin Chemistry to Search for Function.” He described how his group is taking several hundred swabs from the bodies of two individuals and translating the mass spectrometry data onto a 3D model—with the ultimate aim being to find the origin of the molecules. A combined metabolomics and 16S analysis showed no changes when the face and arms were treated with certain personal care products; however, there appeared to be a deodorant-dependent change in the armpit skin. In general, it appears that the profile is resilient, but that certain lifestyle factors can indeed impact the skin.

Day 2 summary

The second day of the Skin Health & Dermatology meeting featured another great lineup of speakers addressing different aspects of the skin microbiome. Amitabha Majumdar, Senior Research Scientist at Unilever, presented on “Commercializing Microbiome-based Beauty & Personal Care Products”.

Majumdar spoke about some of the major challenges in microbiome-focused product development:

  1. Finding the right target: In looking for the cause of malodour, the company found certain microbes, molecules, and pathways that were responsible; when they had the right target, they developed products (like Dove deodorant) to address the problem.
  2. Hitting a target better: In terms of acne, Majumdar says they found that lesions were reduced after a particular 3-week treatment that included natural oils. The company then took two natural oils that were part of this treatment and added them to two facial products already on the market.
  3. ‘Rebalancing’ the microbiota: One of the company’s toothpaste products were studied clinically—and they found that after 14 weeks, some of the bacteria associated with oral health were altered.

Majumdar’s talk was followed by one from Alex Goddard, VP, Research & Development at AOBiome: “Using Ammonia Oxidizing Bacteria to Restore Healthy Skin”. Goddard started with the premise that we are being deprived of certain metabolites because of the nature of our hygiene practices, and this may be altering our overall immune system and general health. He reported that David Whitlock, one of the company founders, noticed animals like horses roll in the soil to relieve an itch on the skin. This led to an investigation of whether the soil somehow had a therapeutic effect—and to the potential of ammonia oxidizing bacteria. These bacteria produce nitric oxide (which is anti-microbial and anti-inflammatory).

The company’s general approach is to discover new environmental bacteria that can be used on the skin. Goddard cited some of the challenges in developing new therapeutics: determining mechanism of action (whether direct or indirect); dosing; and variability in patients (from a physiological and microbial standpoint).

Then, Livia Zaramela, postdoc at UCSD, spoke on “The Role of the active Microbiome in Skin: Emphasis on Atopic Dermatitis”. Zaramela addressed the connection between food allergy and atopic dermatitis, as about one third of children with atopic dermatitis have food allergy. Their group uses a multi-omics approach to identify whether food allergies are intrinsically linked to atopic dermatitis or not.

Zaramela discussed how to overcome the challenges of low biomass samples for metatrascriptomics analysis: they maximize collection, extraction, and mRNA enrichment, and they work to minimize contamination. In terms of contamination, it’s necessary to reduce human content in the samples, but also reagent contamination.

Another speaker in the morning session was Magali Moreau, Associate Principal Scientist, Open Research at L’Oreal. She spoke on “Human Skin Microbiome: Opportunities for Healthy Skin with Aging.”

Moreau described how the company is looking at the skin microbiomes of women of all ages. At four different skin sites across two age groups, the distribution of Staphylococcus appeared to change significantly, while the proportion of Cutibacterium at each site decreased with age. Diversity was higher in the older group, across all sites. Thus, the trend with aging seems to involve a decrease in sebum and an increase in skin microbiome diversity, with some oral bacteria increasing on the skin.

She then addressed how to translate this growing microbiome knowledge into products. Approaches include fostering the growth of beneficial bacteria, controlling the community metabolites to bring back ‘equilibrium’, or perhaps using the virome for precision modulation.

Stephen France, Business Development at SkinBioTherapeutics, was the next speaker, on “Harnessing the Power of the Microbiome for Skin Health.” He focused particularly on some interesting observations on lysates (i.e. fluids containing the contents of lysed cells). They found lysates could inhibit pathogens and change the skin barrier; pretreatment of the skin with lysates protected against S. aureus invasion.

