Publication from Mohn Lab assesses genetic potential of the forest soil microbiome post-harvesting

Harvesting trees from forests, even when replanting efforts are made, has a huge impact on the long-term functioning of the soil microbiome. The unique microbial community in the soil performs essential tasks like decomposing plant material, which recycles nutrients for new plants to use. Plus, these microbes play vital roles in nutrient cycling such as the carbon and nitrogen cycles. To better understand the effects that removing organic matter (harvesting) has on the capacity of the soil microbiome to perform these duties, researchers from the University of British Colombia and the Georgia Institute of Technology assessed the genetic potential of soil communities for biomass decomposition and nitrogen cycling in harvested sites across North America, each representing a unique ecozone.

Using study sites and designs from the Long Term Soil Productivity Study, established during the 1980s, the researchers used shotgun metagenomic sequencing to quantify the diversity and abundance of genes essential to the microbial community’s decomposition and nutrient cycling functions. Harvesting and replanting occurred roughly ten years prior, with three different levels of organic material being taken at each site: stem-only harvesting, whole-tree harvesting, and whole-tree harvesting plus forest floor removal.

Harvesting overall played a role in altering the soil gene profiles, but the level of organic matter harvested did not. Researchers observed a reduced relative abundance of carbohydrate active enzymes genes—which are important for decomposition—and an increase in the abundance of nitrogen cycling genes. However, the increase in nitrogen cycling genes did vary by ecozone, suggesting ecozone-specific nutrient availability plays a role in the sensitivity of the carbon and nitrogen cycles to harvesting.

This was the first large-scale metagenomics study looking at the effects of harvesting on the potential for soil communities to perform some of their natural functions. The team believes that these changes could have an affect on forest productivity as trees grow and their nutrient demand increases, and may also alter a forest’s ability to resist future perturbations. According to the researchers, “our results suggest a mechanism by which harvesting can exacerbate nitrogen losses at sites predisposed to such losses, potentially lowering plant productivity and increasing greenhouse gas emissions.”

Cardenas E, Orellana LH, Konstantinidis KT, Mohn W. Effects of timber harvesting on the genetic potential for carbon and nitrogen cycling in five North American forest ecozones. Sci Rep. 2018; 8: 3142.

PRESS RELEASE: Rebiotix and Microbiome Insights collaborate on a microbiome IBD tool for clinical development

Recent study provides proof of concept for using novel scoring system to define IBD-related changes in microbiome

With a growing body of science linking gut microbiota to inflammatory bowel disease (IBD), a need exists in clinical settings to understand changes in the gut microbial community as they relate to IBD and its management.
Two leading microbiome companies, Rebiotix (part of the Ferring Pharmaceuticals Group) and Microbiome Insights, are collaborating to validate one such tool: a proprietary analysis to determine how closely a patient’s microbiome resembles that of someone with IBD. Microbiome Insights’ bioinformaticians developed an IBD Microbiome Score, based on a vast dataset of over 1600 individuals with IBD and healthy controls. The metric combines the latest understandings of the gut microbiome as a complex ecosystem with information on hundreds of taxa in the bacterial community, rather than the presence or absence of specific taxa. Based on fecal microbial characterization by sequencing, the IBD Microbiome Score can be assigned for each individual patient at diagnosis and at different times throughout treatment, making the Score practical for clinical use. Leveraging Rebiotix’s proprietary Microbiota Restoration Therapy™ (MRT) drug development platform, the Score is being evaluated in active clinical trials to treat IBD.

“The microbiome field is enormously complex,” says Dr. Ken Blount, Rebiotix’s Chief Scientific Officer. “With the use of the first-in-class Rebiotix MRT platform continuing to expand into complex conditions such as IBD, it is critical to have strong, scientifically-validated tools to understand the dynamics of the microbiomes changes within our patients. We’ve seen first-hand how the novel platform and expertise of Microbiome Insights has the potential to rapidly advance not only our understanding of the impact of MRT on patients, but also to uncover valuable microbiome findings for the entire industry.”

“Our scientific team has consulted with leading gastroenterologists to explore ways of leveraging the science on the microbiome and IBD in the clinical setting,” says Microbiome Insights CEO Malcolm Kendall. “Now we have developed the first scientifically robust tool for tracking the microbiome of people with IBD and understanding its link to clinical outcomes. The ability to work with Rebiotix on this path to discovery underscores the future utility of our platform in the clinical setting.”

The companies are continuing to explore applications of Rebiotix interventions and Microbiome Insights’ personal health platform in other microbiome-related diseases.

