Discover Genomics with the Microcosmos App
This visually stunning (free!) app tells fascinating stories about how 4 letters form the building blocks of all life - from an elephant to an onion and so much more.
The Challenge
Microbes are the most abundant and diverse life forms on the planet - out numbering the total stars in the universe by several orders of magnitude. This “microcosmos”, a small part of the macrocosmos, more commonly known as the universe–plays an essential role in creating and sustaining the conditions for life itself. The diversity of microbes provides a vast reservoir of biological sequence data that can both teach us about ourselves, our environment and be central to much needed innovation as we begin to experience the consequences of climate change.
While genomics can be exhilarating for experts, the dense information produced by this field often overwhelms those without specialized knowledge or time for deep exploration. We make it fun to explore the world around us.
The Solution
We created the Microcosmos app as a labor of love - making it free to all. Bridging art and science, the app tells fascinating stories about how four letters form the building blocks of all life–from an elephant, to an onion, and everything in between.
Enter the Microcosmos to delve into genomic stories that bring science to life, meet tree-of-life members and explore their genomes through vivid visuals. Explore the intricate relationship between genes and human diseases like COVID-19 and Lyme disease. Use our genomics portal as a jumping point to other topics in this domain of nooks, crannies, and unexpected connections.
“The cosmos is within us. We are made of star-stuff. We are a way for the universe to know itself” ~ Carl Sagan, an inspiration for the Microcosmos.
Read more or download (free) here: https://apps.apple.com/ca/app/the-microcosmos/id1555443746
Microbes, Hawaiian Lava Tubes, and Life on Mars
We discovered a new genus of species living in Hawiian lava tubes—an important finding when looking for life in similar lava tubes on Mars.
Volcanic Developments, Pink Rocks & New Species
Lava tubes, natural channels formed by flowing volcanic lava, are of special interest in the search for life on other planets. They occur on other planets besides Earth, and their basaltic walls provide protection from radiation and harsh conditions that otherwise make surviving and thriving anywhere other than Earth a challenge - even for microbes.
We worked alongside collaborators at Georgetown University and the National Aeronautics and Space Administration to study microbes living in lava tubes beneath Mauna Loa, Earth’s largest active volcano.
We found a surprisingly high degree of niche partitioning over small spatial scales - meaning that competing species in lava tubes tend to partition resources or space in their niche to exist cooperatively. Based on recent bioinformatic advances in metagenomics, we assembled dozens of high-quality genomes (including those from several novel species!).
Our work was the first to combine 16S SSU rRNA sequencing and whole genome shotgun sequencing to map the microbial diversity and functional potential within a Hawaiian lava tube. Samples taken just centimeters apart revealed significant differences in community make-up, with implications for how to assay a region of interest on Mars.
In addition, the unique metabolism of a new genus discovered here provides a glimpse into the microbial communities in volcanic habitats and how they may evolve with limited nutrient availability in these extraordinary, martian-esque settings. Siliceabacter maunaloa was identified presumably for the first time in pink, gypsum-rich mineral deposits within lava tubes with direct sun exposure. Metabolic inference analysis suggests the microbe itself may contribute to the pinkish colour of the mineral deposit!
Read more here: https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2022JE007283
A Tool for Better Breast Cancer Screening
As an Illumina certified and preferred bioinformatics provider, we created a diagnostic tool for a Canadian hospital to run a cancer detection pipeline.
Creating a Diagnostic Tool for Breast Cancer Biomarkers
Medical researchers are getting closer to understanding the complex biomarkers that can help catch cancer early and save lives. As an Illumina certified and preferred bioinformatics provider, we used Illumina’s Connected Analytics platform to create a secure and HIPPA-compliant web-based tool for a Canadian hospital to run their cancer detection pipeline.
Advancing Health Research with the Microbiome
This nature-published genomics tool enables breakthroughs in disease prevention and intervention for several significant human diseases.