A talk from Greg Hillebrand, Senior Principal Scientist at Amway, capped off the morning sessions: “Changes in the Facial Skin Microbiome: A One-Year Longitudinal Study in Normal Healthy Men and Women.”

Hillebrand began by describing the company’s investigations into the meaning of skin health, with input from 70 individuals. The resulting points were: “it has to perform, but needs to be resilient when stressed; it needs to look even color-toned, and fairly unremarkable (you don’t notice your skin)”.

Hillebrand described the company’s ‘Cinco de mayo’ study, done in collaboration with Microbiome Insights. Skin samples from the forehead and cheek were taken from 150 Amway employees (aged 20 to 60) in 2017, with a repeated measure on 137 of the individuals in 2018. They measured other parameters like elasticity. Microbiome analysis using 16S V4 and V1-V3 revealed overlap in the microbial communities of the forehead and cheek, with some differences. Individuals’ skin microbiomes were relatively stable, and the individuals who had low diversity of their skin microbiome in 2017 also had low diversity the following year.

Barrier function was stronger with a more diverse skin microbiome; as water loss went up, barrier function went down. The other striking finding was that bacteria from the genus Corynebacterium increased with age. Amway is looking to build on these findings, with Microbiome Insights acting as an external R&D arm, to rapidly develop microbiome-focused solutions for skin health.

Better skin microbiome analyses using new 16S V4 region primers developed by Microbiome Insights’ scientific team

Over the past several years the Microbiome Insights team has invested in the development of new tools and techniques for obtaining high-quality, actionable skin microbiome data for our partners and clients in the cosmetics and dermatology industry.

When designing a new skin microbiome study, we always have an important discussion: which variable region should be sequenced? Although many assume that, for characterizing skin bacteria, primers targeting regions V1-3 are superior to those targeting the V4 region, it’s not so straightforward.

All current primers have their limitations—namely, that they underestimate the abundance of some skin-dwelling bacteria, poorly capturing skin commensals.

Our team members Pedro Dimitriu and Hilary Leung redesigned the V4 primer pair under the direction of Microbiome Insights co-founder Dr. Bill Mohn, and found that the new primers resulted in the detection of more bacterial genera, while improving error rates. The new primer also addressed a main limitation of common primers used for the v4 region: it can detect Propionibacterium acnes—the most abundant human skin bacterium.

Thus, we are now pleased to offer our clients this exclusive V4_skin primer in order to help them make the most of their skin microbiome surveys.

Improved bacterial 16S rRNA gene (V4 region) primers for skin microbiome surveys

Download the PDF version of this v4_skin poster.

If you’re thinking about designing a skin microbiome study, be sure to read our blog posts on both sampling and amplicon sequencing.

Contact our scientific team to learn more, or catch us in person at the upcoming Hanson Wade Skin Health & Dermatology Conference, September 10th to 12th in San Diego!

How Microbiome Insights can help with your Canadian microbiome research grant application

Competition for funding can be tough—but if you’re applying to a Canadian granting agency to fund a microbiome study, the Microbiome Insights team will be pleased to help. Some granting agencies require you to name an industry partner—and as the leading Canadian industry partner dedicated to microbiome testing and bioinformatic analysis, we are positioned to help your application be as successful as possible.

Here are some frequently asked questions about how we can help with microbiome research grant applications in Canada.

What kinds of testing does Microbiome Insights do?

Microbiome insights has a full suite of sequencing options—some of which may not be readily available at your own institution. Our services include amplicon sequencing (16S V4, 16S V1-V3, 16S V4_skin, 18S, ITS2 and Archaeal V4-V5), shotgun metagenomics, and bacterial whole genome sequencing; in addition to sequencing we run short-chain fatty acid analyses and calprotectin testing. If these are relevant to your research, please contact us to for more information on pricing, turnaround time, and support. Feel free to include our details in your grant application to show you’ve got everything lined up and ready to go for your research.

How flexible are the services?

While an end-to-end service is appealing to some, it doesn’t suit everyone. We can provide the full end-to-end service if needed or we can provide only the parts that make sense to you: for example, if you’re interested in learning more about bioinformatics yourself, you can obtain raw data from our team and explore the data on your own. Under this model, you’ll be able to leverage our wet lab standards while continuing to grow your own understanding of the microbiome.

