Microbial ecology and molecular diagnostics
Released to the public in August, 2004, cpnDB is a curated database of chaperonin sequences. Chaperonins are a diverse family of molecular chaperones that are present in the plastids, mitochondria, and cytoplasm of eukaryotes, bacteria and archaea. The family is divided into group I (CPN60, also known as Hsp60 or GroEL, found in bacteria, some archaea, mitochondria and plastids) and group II (CCT or TriC, found in archaea and the eukaryotic cytoplasm).
Chaperonin sequences are useful for phylogenetic studies and have been widely exploited in studies of prokaryotic and eukaryotic evolution. Group I chaperonin sequences have also been employed as targets for detection and identification of organisms since a 549-567 bp segment of the cpn60 coding region, the 'universal target', can be amplified with universal PCR primers. Compared to the more widely used 16S rRNA gene target, cpn60 sequences generally offer more disriminating information, especially for closely related organisms.
cpnDB continues to grow with the support of a consortium of researchers and clinicians using cpn60 sequence-based methods in their work. You can read more about the 'cpn60 advantage' on the cpnDB website.
Bacteria in nature rarely live in pure culture; rather, they form complex communities that have profound effects on our world. For example, the numbers and types of nitrogen-fixing bacteria in soil can affect the quality of a crop, and the disruption of bacterial populations in the human intestine with antibiotics can lead to life-threatening infections. Since most bacteria cannot be cultivated in the lab, our knowledge of natural microbial communities is largely based on analysis of sequences of universally conserved genes found in all bacteria. At the same time, studies of culturable bacteria have revealed significant gene content differences between strains of bacteria that would be considered members of the same species if only universal gene sequence data were considered.
There are clues in the results of sequence-based studies of microbial communities that the significance of genomic diversity in natural communities has been underestimated. Perturbation of microbial communities may select for strain-specific genes and result in population shifts at the 'sub-species' level that would be undetected by universal gene sequence-based approaches. An inventory of genomic diversity in a microbial community is an essential first step to understanding population dynamics at the strain level.
We are using conventional microbiology and molecular methods to characterize sub-species genomic diversity and population dynamics in the Enterococcus community of the pig intestine. The pig intestinal microbial community is significant from the perspective of livestock management, animal and human health and welfare and offers a powerful model for studying microbial community dynamics. Our goal is to observe, predict and modify the effects of environmental variables and perturbation on intestinal microbial diversity.
This project is supported by an NSERC Discovery Grant.
Under normal circumstances, the vagina is home to many different microorganisms. A shift in the balance of vaginal microbiota can result in infections such as bacterial vaginosis (BV), the most common cause of vaginal infection. BV and other infections are associated with early pregnancy loss, preterm labour, and an increased risk for HIV. Our primitive understanding of the complex microbial ecosystem of the genital tract greatly hampers our ability to identify and describe normal vaginal microbiota. This hinders the development and evaluation of appropriate, focused therapies for genital infections. The use of high throughput molecular methods promises to be very effective for characterizing vaginal microbiota.
This project is supported by the Saskatchewan Health Research Foundation.
Diarrhea in grow‐finish pigs is a highly prevalent and significant condition on commercial farms. It reduces performance and economic competitiveness, affecting daily gain, feed conversion, morbidity, mortality, variation, and medication costs. Brachyspira hyodysenteriae is the most common cause of haemorrhagic colitis in pigs and causes a disease known as swine dysentery. However, other related species of Brachyspira are associated with intestinal disease in pigs, including some poorly characterized, novel members of this genus including "Brachyspira hampsonii". We are using a combination of clinical investigation, epidemiology, pathology, molecular microbiology and metagenomic approaches to investigate these diseases and determine possible risk factors for their (re)emergence.