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.

What can metagenomics do for you?

Microbiome data is leading to innovative solutions in diverse industries, from human and animal health to agriculture and the built environment. Next-generation sequencing has allowed researchers new insights into the microbial world with high levels of resolution—that is, they can precisely identify many of the bacteria and other microorganisms present. Not only that, but these technologies have enabled higher throughput than ever before. Foundational technologies, such as amplification and sequencing of phylogenetic markers, including the 16S rRNA gene, have become standard tools for understanding how microbial communities are structured and how they respond to changes in their environment.

However, amplicon sequencing does have some limitations in the type and resolution of the information it provides. This is where metagenomics — the direct recovery of total genomic information from the environment — can make a difference. Amplicon sequencing readily provides information at roughly the genus level; with care, it can identify microbial species and strains only under specific circumstances. Metagenomics reliably provides up to strain-level resolution (Figure 1). It also provides information about function—what the microorganisms’ genes equip them to do.

Figure 1. Species level classification of Staphylococcus species in skin samples recovered from amplicon sequencing and metagenomics. Metagenomics was able to resolve the taxonomy up to species and show that different body types select for different Staphylococcus species. Data from patient HV07 from Oh et al. 2014 (doi: 10.1038/nature13786).

Functional information is useful to understand the mechanisms underlying the changes in the microbial community, to reconstruct the metabolism of the community as an entity, and to discover new genes and pathways (Figure 2). The addition of functional information is also helpful to understand what groups provide what functions and how much redundancy exists for that function, which can have implications for the degree of resilience of the community (how it can bounce back after perturbations).

Figure 2. A. Changes in the abundances of key carbohydrate active enzymes in the soil ten years after forest harvesting. Differences were present in enzymes involved in the degradation of plant carbohydrates such as cellulose and hemicellulose. Modified from Cardenas et al. 2014 (doi:10.1038/ismej.2015.57) B. Metabolic reconstruction of the aerobic n-alkane degradation by partially-recovered genome from a metagenome of an oil reservoir. Expression levels are represented in blue barplots. Modified from Liu 2018 (DOI 10.1186/s40168-017-0392-1)

A second advantage of metagenomics is that it recovers data from all microbial community members, so the information will not be limited to bacteria (as when using a 16S rRNA) but also include data for fungi, viruses, and other groups. One example: using metagenomics, Oh et al. 2014 (Figure 3) mapped the abundance of bacterial and fungal species, and viral groups to different skin locations, identified functional gene differences across sites, and recovered 67 partial genomes (bacterial, viral, and eukaryotic). When samples have low diversity (e.g. enrichments), metagenomics can recover high quality draft genome sequences from community members. The genome of Kuenenia stuttgardiensis, one of the first characterized anaerobic ammonia oxidizers, was obtained from a metagenome of a bioreactor sample (see doi:10.1038/nature04647) without the need for cultivation.

Figure 3. (A) Average multi-kingdom relative abundances for 15 healthy adults stratified by skin characteristics. (B) Detailed phyla-level composition for two of those patients. Data from Oh et al. 2014 (doi: 10.1038/nature13786).

Metagenomics also comes with its own limitations. Since sequencing is done for the whole community, analysis can be challenging if too much host DNA is present or for samples with very low biomass. In the first case, most of the data will be of little interest since the host is not the target. In the second case, only a small part of the community will be reflected in the data, leading to a biased understanding of the microbiome. Finally, the applications of metagenomics depend on the depth of sequencing (Figure 4). Having higher sequencing coverage allows for recovery of data from more community members, assembly of short reads into larger contigs, and the use of those contigs to reconstruct genes, pathways, and genomes.

Figure 4. Effect of sequencing effort on the range of possible analyses of metagenomes.

