Bioinformatics for the seed microbiome, GRDI

Example of how a beneficial bacterium can protect seeds from fungal spoilage. Composite figure is based on our work at  doi:10.1111/nph.12693

Example of how a beneficial bacterium can protect seeds from fungal spoilage. Composite figure is based on our work at doi:10.1111/nph.12693

Microbes have a profound effect on the health of the host organism with which they associate. Recently AAFC and the University of Saskatchewan have developed a novel method for microbial profiling using metagenomic assembly (doi:10.1186/2049-2618-1-23). AAFC has also shown recently that there is a shared microbiota within the epiphytic seed microbiome of Brassica spp. and Triticum spp. (doi:10.1111/nph.12693). We have also shown that these patterns can lead to the identification of microbial interactions within the seed microbiome that have a direct connection to seed health; e.g. patterns revealed that there is a specific group of bacteria (Pantoea spp.) that have an antagonistic effect on the growth of some fungal pathogens. 

Beneficial Biotic Interactions, Wheat Alliance

Ralph Stevenson @ harvest.

Ralph Stevenson @ harvest.

Applying a powerful metagenomics platform to identify wheat‑microbe interactions that will reduce nitrogen requirements and define the microbiological characteristics of healthy productive soils for wheat varieties.

Next generation bioinformatics platforms, AAFC

Next-gen Canadian Lynx kitten.

Next-gen Canadian Lynx kitten.

Modern sequencing technologies have driven a data explosion in the genomics space, with data generation advances outpacing computational advances since ca. 2007. As a consequence, the information systems supporting data management and analysis have become increasingly complex, and they have moved from the lab domain (e.g. standalone desktops) to the Information Technology (IT) domain (e.g. server clusters backed by large capacity storage clusters). This requires that research-computing strategies be adapted to reflect IT trends and IT policy changes. However, current cluster-based solutions are often tightly coupled to the physical infrastructure, making transformative IT changes potentially disruptive to research end-users. One current trend is a shift towards an Infrastructure as a Service (IaaS) model based on virtualized (“cloud”) rather than physical infrastructure. 

Vogue (Vaginal micrObiome GroUp initiativE): Advancing Women’s Health through Microbiome Research. CIHR

Women’s health and healthy pregnancies are intimately linked to the balance of bacteria and viruses that live in a woman’s body. The fine balance of microorganisms in a woman’s reproductive system is vitally important to the maintenance of health and the prevention of disease. For example, a healthy balance of bacteria can protect against infections such as Herpes and HIV, whereas an unhealthy balance can increase risk of infection in the uterus and fallopian tubes, and may ultimately result in cancer. We know that if the balance of bacteria in the vagina is not ideal in pregnancy, there are serious health consequences – one of which is risk of preterm birth. Preterm birth is one of the most serious complications facing infants, occurring in 7-8% of births in Canada but causing over 70% of newborn deaths and 50% of newborn health problems. This has been one of the hardest health problems to tackle worldwide with rates of preterm births increasing despite improvements in overall pregnancy care for women and their newborns. New advances in genomic research make it possible to study the composition of microbial communities in a women’s reproductive system.