About Rebiotix
Rebiotix Inc., part of the Ferring Pharmaceuticals Group, is a late-stage clinical microbiome company focused on harnessing the power of the human microbiome to revolutionize the treatment of debilitating diseases using drug products built on its pioneering Microbiota Restoration Therapy™ (MRT) platform. The MRT platform is a standardized, stabilized drug technology that is designed to rehabilitate the human microbiome by delivering a broad consortium of live microbes into a patient’s intestinal tract via a ready-to-use and easy-to-administer format. For more information on Rebiotix and its pipeline of human microbiome-directed therapies, visit www.rebiotix.com.

About Microbiome Insights
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 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.

See the original Business Wire press release here.

Study led by Afribiota investigators shows stunted growth in children is associated with gastrointestinal ‘de-compartmentalization’

Stunting, the impaired growth and development of children, affects an estimated 155 million children per year. This represents roughly 25% of the world’s children and there exists a substantial lack of knowledge regarding the underlying causes and potential treatments. Current thinking on stunting hypothesizes that contributing factors such as inadequate psychosocial stimulation, poor nutrition, and recurrent infection are to blame. New research, however, is indicating that the microbial community of the small intestine, an organ essential for digestion and nutrient absorption, may be another contributing factor.

New data, published in PNAS by Afribiota investigators, including Microbiome Insights co-founder Dr. Brett Finlay, found that children suffering from stunting are affected by bacterial overgrowth in the small intestine and possess a microbial community made up from mainly oropharyngeal bacteria. Researchers studied duodenal and gastric samples of children with stunting, aged 2-5 years, in comparison with healthy children living in sub-Saharan Africa. Using 16S Illumina amplicon sequencing and semi-quantitative culturing methods they characterized the microbial communities of these children and found the small intestinal bacterial overgrowth in children with stunting.

The small intestines of children with stunting harboured bacterial species normally found in the oropharyngeal cavity. This overgrowth was also represented in fecal samples from the stunted children—which suggested a path toward developing non-invasive biomarkers for this condition. Furthermore, in stunted children Escherichia coli, Shigella species and Campylobacter species were more prevalent and Clostridia, well-known butyrate producers, were reduced.

These results indicate stunted children are experiencing a de-compartmentalization of the gastrointestinal tract, possibly a result of poor oral hygiene, recurrent or chronic rhino-pharyngeal infections, a hypo-chloric environment in the stomach (which weakens the natural barrier of stomach acidity), or other changes to the stomach environment which reduce its ability to kill unwanted bacteria. Importantly, these changes were seen in two geographically and nutritionally distinct populations, providing strong evidence that bacterial overgrowth is a conserved feature of the stunting condition itself.

The exact role of the oropharyngeal bacteria in intestinal inflammation, while yet to be determined, may provide vital information toward understanding the pathophysiology of stunting and potential new treatments.

Vonaesch P, Morien E, Andrianonimiadana L, et al. Stunted childhood growth is associated with decompartmentalization of the gastrointestinal tract and overgrowth of oropharyngeal taxa. Proc Natl Acad Sci U S A. 2018; 155: E8489-E8498.

PRESS RELEASE: Microbiome Insights receives funding from the Government of Canada to develop new microbiome testing platform for managing chronic disease

Vancouver, British Columbia (September 12, 2018)—Microbiome Insights, Inc. is pleased to announce that it will receive a contribution of up to $190,249 from the National Research Council of Canada Industrial Research Assistance Program (NRC IRAP) to help support the development of a new personal health platform of microbiome testing.

Co-founded by Drs. Brett Finlay and Bill Mohn at University of British Columbia in 2015, Microbiome Insights is a rapidly growing company and a global leader in microbiome testing and bioinformatic analysis. The advisory services and financial assistance from the Government of Canada, through NRC IRAP, will help the company expand in a new direction—continuing to develop tools for use in clinical settings as new data emerge on the gut microbiome and health.

“We’re leveraging our expertise in microbiome testing to develop a suite of tools for monitoring chronic disease in clinical practice,” says Microbiome Insights CEO Malcolm Kendall. “From the practitioner interface to the educational components of the test, our team is taking a fresh approach that is going to change the game for microbiome testing.”

The primary aim of the company’s personal health platform is to help address the challenges both healthcare practitioners and individuals face in the management of chronic disease.  Microbiome monitoring in those with chronic disease may provide a tool for assessing response to therapies or to various lifestyle changes (including diet), particularly when integrated with robust research findings and ongoing data collection.