In addition to these challenges, the public databases which are used for data comparison are constrained. These databases contain sequence information as well additional data such as the organism the sequences came from, the location and date of sampling, functional annotation, and links to related publications. Databases link sequence information with taxonomy and function and represent the historic efforts of researchers worldwide (and consequently their biases). These databases are limited first because most genes in any genome, even those from well-studied groups, lack biochemical characterization; and second, databases are biased towards human-related and pathogenic groups. Poorly represented groups in the databases include the archaea, fungi, viruses, and small eukaryotes; poorly represented environments include soils. Yet, this may not be a roadblock, but a challenge that will lead us to a better understanding of the microbial world.

“Both the cost and complexity barriers to metagenomic and metatranscriptomic sequencing have been greatly reduced, meaning these shotgun approaches are now practical ways to very precisely profile the human microbiome and other microbial communities,” says Curtis Huttenhower, Microbiome Insights Scientific Advisory Board member and Associate Professor of computation biology and bioinformatics at the Harvard T.H. Chan School of Public Health (Boston). “Metagenomics can now easily provide strain tracking and functional information that is difficult to obtain using amplicon sequencing, and these can further be integrated with metatranscriptomics, metabolomics, or other culture-independent molecular data to understand microbial community bioactivity.”

Microbiome Insights provides a full suite of services, including both amplicon sequencing and metagenomics. We can help you answer the question: where will metagenomics can take you?

 

How microbiome science is leading to human nutritional innovations

We all know food plays a critical role in health, but can anyone really answer why or how it is so important? Scientists have made numerous links between particular foods and health outcomes over the past few decades, enabling dietitians and other professionals to give guidance, with some level of certainty, toward dietary choices that will maximize their ability to live longer, fuller lives. But many of these links between diet and health remain associative, gleaned from epidemiological studies with little evidence of causation. One example is dietary fiber—while it is clear that a higher consumption of fiber is associated with a myriad of health benefits and even lower mortality, the underlying mechanisms have remained elusive.

Microbiome science is playing a role in changing this uncertainty. Population cohort studies show that, aside from medication, diet is the leading environmental factor that predicts the composition of the gut microbiome from person to person. Meanwhile, experimental studies are showing the gut microbiome influences various aspects of human immune and metabolic health. Thus, many see the potential for diet to become a powerful means of manipulating the human gut microbiome for better health.

Under this framework, a number of companies are already focusing on the development of foods that better support the microbiome and health at different points in the lifespan, from infancy to older adulthood. Microbiota-modulating ingredients may be deliberately included in foods or concentrated into supplements—and then, of course, tested for their measurable effects on the health of the host.

Thinkstock image, used with permission

Below are some examples of microbiome-enabled innovations that may be around the corner for nutrition, both for healthy populations and for those with disease:

Nutritional interventions that support brain health

Alzheimer’s disease places a significant burden on both health services and patients’ family members, and prevalence is estimated to increase dramatically in the coming decades. Could nutritional interventions play a part in preventing this condition? Jared D. Hoffman of the University of Kentucky (USA) is studying a microbiota-modulating prebiotic intervention as a possible way to prevent Alzheimer’s disease in those who carry the APOE4 gene; in a mouse model, he found that increased intake of inulin led to gut microbiota alterations (e.g. more Bacillus subtilis), increased scyllo-inositol (which moves through the blood-brain barrier into the brain), and decreased amyloid beta in the brain.

Supplements to change the microbiome for healthy aging

While extremely healthy older individuals show gut microbiota compositions that resemble much younger individuals, it’s not clear whether the gut microbiota itself confers youthfulness or good health. However, interventions targeting the gut microbiota may show promise. One company recently carried out a placebo-controlled clinical trial of its resistant starch product in older adults, testing both gut microbiome changes and the resultant health effect; they found increases in bifidobacteria, which accompanied significant differences in blood glucose, insulin levels, and insulin resistance.