Everything we do it price sensitive, so we have the ability charge per sample rather than having you lock into a full plate or a full run.

How can partnering with Microbiome Insights make the grant application stronger?

Including us in your grant applications shows you have strong collaborators and leading expertise on your side, bridging to the knowledge of our team and our co-founders (Drs. Brett Finlay and Bill Mohn). Through us, you’ll be able to secure expertise and support in the areas where you need it, and you’ll be able to access industry standards and proven pipelines. Moreover, you can be assured that all of this is done in Canada, with leading Canadian experts in the field.

What specific assistance can the Microbiome Insights team offer for grant applications?

We’ll consult with you to better understand (and draft, if necessary) the study design. We can give you guidelines on collection and transport to insert into your application, and can provide a mock report of the results if required. Our team members can also be hired to write a detailed results or methods section for your application.

Most importantly, we also offer a letter of support which details your study objectives, our deliverables for services and reporting, along with workflows and pricing. These details are key features of your submission, and we are always able to edit the details as funding is released.

How many Microbiome Insights clients come from academia?

The majority of our clients at present come from academia and publish their results in leading journals. If you choose to partner with us, you’ll have access to the same exceptional team that’s used by well-known researchers worldwide.

Contact us today using the form below!

On World Microbiome Day, Here Are Ten Microbiome Thought Leaders You Need to Know

Day in and day out, the Microbiome Insights team is immersed in scientific work on the microbiome. But on this very first World Microbiome Day, we’re taking a moment to step back and consider what—and who—made this remarkable field what it is today.

Although microbiome science is relatively young, the newest discoveries are only possible because of the preceding decades of research in fields as diverse as microbiology, genomics, molecular genetics, infectious diseases, and ecology. In this way, every microbiome researcher stands on the shoulders of those who came before.

With the help of Microbiome Insights co-founders Dr. Brett Finlay (Professor of Biochemistry and Molecular Biology, and Microbiology and Immunology at the University of British Columbia) and Dr. Bill Mohn (Professor of Microbiology and Immunology at the University of British Columbia), and our Scientific Advisory Board member Dr. Janet Jansson (Division Director of Biological Sciences at the Pacific Northwest National Laboratory)—all of whom qualify as thought leaders in their own right—we’ve compiled a list of ten scientists who have built a foundation for today’s microbiome researchers. These are individuals who, through their hard work and vision, have inspired their contemporaries to think differently and, in doing so, have shaped the field of microbiome science into what it is today.

Carl Woese

Dr. Carl Woese (1928-2012) was a biophysicist turned evolutionary microbiologist whose influence on the microbiome field cannot be understated. He was the first to show that bacteria evolve—and he demonstrated the phylogenetic relationships that backed this claim. Through this work he redefined the taxonomic scheme used to describe all forms of life on Earth and introduced us to the three domains of life we recognize today: Bacteria, Archaea and Eukaryota. His legacy is still seen in state-of-the-art lab techniques today, as he established phylogenetic methods using small subunit RNA and culture-independent methods that allow researchers to characterize microbial communities without first culturing them.

Norman Pace & trainees, including David Stahl

Dr. Norm Pace is, among many other things, a Distinguished Professor of Molecular, Cellular and Developmental Biology at the University of Colorado as well as a member of the National Academy of Sciences, a Fellow of the American Association for the Advancement of Science, the American Academy of Microbiology, and the American Academy of Arts and Sciences. His distinguished research career began with the breakthrough idea that, rather than trying to culture all of the unknown microbes of the world, one can instead scoop up genes from the environment and sequence them—essentially creating the many areas of microbiome study that are now among the most active in biology. Many trainees of his lab have gone on to make major contributions to many microbiome areas—in particular, Dr. David Stahl with his unique application of microbial ecology to environmental engineering.