The company’s new testing platform will be aimed at health practitioners helping individuals who live with inflammatory bowel disease. The efforts are led by Nataša Jovic, MBA, who brings to the company twenty years of experience in therapeutic and diagnostic commercialization. The company is currently exploring opportunities to commercialize its platform of microbiome tests for healthcare practitioners through research collaborations and distribution or joint commercialization efforts.

See the original BusinessWire press release here.

New paper from Microbiome Insights co-founder on critical window for the gut microbiome in infants and the later occurrence of asthma

Among serious and chronic childhood diseases, asthma is the most prevalent. Currently there exists no cure for asthma—only treatments designed to help manage symptoms. Recently, a body of research attempting to unravel how this condition develops  in young children has emerged, so that prevention may one day eliminate or reduce the burden of this chronic condition.

Recent work identified the existence of a critical window during the early lives of both mice and children, during which gut microbial changes are associated with the development of asthma. This provided an avenue to explore the role of the gut microbiome during early childhood development and the onset of chronic diseases like asthma. Importantly though, we know the gut microbiome varies greatly among those raised in different geographic regions. Therefore, understanding how changes in gut microbiota related to asthma development differ globally may provide valuable insights into the mechanism of asthma development.

A new paper, led by Microbiome Insights co-founder Brett Finlay and published in The Journal of Allergy and Clinical Immunology, evaluated the associations of fungal and bacterial changes (dysbiosis) in infants raised in the non-industrialized setting of rural Ecuador. The research was conducted as a collaboration between members of the Universities of British Colombia and Calgary, the BC Children’s Hospital, and Universidad Internacional del Ecuador. Children with atopic wheeze (27 in total) along with 70 healthy controls were identified and their bacterial and eukaryotic gut microbiota analysed at age 3 months. Stool samples were collected and sequencing of the 16S and 18S regions predicted bacterial metagenomes while fecal short chain fatty acids were determined via gas chromatography.

Results indicated that, similar to the previous findings in Canadian children, microbial dysbiosis in Ecuadorian infants at 3 months was associated with the subsequent development of atopic wheeze. Surprisingly though, the dysbiosis observed in Ecuador involved different bacteria taxa as well as some fungal species, and this was more pronounced than in Canada. Some predictions based on the metagenome analysis also emphasized significant dysbiosis-associated differences in genes involved in carbohydrate and taurine metabolism. The fecal short-chain fatty acid acetate was reduced while caproate was increased in children at 3 months who later developed atopic wheeze.

This work continues to provide evidence that there is a critical window during the first 100 days of life during which microbial dysbiosis is strongly associated with development of atopic wheeze. The study also yielded several valuable pieces of information. Despite the involvement of different bacteria taxa, both the Canadian and Ecuadorian populations had decreased fecal acetate, suggesting alterations to fermentation patterns may be a common factor associated with atopic wheeze. Furthermore, the pronounced role of fungal dysbiosis in this study led researchers to recommend that “the role of P. kudriavzevii and other yeasts should be explored in mechanistic studies using animal models.”

Along with more studies characterizing the early microbiome in more communities around the world, optimized biomarker studies of microbial taxa and metabolites could lead to better predictions of risk and therapeutic strategies to restore gut microbial health as a prevention method.

 

As founding sponsor of Hanson Wade Skin Health & Dermatology conference, Microbiome Insights speaks about skin microbiome study design

With its globally leading expertise in skin microbiome testing, Microbiome Insights was a proud founding sponsor of the Skin Health & Dermatology Conference, held in San Diego September 10th to 12th, 2018. According to conference organizers Hanson Wade, the aim of the event was “understanding the underlying biology of the skin microbiome for translation into safe, effective, and commercially viable dermatological therapeutics & cosmetic products”. Participants heard about microbiome-focused skin products already on the market and those under development by companies around the world.,

Microbiome Insights CEO Malcolm Kendall spoke at the conference, with a presentation entitled: “Swab to Data – Considerations for Designing Skin Microbiome Studies”. The talk covered expertise developed by the Microbiome Insights team by working with leading scientists and industry partners in cosmetics and dermatology, and explained how the company has developed new 16S V4 region primers for improved skin microbiome analyses.

Also on the speakers’ list was Greg Hillebrand, Senior Principal Scientist at Amway, who spoke about a study carried out in partnership with Microbiome Insights: “Temporal Changes in the Facial Skin Microbiome: A One-Year Longitudinal Study in Normal Healthy Men and Women”.

To find out more about the conference, see here.

Microbiome Insights co-founder Dr. Brett Finlay to speak at Institut Pasteur event

Microbiome Insights co-founder and co-CSO Brett Finlay will be one of the distinguished speakers heading to Paris from October 15th to 16th 2018 for the Institut Pasteur meeting: Modeling the Mammalian Microbiota Host Superorganism, Current Tools and Challenges.