Dietary therapeutic interventions for IBD

Anecdotally, many people with inflammatory bowel disease (IBD) report an influence of diet on their symptoms; yet dietary research in IBD has been inconclusive, and diet is currently not a part of the standard therapeutic regimen for IBD. The exception is with exclusive enteral nutrition (EEN) for certain cases of Crohn’s disease—this diet appears effective at inducing remission. Gut microbiota is under investigation as the mechanism behind this effect, with recent research suggesting the gut microbiota of the patient at baseline may predict the success of EEN. In future, the idea of using microbiome composition to predict responders may be extended to other food items or dietary patterns in IBD, expanding the therapeutic toolbox for both Crohn’s disease and ulcerative colitis.

Nutritional interventions that boost bacteria with therapeutic potential in obesity and metabolic disease

Akkermansia muciniphila is a member of the human gut microbiota that may have particular importance in metabolic health; it stimulates butyrate production and prevents the development of obesity in animal models, and is currently being tested in a human clinical trial. Many regulatory hurdles, however, will need to be cleared before bringing these “bugs as drugs” to market. In the meantime, research may help uncover specific nutritional interventions that can increase Akkermansia in the gut environment for potential effects on metabolic disease and obesity.

These are just some examples of experiments in food science that have shown manipulation of health by way of the gut microbiome. As such, leaders in the food industry are beginning to use microbiome science to develop products that better support health, but not all companies have the internal expertise to tackle the challenge. Microbiome Insights addresses this gap in expertise by working closely with clients to plan and execute all aspects of nutrition-related microbiome studies. Our team is collaborating with several industry clients to help advance new food products and supplements that enhance health through the microbiome—confident that microbiome science will help guide us toward knowledge of who should eat what, and when, for better health.

 

Banff Keystone Symposia on Gut Microbiota: Day Three Summary

Wednesday was the third day of the joint Keystone Symposia in Banff, Canada: (1) “Manipulation of the Gut Microbiota for Metabolic Health” and (2) “Microbiome, Host Resistance and Disease”, and the great talks kept on coming!

One track opened the day with a group of lectures on nutrition and gut microbiota. Jens Walter (a local, from University of Alberta) talked about modulation of the human gut microbiota with non-digestible carbohydrates—taking an ecological perspective. Then Nathalie Delzenne (Université catholique de Louvain) spoke about the links between prebiotics, gut microbiota, and human health, describing her intervention study on increasing inulin-rich vegetables in the diet. On the mechanism side, André Marette (Université Laval) described mouse work on the interaction between dietary polyphenols—for example, arctic fruit extracts—and the gut microbiota to alleviate obesity-related diseases. And regarding the early life period in humans, Maria Carmen Collado gave an apt overview of what we know about how the maternal microbiome (in breast milk especially) affects the infant gut microbiome and health. Meanwhile, in the other track, the account by Kerwyn Casey Huang (Stanford) of how the gut microbiota can be resilient to perturbations proved popular.

At 5:00 pm the action continued with a track on xenobiotics-microbiota interactions in metabolic diseases and another on disease tolerance, pathology, and the microbiome. In the latter, Yasmine Belkaid (NIAID, NIH) spoke about her extensive work on control of skin tissue immunity and repair by the microbiota, discussing how homeostatic immunity to the skin microbiota occurs through diverse mechanisms that may or may not involve inflammation. Janelle S. Ayres (Salk Institute) then talked about what she has learned about host-microbe interactions (and adaptations); she described her mouse model findings on how micronutrients—for example, iron—mediate healthy host-pathogen interactions.

Thursday will be the last day of these joint conferences! But don’t forget—you can still re-live the action on Twitter by searching the conference hashtags, #KSmicrobiome and #KSgut.

Banff Keystone Symposia on Gut Microbiota: Day Two Summary

March 6, 2018 marked the second day of the joint Keystone Symposia in Banff, Canada: (1) “Manipulation of the Gut Microbiota for Metabolic Health” and (2) “Microbiome, Host Resistance and Disease”.