James Tiedje

Dr. James Tiedje is a pioneer in the molecular exploration of soil and non-human environments. His work was instrumental in advancing many fields of microbiome research and addresses environmental concerns like climate change and bioremediation. His expertise in the field was even used for space exploration, as he designed experiments for the Viking Rover aimed at finding life on Mars. He is now a Distinguished Professor of Microbiology and Molecular Genetics and of Plant, Soil and Microbial Sciences as well as the Director of the Center for Microbial Ecology at Michigan State University.

Maria Gloria Dominguez-Bello

Dr. Maria Gloria Dominguez-Bello is Research Professor in the Department of Medicine at New York University whose work spans the fields of microbiology, anthropology, and agriculture. Collecting data from different populations across the globe, including populations in remote geographical areas, her work has focused on the immune and metabolic functioning of the microbiota through development, and how modern practices might impact this functioning. She is well known for her pioneering research on how Caesarean section birth impacts infant microbiome development, and possible microbiome ‘restoration’ techniques.

Martin Blaser

Dr. Blaser is Director of the New York University (NYU) Human Microbiome Program, and Professor of Microbiology at NYU School of Medicine. His early work with Helicobacter pylori confirmed its role in diseases like gastric cancer, providing one of the first examples for a bacterial role in these human diseases. He also brought attention to the importance of the early life microbiome and the dangers of antibiotics to a healthy microbiome and drug resistance—concepts covered for the general public in his highly praised book, Missing Microbes.

Jeff Gordon

How does the gut microbiome develop after birth, and how might this affect one’s nutritional status? These are the questions that drive Dr. Jeff Gordon, the Dr. Robert J. Glaser Distinguished University Professor at Washington University in St. Louis. He has shone a light on the role of the gut microbiota in metabolism and has taken on two pressing global health challenges: obesity and childhood malnutrition. By exploring interactions between the diet and gut microbiome he is discovering potential new ways of optimizing gut community development during the first few years of life.

Patrick Schloss

Dr. Patrick Schloss, now Professor in the Department of Microbiology and Immunology at the University of Michigan, took an interest in bacteria early in his career—not only the bacteria present in samples, but also what they were doing there. To answer this, he used gene sequencing and developed critical tools for analyzing microbiome data and making the interpretation of this data more accurate. With his flair for bioinformatics, his work has helped others make sense of the vast amounts of data generated by microbiome studies.

Stanley Hazen

Dr. Stan Hazen, chair of the Department of Cellular & Molecular Medicine in the Lerner Research Institute at Cleveland Clinic, changed the way researchers think about diet, the gut microbiome, and heart diseases by showing for the first time that a microbial metabolite (TMAO) was linked to cardiovascular disease. With his groundbreaking work in atherosclerosis and inflammatory disease research, he has impacted clinical practice and has laid the foundation for FDA-cleared diagnostic tests and cardiovascular disease drug development. Among his many accolades is his recognition as 2017 Distinguished Scientist by The American Heart Association for his many contributions to the field.

Eran Elinav

After completing his medical specialization as a doctor of internal medicine, Dr. Eran Elinav moved to the Department of Immunology at the Weizmann Institute in Israel. His work has uncovered the very personal links between humans, their diet, and gut bacteria. This has led to microbiome-focused research on personalized physiological responses to nutrition, and has garnered him several accolades including The Rappaport Prize for Excellence in the field of Biomedical Research.

Highlights of the Microbiome Drug Development Summit 2018 in Boston

Development and commercialization of microbiome-based therapeutics was the focus of a recent event in Boston (USA): the Microbiome Drug Development Summit 2018, organized by Hanson Wade. The Microbiome Insights team was in attendance – and here we share some of the highlights from this exciting event:

DAY 1

Jennifer Wortman, Senior Director, Bioinformatics, Seres Therapeutics

Unraveling Microbiome Signatures for Drug Design

Seres Therapeutics, one of the top 5 microbiome biotechnology companies in the world by funding, has a robust microbiome development pipeline. Their approach for addressing disease is to supply bacterial species that are associated with health in an attempt to change disease course.

Wortman explained the company has an extensive strain library isolated from healthy donors. They design consortia for their treatments using in silico design models (e.g. species and functions to reduce inflammation and increase epithelial barrier integrity) and by looking at species that are naturally co-occurring.