Knowledge about the role of microbiota and microbial metabolites in host functions and health has steadily increased over the past two decades. With mechanistic insights enabled by animal models and an increasing ability to characterize microbial communities during both development and adulthood, researchers are on the cusp of real therapeutic treatments. The Institut Pasteur meeting will bring together academic and industry leaders from this field to share new visions on host-microbiota mutualisms and parasitism, and to discuss the latest techniques and models. Along with Dr. Finlay, some exciting names on the program include Dr. Andrew Macpherson of Inselspital in Bern, Switzerland, giving the keynote address, and Marion Leclerc from the MICALIS Institute in Jouy-En-Josas, France and Philippe Sansonetti of Institut Pasteur.

Finlay will present his talk, entitled The Role of the Early Life Microbiota in Malnutrition and Environmental Enteropathy during the ‘Models of Pathogenesis’ session on Monday, October 15th. He has published over 500 papers and, as a principal investigator at the University of British Columbia he studies how microbes interact with hosts to influence health and disease. His lab developed the first animal model for the study of environmental enteropathy, a key feature of childhood malnutrition. Ongoing work with this model is now funded by the Gates Foundation in order to explore how it can better our understanding of the consequences of malnutrition. The Finlay lab also investigates the risks for childhood asthma stemming from microbiota and metabolic alterations during infancy, and were the first lab to demonstrate that early life intestinal microbiota plays a crucial role in asthma susceptibility.

By understanding how microbes colonize the small intestine and cause stunted growth and inflammation, Finlay and his collaborators hope to develop new nutritional therapies for human malnutrition. His lab’s work is essential for understanding the microbiota-host superorganism and the associations that are essential to maintain good health and development—making Finlay a “can’t miss” speaker at this prestigious meeting.

Microbiome Insights hosts students for educational laboratory tour

JUNE 15, 2018 — Microbiome Insights was pleased to welcome an enthusiastic group of post-secondary students from Vancouver’s Alexander College this week for a laboratory tour and presentation.

During the visit team member Ben Tantika, Senior Next-generation Sequencing Technician, described the cellular and molecular biology techniques used in research labs to answer scientific questions.

The second year biology students heard about the importance of knowing the ways in which biological sciences techniques can be applied in both research and industrial settings. Tantika also helped the students understand how a career in life sciences can take shape, giving anecdotes about his own previous experiences as an international student studying at UBC Okanagan.

 

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

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

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

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

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

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

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

See here for some photos from the event:

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

 

 

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

 

 

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

 

 

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

 

 

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

 

 

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

 

PRESS RELEASE: Microbiome Insights, Global Leader in Microbiome Testing, Expands to New Lab Facilities on UBC Campus

Company’s rapid growth spurs move to new state-of-the-art facility

VANCOUVER, British Columbia–(BUSINESS WIRE)–Microbiome Insights, Inc. has announced the opening of its new laboratory on the campus of the University of British Columbia (UBC). The company, a leading end-to-end service provider for microbiome DNA sequencing and bioinformatic analysis, has expanded into its new state-of-the-art lab in order to meet the needs of over 100 clients.

“We have experienced rapid growth in our business and across the microbiome testing industry,” says CEO Malcolm Kendall. “This move is a major milestone for our company and helps us meet the needs of our growing client base, to deliver the high-quality service they have come to expect from us.”

Founded by two world-leading microbiome researchers, Drs. Brett Finlay and Bill Mohn of UBC, Microbiome Insights has grown rapidly since its incorporation in 2015—supporting over 200 microbiome studies across academia and industry. The new laboratory, located in the UBC Pharmaceutical Sciences Building, enables the company to expand its capacity, hire additional laboratory technicians and initiate clinical laboratory (CLIA) certification.

Brad Popovich, former Chief Scientific Officer at Genome British Columbia and Chair of Microbiome Insights’ Board of Directors, says, “The emergence of leading companies like Microbiome Insights is a sentinel for the growth of the microbiome testing marketplace; they are following a similar pattern of accelerated growth the field of genomics testing experienced over the past two decades.”

Microbiome Insights marked the opening of the new laboratory on May 28th with a reception and microbiome poster competition. Dr. Julian Davies, one of the scientists that spearheaded the NIH Human Microbiome Project (HMP) and Chair of the HMP External Scientific Board until 2015, spoke about the importance of microbiome research and the unique benefits of a UBC-based microbiome testing company.

See the original BusinessWire press release here.