Morning sessions were split into two tracks. The first track covered microbiota and metabolic disorders, with two initial talks by François Leulier (Institut de Génomique Fonctionnelle de Lyon) on gut microbiota and host mutualism in chronic undernutrition, and Emily P. Balskus (Harvard University) on microbiota-drug interactions.

The complex development of early life gut microbiota and immune function was the topic covered by the second track. Maria Gloria Dominguez-Bello (Rutgers University) gave an overview of what we know about how C-section birth is linked with later-life disease through the gut microbiota, showing the associations that exist in human populations and the causal evidence that exists in mouse models. Andrew J. S. Macpherson (University of Bern) then gave a detailed account of early postnatal innate immune development, showing how the site of microbe administration shapes distinct repertoires of IgA and IgG antibodies from mature B cells, and how these antibodies are found in several sites through the host. Subsequent talks branched out to other immune-related topics linked to skin commensals, and also the gut-brain axis (i.e. a gut bacterial metabolite that causes behavioural abnormalities related to anxiety and autism spectrum disorder).

The evening’s sessions were divided into one track on gut barrier alterations and host metabolic disorders, and one on mechanistic microbiome function in physiology and aging. A highlight of the evening was the account given by Lora Hooper (University of Texas Southwestern Medical Center) of mechanisms linking circadian rhythm with adipose tissue development: in mouse models, she found a conventional microbiota drives immune system regulation of circadian rhythms, resulting in more long-chain fatty acid uptake on a high-fat diet, and ultimately an increase in adipose tissue. Participants in the evening session also heard a talk by Michiel Kleerebezem focusing on the microbiota of the small intestine and how a robotic capsule can be used to track the effects of a dietary intervention.

We’ll be tweeting again on Wednesday! Look for the conference hashtags, #KSmicrobiome and #KSgut.

Banff Keystone Symposia on Gut Microbiota: Day One Summary

Gut microbiota researchers from across the globe gathered in Banff, Canada for two joint conferences: (1) “Manipulation of the Gut Microbiota for Metabolic Health” and (2) “Microbiome, Host Resistance and Disease”. On day one of the conference—March 5, 2018—all sessions were held concurrently.

For several human diseases, observed differences in gut microbiota composition between disease populations and healthy controls are well known. What’s of greater interest is mechanism: the steps causally involved in disease pathogenesis or maintenance. On March 5th, to a packed room, the presenters delved deep into the gut-microbiome mechanisms responsible for human disease states ranging from obesity and diabetes to cardiovascular disease.

The morning sessions focused on the mechanisms of pathogen infection as well as obesity and type 2 diabetes. In the keynote address, Andreas J. Bäumler (University of California, Davis) gave a detailed account of something that could be a driver of gut dysbioses: oxygen becoming available to gut pathogens. Then Fredrik Bäckhed (University of Gothenburg) described how a bacterial metabolite—imidazole propionate—may be related to type 2 diabetes, and Liping Zhao (Shanghai Jiao Tong University & Rutgers University) delivered a talk on various aspects of the gut microbiota in obesity, underscoring the necessity of considering microbial ecology.

After an afternoon workshop by Microbiome Insights’ Scientific Advisory Member Curtis Huttenhower (Harvard), which gave an overview of different microbial community analysis workflows, the afternoon sessions focused in on the gut microbiota’s role in the control of fat metabolism. The wide-ranging topics covered how the gut microbiota may be involved in liver disease pathogenesis; how cold temperatures transform fat (a process called “browning”) in order to use more energy and decrease adiposity; and extensive work from the lab of Patrice D. Cani on the endocannabinoid system and how intestinal NAPE-PLD appears to be a key sensor controlling food intake and energy metabolism upon fat exposure.

Follow our Twitter feed tomorrow — and don’t forget to check out the hashtags #KSmicrobiome and #KSgut for more of the action from the Banff Keystone Symposia!