One product, SER-287, is an orally delivered community of purified Firmicutes spores associated with gastrointestinal health; it has efficacy in mild to moderate ulcerative colitis and is currently in phase 2B clinical trials. No serious drug-related adverse effects were noted in the trials. Research on SER-287 looks at engraftment: which species were absent at baseline but present after treatment? In all groups, they have seen engraftment of the spore-forming species following treatment: 19 species were more prevalent in patients achieving clinical remission; 13 species were more prevalent in patients not achieving remission.

Julia Cope, Director Scientific Operations, Diversigen

Microbiome Tools and Trends for the Pharmaceutical Industry

Cope spoke about the process for developing drugs to address various microbiome-linked diseases, including obesity, IBD, and cancer. To treat a disease, you need to know what to target. She cautioned that not all targets are likely to be bacterial in origin; researchers should also pay attention to viruses or fungal members of the microbiota.

Cope gave an example of four different studies that revealed four different microbiome-disease associations: taxonomy was similar but the specific biomarkers were different. She advised integrating as many cohorts as possible in order to prevent confounds.

Cathryn Nagler, President ClostraBio & Professor, University of Chicago

The Gut Microbiome, Immunity, and Allergic Disease

Nagler’s central question was whether we’ll be able to develop new microbiota-based strategies to regulate or prevent food allergies. She explained that certain populations of bacteria (classified as clostridia) make barrier-protective cytokines; they also stimulate the production of mucus, antibacterial peptides, etc.

Nagler’s data showed that lactobacilli were depleted in infants allergic to cow’s milk, with an increase in microbes that typically characterize an adult microbiome. Treatment with LGG increased tolerance of cow’s milk in these infants, and increased fecal butyrate. ClostraBio is engineering synthetic drugs to mimic the protective function of the health-associated bacteria.

Mark Smith, CEO Finch Therapeutics Group

Leveraging Reverse Translation to Develop Microbial Therapies

Smith described how broad-spectrum microbial interventions (i.e. fecal microbiota transplantation, or FMT) have good safety profiles in different therapeutic areas. Finch is using data from FMT trials to identify the bacteria linked with positive clinical outcomes, and then making these into bacterial cocktails for the treatment of disease. Smith described their product FIN-524 (developed with Takeda)–noting the challenges in understanding which organisms are driving the response.

An afternoon panel discussion, called Clinical Development of Microbiome-Based Therapeutics, covered a range of questions: clinical trial design in the development of microbiome-based therapeutics; key learnings from existing clinical programs for these therapeutics; and the relative importance of clinical efficacy and mechanism of action.

The panel discussed ‘hype’ in the media: some outlets inflate the importance of the scientific results, but companies need to temper the enthusiasm and stay focused on robust science. As for health professionals, they may be aware of this area but they are uncomfortable talking to patients about it until new products are approved and released into the market.

Regulation was another topic of interest: in particular, the need for flexibility in regulating new microbiome-related drugs. Panelists noted that there’s very little guidance in both the US and Europe, and it might make sense to develop guidelines or have guidance to expedite the development of some of these products. The Parallel Scientific Review is one mechanism that could help.

DAY 2           

Evgueni Doukhanine, R&D Scientist, Microbiome, DNA Genotek

Establishing Techniques for Reproducible and Insightful Microbiome Studies

Doukhanine discussed the necessary steps to design microbiome studies for scalability and innovative analysis. Many people pay attention to the sequencing technology—but the bioinformatics pipeline is also a very important factor. For 16S, they have seen that depending on the bioinformatic pipeline, the relative abundance recovery is quite different. DNA Genotek has moved from collection kits into study design consultation.

Phil Strandwitz, Co-founder & CEO, Holobiome

GABA-Modulating Bacteria of the Human Gut Microbiota

Strandwitz gave an overview of the microbiota-gut-brain axis and described the identification of a bacterium from the human microbiota that’s completely dependent on GABA for growth; Holobiome is using it to identify and culture a panel of diverse GABA-producing bacteria with the hopes that they can modulate levels of this important neurotransmitter.

