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.

 

Microbiome Insights included in list of BC’s top emerging life sciences companies

 

MARCH 14, 2018 — Microbiome Insights is honoured to be featured in the 2018 Emerging Rocket List by the management consulting firm Rocket Builders. The Emerging Rocket List is part of “Ready to Rocket”, a business recognition program that showcases British Columbia’s technology companies with the greatest potential for revenue growth as well as investment and market breakthrough.

The Ready to Rocket program encompasses 4 technology sectors: Information and Communications Technology, Cleantech, Life Science, and Digital Health. Microbiome Insights was one of the 10 companies included in the Emerging Rocket Life Science List, winning this recognition for the second year in a row.

Lists in the Ready to Rocket program are predictive of success; since 2003, the program has accurately identified future growth leaders in each category through rigorous sector and company analyses spanning several months.

To qualify as a candidate in the Life Science category, companies must have established industry relationships and must also be undergoing customer validation and regulatory approval. The selection committee assesses candidates based on early indicators of long-term potential and increasing shareholder value, such as passing key regulatory hurdles and achieving related validation steps.

“We identify companies that have both innovative technology and a fit within the industry value chain. Our analysis of the market and the company progress led to our selection of Microbiome Insights as a Ready to Rocket Life Science company,” said Thealzel Lee, Senior Partner, Rocket Builders.

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!