Four important areas for harnessing the microbiome in agriculture

Microorganisms form the foundation of every ecosystem on Earth, coexisting and interacting with a variety of host organisms. Of interest in the agricultural field are the plant microbiome and the soil microbiome, and how the two interact with one another. Microbes are associated with every plant tissue: they are found in the stems, leaves, and seeds (where they are known as endophytes), and on the surfaces of these same tissues (where they’re known as epiphytes). The most studied agricultural microbiome is the plant’s rhizosphere: the bacteria, archaea, and fungi (such as mycorrhizal fungi) living in and around the plant’s root system. To the plant they provide fixed nitrogen, access to micronutrients, and protection from pathogens in the soil; in turn, the plant roots release nutrients (for example, sugars and amino acids) that sustain the microbes. Whereas the rhizosphere is mainly recruited from the soil to provide support to the growing plant, the seeds containing their own microbiomes provide support for the plant’s next generation.

Scientists in the field of agricultural biosciences (or agbio) are combining old and new techniques to find out the impact of the agricultural microbiomes, and how to manipulate them over time. The tools they use include conventional culturing techniques, community snapshots via sequencing of universal barcode regions, as well as shotgun metagenomics and transcriptomics. By harnessing the microbiome, they hope to render the agricultural output ever more bountiful, resilient, nutritious, and flavorful.

Thinkstock photo, used with permission.

Here is a brief summary of four areas of potential for the microbiome in agriculture:

Yield Improvement

Plants depend on their root microbiome, and the microbiome of the surrounding soil, for access to organic nitrogen, phosphorus, and micronutrients which are necessary for their growth. Therefore, the root and soil microbiomes are a logical place to start when considering agricultural improvements.

Soil health is an important part of improving crop yields. Legumes have been used since antiquity in crop rotation because of their ability to improve soil health—and more recently it was found they do this though their impact on nitrogen and nitrogen-fixing microbes (rhizobia) in root nodules. These rhizobia have been commercially available for decades and are still used as inoculants when legumes are first planted.

Now biological inoculants of soil and root microbes are also available to provide a variety of benefits including: increasing bioavailability of phosphorus, nickel and potassium; relieving drought and salinity stress; and increasing oil production. One product in development is aimed at providing nitrogen fixation to non-legumes, while another early stage product is focused on increasing seedling vigor. The benefits of microbes beyond the roots is leading to a push for research into inoculum for endophytes of the stems and leaves. These are just a few examples of microbiome inoculation in agriculture.

Many new technologies are shifting focus from single organisms to a community view, and inoculation is no exception. LCO (lipochitooligosaccharide) is the signaling molecule used by nodule forming plants and their rhizobia to communicate, and application of this hormone accelerates root colonization by natural microbiota and inoculated bacteria. On the cutting edge of the microbial inoculate market is the modulation of whole microbial communities rather than just a few organisms.

Nutritional improvement

Although crop yield is an important focus of crop improvements, nutritional content is also a concern. It has been demonstrated that many of our food crops have decreased in nutrient content over the past century. This decline is likely caused by many factors including industrial selection of fast growing/low nutrient crop varieties, depletion of nutrients in the soil, and perturbations of microbes in the plants and surrounding soil. Recent efforts have gone into understanding the role that both rhizobia and endophyte communities play in reinvigorating the nutrient profiles of these crops. In future, microbes may play a role in bringing more nutritional value to existing crops.

Flavour Alteration

Foods grown in soil with high organic matter will taste different—often richer and more flavourful—than foods grown in sandy soils. The organisms of the microbiome modulate the metabolisms of their host plants, and perhaps even produce flavor altering chemicals themselves. This may be of particular interest in end products that depend on flavor profiles such as wine, coffee, chocolate, and herbs/spices. For instance, the bacteria and fungi in wine fermentations, which are shaped in part by conditions in the vineyard, correlate with the chemical composition of finished wines – contributing to ‘terroir’. Herbs grown in enriched environments will have heightened herbaceous qualities of smell and taste.  We continue to seek understanding of the ways in which particular bacteria and fungi impact these specific ecosystems.