The Challenge
Despite decades of research into the human microbiome, we haven’t been able to harness the microorganisms living in human bodies for widespread disease prevention and therapeutic interventions. While a promising field of research, a major barrier to breakthroughs in this area are data analysis and interpretation issues faced by medical researchers.
The most densely populated area of the human microbiome is the lowest region of the gut, home to microorganisms that play critical roles in nutrition, detoxification, and immune system conditioning. Large scale datasets about the metabolic activity of these organisms are available, but differences in how that data was originally processed make comparative analyses difficult.
Being able to understand and use these data will help advance research on significant human diseases such as inflammatory bowel disease, Crohn's disease, type 2 diabetes, and others.
Koonkie’s Approach
To help overcome this data compatibility barrier and enable new discoveries, we created GutCyc, a software pipeline and a collection of pathway genome databases. GutCyc transforms this data into a format that both domain experts and machines can understand. GutCyc provides the consistent annotations and metabolic pathway predictions needed to analyze differences in microbial communities between health and disease states.
Visit the GutCyc website here: http://www.gutcyc.org/
Read our paper in Scientific Data: https://www.nature.com/articles/sdata201735
Surveying Oceanic Microbial Communities
Microbial communities in oceanic Oxygen Minimum Zones (OMZs) that are integral to marine ecosystem health are currently facing disruption.
OMZs, a Growing Concern
Microorganisms in oceanic oxygen minimum zones (OMZs) are vital for nutrient cycling and ecosystem health. In a study presented at the 2018 Ocean Sciences Meeting, we harnessed the microbial data with bioinformatics to reveal intricate relationships within these vulnerable microbial communities that are facing disruption due to the OMZ expansion that is a direct consequence of warming global temperatures.
We used a pathway-centric approach to analyze microbial community metabolism in the expanding northeast subarctic Pacific Ocean OMZs. Using a powerful bioinformatics pipeline, we analyzed data collected at various stations along the Line P transect, stretching from Saanich Inlet on Vancouver Island to open ocean station “Papa”.
Our analysis uncovered a rich story of delicately balanced microbial communities sharing resources with their neighbours - from sunlit to dark, oxygenated to oxygen-starved, energy rich to energy poor OMZ neighbourhoods, all on the edge of climate change-driven disruption. The metabolic activities of the communities we studied have a profound influence on ecological and climatic balance, and ongoing deoxygenation of these waters due to rising temperatures and changes in ocean circulation could push these ecosystems past a critical point.
Read more here: https://agu.confex.com/agu/os18/meetingapp.cgi/Paper/323897
The Mining Microbiome Analytics Platform (M-MAP)
Supported by Canada’s Digital Technology Supercluster, this platform is accelerating microbial solutions to some of mining’s biggest challenges.
Industry-Sized Questions, Microscopic Answers
The global adoption of greener technologies like electric vehicles and wind turbines requires the extraction of raw minerals at rates that exceed what traditional mining practices can deliver. Backed by Canada’s Technology Supercluster, this consortium-led project is revolutionizing the mining industry by looking for solutions to mining’s biggest challenges in their tiniest miners – the resident microbial community.
We worked with our consortium partners (including mining giants Teck Resources and Rio Tinto) to develop the Mining Microbiome Analytics Platform (M-MAP), an online platform that is accelerating the development of eagerly-awaited microbial solutions for mining. With this platform, our team is extracting key information about microbial communities from mining-related environments to understand “who” is there and “what” they are doing. These insights empower mining companies to embrace next-generation biomining technologies, and to deploy custom data-backed solutions.
Microbiome analytics is catalyzing the development of state-of-the-art environmental practices across the mining lifecycle: a “green” approach to resource extraction and mine site remediation that aims to significantly reduce, and ultimately eliminate, the use of toxic chemicals, develop more efficient mining practices, and reduce adverse environmental impacts. M-MAP represents the largest investment in planned natural resource genomic bioinformatics in the history of the sector.
Learn more here: https://www.m-map.ca/