Research
Projects
Genomic
diversity in natural microbial communities
Campylobacter ecology in people, pets and livestock
Microbial ecology in reproductive health and disease
Interactions of diet and intestinal microbial ecology in rainbow trout
Ecology of Brachyspira-related colitis in pigs
The cpnDB
project
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.
Genomic diversity in natural microbial communities
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.
Diagnostic
tools for understanding Campylobacter
ecology in people,
pets and livestock
Campylobacter
infections are
the major cause of gastrointestinal disease in Canada, constituting a
major burden to the healthcare system. Most research on Campylobacter
disease is focused on
foodborne and waterborne Campylobacter
jejuni and C.
coli
originating from livestock. However, there is mounting
evidence
that other species of Campylobacter
are clinically significant emerging pathogens. 
The
largest obstacle
to
understanding Campylobacter
ecology and the contribution of the 'unusual' campylobacters has been
the lack of specific diagnostic methods for the detection,
identification and quantification of individual Campylobacter
species. Inadequate
methods have also impeded the identification of sources of Campylobacter
infections and limited diagnostic capabilities for detection of important veterinary pathogens like C. fetus subsp. venerialis, the causative agent of bovine genital campylobacteriosis.
We developed species and subspecies-specific diagnostic methods
for
Campylobacter
identification
and are applying these methods in increasing the diagnostic capabilities of
animal and human health laboratories and in understanding the
contribution of both the commonly recognized and 'unusual'
campylobacteria to disease in humans, pets and livestock.Microbial
ecology in reproductive health and disease
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. The Hill Lab is a member
of the Vaginal Microbiome Project: a multidisciplinary team of
researchers with links across Canada, led by Dr.
Deborah Money (UBC). The team is supported by the Women's Health Research Institute, CIHR and the March of Dimes
Sustainable,
plant-based diets
for
salmonid aquaculture
Collaborators:
Dr. Murray Drew and Dr. Andrew Van Kessel
Department
of Animal and Poultry Science
University of Saskatchewan
To meet growing demands for fish products and encourage
healthier
diet choices by Canadians, the aquaculture industry has been growing at
an annual rate of 8-10%. Growth has brought challenges to the industry,
including the need to decrease reliance on declining global supplies of
fish meal as the major protein source for carnivorous fish such as
salmon and trout.
Plant ingredients have
potential as feed ingredients for carnivorous
fish and developing this opportunity has the added benefit of creating
another market for Canadian producers of crops such as soybean, canola
and peas. Unfortunately, plant ingredients cause intestinal
inflammation
in salmonid fish, which has a negative impact on fish growth and
health.
The negative effects of plant ingredients on salmonid fish may
be
due to direct interactions of ingredients with the intestine or they
may be indirect effects, resulting from feed ingredients causing
changes in the complex intestinal microbial community that in turn
affect intestinal physiology. By studying the effects of various
individual plant ingredients and mixtures on fish growth, intestinal
health and the intestinal microbial community, components of the
ingredients responsible for the negative effects can be identified and
insight gained into the mechanisms responsible. Results of this work
will determine the type and degree of processing of plant ingredients
required to reduce their negative impact on fish growth and health. An
understanding of the mechanisms at work in the interaction between diet
composition and intestinal health will lead to the formulation of
improved, sustainable diets for the aquaculture industry and in the
future selection and formulation of diets including new plant
ingredients.
This project was supported by an NSERC
Stragetic Project Grant.
Ecology of Brachyspira-related colitis in pigs.
Coinvestigators:
Department of Large Animal Clinical Sciences
Dr. Manuel Chirino
Department of Veterinary Microbiology
Department of Veterinary Pathology
This ongoing work is supported by the WCVM Disease Investigation Unit sponsored by Saskatchewan Agriculture and Food, and by the Canadian Swine Health Board.
Updated 2011-09-12