Pest and pathogen management

During the plant’s growth there are several risk factors that may disrupt its life cycle. The plant has its own protective mycobiome through its endophytes. These microorganisms produce secondary metabolites such as alkaloids and terpenes that are toxic for insects and other herbivorous pests.

Biopesticides are a rapidly developing technology, driven in part by consumer demand for alternatives to chemical pesticides. These products take advantage of ways to resist the crop’s pathogens. A variety of microorganisms can be used control other organisms such as insects, fungi, nematodes, bacteria, and viruses that may be playing a detrimental role in the ecosystem and in the growth of plants.

Like the next generation of yield enhancing technologies, new biopesticides will consider not only single advantageous organisms, but also the complex network of cooperating microorganisms.

The Future

Through our clients, we see agricultural biosciences starting to embrace the impact of the microbiome and its importance to plant and soil health and the agricultural production process. At Microbiome Insights we see the role of the microbiome as essential for industry-leading agricultural innovation, and provide a suite of services that help advance this science.

 

How to Design a Skin Microbiome Study, Part II: Amplicon Sequencing

In this post, the second of a 2-part series on skin microbiome research, we will discuss technical issues surrounding sequencing of human skin microbes. Read the first blog post here.

At this point, the microbial ecologist conducting a skin microbiome study has now collected all the skin samples she needs, and the DNA has been extracted. We turn to the question of how to decide on the sequencing strategy. Metagenome shotgun sequencing, in which the entire community of microbes is sequenced in an untargeted manner, can provide invaluable information about the functional potential of the microbiome, but – despite continually dropping sequencing costs – it is still expensive. The researcher in this case settles for 16S marker gene sequencing, which targets a specific region of the gene. Now, which primer pair should she choose?

The current dogma in the field is that primers targeting regions V1-V3 are better at describing skin bacterial communities than the V4 region primer pair. (The V4 region is commonly used for studying gut communities and other environments.) This is because V1-V3-sequenced communities better recapitulate the taxonomic composition and relative abundance of “mock community” controls (Meisel et al., 2016). And V4 primers poorly amplify typical skin microbes, notably Propionibacterium and some Staphylococcus species (Meisel et al., 2016). But should V4 be discarded in favor of V1-V3?

The reason behind the V4 region’s underestimation of Propionibacterium is a single mismatch at the end of the primer that prevents efficient binding to a specific group of bacteria. To evaluate if V4 region may be a suitable target for characterizing skin bacteria, our team re-designed the V4 primer pair and tested in silico its ability to improve the coverage of underrepresented propionibacteria. With these new candidate primers, we are able (theoretically) to increase the coverage of Propionibacterium to over 67%–from less than 3%–without losing coverage of the other bacterial groups. Our next step is to evaluate the accuracy of this approach using a mock community as the standard.

There are advantages to using existing V4 primers. They can detect the genera Finegoldia and Peptoniphilus, which are increased in persons with primary immunodeficiencies (Oh et al ., 2013). Zeeuwen et al., citing previous work, also pointed out that the 27F primer used for the V1-V3 region inefficiently amplifies Gardnerella and Lactobacillus, which have been found to be associated with females (Zeeuwen et al., 2012). In general, V1-V3 classifies fewer populations down to the genus level (Meisel et al., 2016). Because the V1-V3 region is longer than the V4 region, paired-end reads generated with the Illumina MiSeq will not fully overlap. And without full overlap, denoising of reads is not as effective. Using the V3 chemistry (a 600-cycle kit, longer than the 500-cycle kit of the V2 version) will not solve the problem and may even make it worse, because the sequence quality drops after 500 cycles.

In this two-part blog series, we have discussed how to collect enough microbial biomass to run a skin microbiome study, and how to deal with environmental contamination. We have seen that even relatively minor changes in primer sequences may improve the detection of bacteria relevant to skin microbiomes. Feel free to reach out to our team for more information on designing your own skin microbiome study!