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

New tools could mean profound changes ahead in medicine, says Canadian Medical Hall of Fame inductee Dr. Brett Finlay

Six exceptional individuals have been inducted into the Canadian Medical Hall of Fame in 2018 — and one of them is Microbiome Insights’ co-founder Dr. B. Brett Finlay, University of British Columbia Professor of Biochemistry and Molecular Biology at the Faculty of Medicine, and Peter Wall Distinguished Professor at the Michael Smith Laboratories.

The honour recognizes contributions to medicine and the health sciences that have had an extraordinary impact on human health.

Dr. Finlay is a microbiome knowledge leader whose work has explored the role of microorganisms in human health and disease — in particular, asthma and malnutrition. His discoveries have led to the development of several human and animal vaccines, and to treatments for drug-resistant infections like Severe Acute Respiratory Syndrome (SARS). (See Finlay’s full biography here.)

Below, we share a conversation with this esteemed member of our team — covering his career accomplishments and what he sees as the future of medicine.

Over the years, you must have overcome many challenges. What has driven you to do the things you’ve done in science and medicine?

I have always loved science, and the idea of using science to improve the world, including peoples’ lives, has always been a driving factor for me. Of course there are challenges, but as scientists we have the privilege to explore an exciting frontier, and find things never found before. Of course there are challenges, but all things worth doing have them, and being able to do science that has the potential to change the world is the greatest gift a scientist can have.

In your long and broad-ranging career, what medicine-related accomplishment or recognition are you most proud of?

The neat thing about science is you never know where it will take you. We are fortunate to have many successes. Some of the highlights include developing a vaccine to E. coli O157, developing the first SARS vaccine, and showing the early life microbiome plays a role in determining asthma are but a few. I am also proud of the book I co-wrote, Let Them Eat Dirt, and the new one I am finishing, The Whole Body Microbiome: Healthy aging with your microbes. This has allowed us to share the wonder and excitement of the microbiome with so many people. It is also changing how they look after their children with healthy benefits, which excites me tremendously, being able to promote child health through science education.

How do you think medicine is changing now?

I am biased, but I think medicine is about to undergo a profound change. Genomics, personalized medicine, and the microbiome will all play a major role in this upheaval. The ability to sequence a person’s genome or microbiome, to do a metabolomic analysis of a person’s urine, or a proteomic analysis of they blood all provide wonderful new tools to really figure out what is going on in a person, and then hopefully be able to treat based on molecular knowledge. The development of Crispr-Cas 9 could easily revolutionize gene therapy as well.

What innovations or directions in medicine do you see as uniquely Canadian?

Canada hits above its weight in science [but] science is global, and builds upon the shoulders of others, so to claim a geographic specialty is difficult. Canadian scientists are involved in many of the groundbreaking findings worldwide.

How do you hope your own work will lay the foundation for a different kind of medicine in future?

I strongly believe the microbiome will radically change medicine. If you take the top 10 reasons Canadians die, 9 of those 10 now have microbial links. Similarly, we know the microbiome plays a profound role in how our body develops early in life. There are so many areas of medicine the microbiome is impacting, the inside joke is “what area isn’t affected”! The other advantage of the microbiome is that we can change it easily, unlike our own genes. This means its application should be easier than gene therapy or developing drugs — drugging the “bugs” will be a whole new area of pharmacy in the future.

The 2018 Canadian Medical Hall of Fame (CMHF) induction ceremony was held on April 12, 2018, in London, Ontario (Canada). See the CMHF video of Dr. Finlay here.

About the company:

Microbiome Insights, Inc. is a global leader providing end-to-end services for microbiome DNA sequencing, including state-of-the-art bioinformatic analysis. Based in Vancouver, Canada, the company’s customized suite of services enables researchers and clinicians to easily and effectively include microbiome analysis in studies across a range of human, animal, agricultural and environmental applications. The multidisciplinary team of researchers and knowledge leaders at the company’s helm provide access to decades of expertise in traditional sciences such as ecology, microbiology, infectious diseases, and genetics. Microbiome Insights’ award-winning team is committed to providing clients with fast, dependable, cost-effective results.