A5049436371- Microbial Community Ecology and Physiology
- Genomics and Phylogenetic Studies
- Microbial bioremediation and biosurfactants
- Gut microbiota and health
- Landfill Environmental Impact Studies
- Microbial Fuel Cells and Bioremediation
- Methane Hydrates and Related Phenomena
- Wastewater Treatment and Nitrogen Removal
- SARS-CoV-2 detection and testing
- Biofuel production and bioconversion
- Reproductive tract infections research
- Infection Control and Ventilation
- Anaerobic Digestion and Biogas Production
- Bioinformatics and Genomic Networks
- Mine drainage and remediation techniques
- Enzyme Production and Characterization
- Metal Extraction and Bioleaching
- biodegradable polymer synthesis and properties
- Bacteriophages and microbial interactions
- Microplastics and Plastic Pollution
- Antimicrobial Peptides and Activities
- Studies on Chitinases and Chitosanases
- COVID-19 diagnosis using AI
- Mining and Resource Management
- Arsenic contamination and mitigation
University of Waterloo
2016-2024
University of Toronto
2012-2013
Polyhydroxyalkanoates (PHAs) are a family of microbially made polyesters commercialized as biodegradable plastics. PHA production rates predicted to increase concerns around environmental plastic contamination and limited fossil fuel resources have increased the importance bio-based alternatives. Microbially produced depolymerases key enzymes mediating biodegradation, but only few been well-characterized screens employing metagenomic sequence data lacking. Here, we used 3078 metagenomes...
Reductive dehalogenases are the critical enzymes for anaerobic organohalide respiration, a microbial metabolic process that has been harnessed bioremediation efforts to resolve chlorinated solvent contamination in groundwater and is implicated global halogen cycle. dehalogenase sequence diversity informative dechlorination potential of site or enrichment culture. A suite degenerate PCR primers targeting comprehensive curated set reductive genes was designed applied twelve DNA samples...
Phylum Cloacimonadota (previously Cloacimonetes, WWE1) is an understudied bacterial lineage frequently associated with engineered and wastewater systems. members were abundant diverse in metagenomic datasets from a municipal landfill, prompting examination of phylogenetic relationships, metabolic diversity, pangenomic dynamics across the phylum, based on 30 publicly available genomes 24 new metagenome-assembled (MAGs) landfill samples. We found that have distinct evolutionary histories...
Landfills generate outsized environmental footprints due to microbial degradation of organic matter in municipal solid waste, which produces the potent greenhouse gas methane. With global waste production predicted increase substantially next few decades, there is a pressing need better understand temporal dynamics biogeochemical processes that control methane cycling landfills. Here, we use metagenomic approaches characterize was landfilled over 39 years. Our analyses indicate newer...
Abstract Across the tree of life, gene lengths vary, but most are no more than a few thousand base pairs in length. The largest protein often reported is ∼40,000 aa eukaryotic Titin. Even larger proteins may occur rapidly expanding set metagenome-derived sequences, their existence be obscured by assembly fragmentation. Here, we leverage genome curation to complete sequences that encode predicted up 85,804 aa. Overall, findings illuminate huge knowledge gap related giant proteins. Although...
Predicting the total number of microbial cells on Earth and exploring full diversity life are fundamental research concepts that have undergone paradigm shifts in genomic era. In this issue, Lloyd colleagues (K.
1,4-Dioxane (dioxane) is an emerging contaminant of concern for which bioremediation seen as a promising solution. To date, eight distinct gene families have been implicated in dioxane degradation, though only monooxygenase (DXMO) from Pseudonocardia dioxanivorans routinely used biomarker environmental surveys. In order to assess the functional and taxonomic diversity bacteria capable we collated existing, poorly-organized information on known biodegraders create curated suite biomarkers...
Microbial communities in landfills transform waste and generate methane an environment unique from other built natural environments. Landfill microbial diversity has predominantly been observed at the phylum level, without examining extent of shared organismal across space or time. We used 16S rRNA gene amplicon shotgun metagenomic sequencing to examine taxonomic functional inhabiting a Southern Ontario landfill. The capacity for volatile organic compound degradation leachate groundwater...
The Riverton City dump is Jamaica's largest solid waste disposal site, but it lacks engineered protection for leachate containment and treatment. Shotgun metagenomics was used to survey the microbial communities in surface waters of Duhaney River, an urban waterway abutting dump. community within pond taxonomically distinct from that found River. Higher diversity observed leachate, with members Bacteroidetes, Firmicutes, Gammaproteobacteria, Deltaproteobacteria, Tenericutes being most...
ABSTRACT Background Environmental surveillance of SARS-CoV-2 via wastewater has become an invaluable tool for population-level surveillance. Built environment sampling may provide complementary spatially-refined detection viral in congregate settings such as universities. Methods We conducted a prospective environmental study at the University Ottawa between September 2021 and April 2022. Floor surface samples were collected twice weekly from six university buildings. Samples analyzed...
Viruses are the most abundant microbial entity on planet, impacting community structure and ecosystem services. Despite outnumbering Bacteria Archaea by an order of magnitude, viruses have been comparatively underrepresented in reference databases. Metagenomic examinations illustrated that specifically understudied engineered environments. Here we employed metagenomic computational biology methods to examine diversity, host interactions, genetic systems predicted from 27 samples taken three...
Abstract Bacterial genomics has revolutionized our understanding of the microbial tree life; however, mapping and visualizing distribution functional traits across bacteria remains a challenge. Here, we introduce AnnoTree - an interactive, functionally annotated bacterial life that integrates taxonomic, phylogenetic, annotation data from nearly 24,000 genomes. enables visualization millions precomputed genome annotations phylogeny, thereby allowing users to explore gene distributions as well...
Abstract Global waste production is increasing rapidly, with the majority of destined for landfills. Microbial communities in landfills transform and generate methane an environment unique from other built natural environments. Previous work has largely considered landfill microbial diversity only at phylum level, identifying complex variable communities. The extent shared organismal across or over time more precise levels classification remains unknown. We used 16S rRNA gene amplicon...
ABSTRACT Landfills are engineered, heterogeneously contaminated sites containing large reservoirs of paper waste. Cellulose degradation is an important process within landfill microbial ecology, and these anoxic, saturated environments prime locations for discovery cellulases that may offer improvements on industrial cellulose efforts. We sampled leachate from three a municipal landfill, collection cistern, groundwater adjacent aquifer to identify cellulolytic populations their associated...
Abstract While a number of amphibian microbiomes have been characterized, it is unclear how microbial communities might vary in response to seasonal changes the environment and behaviors which many amphibians exhibit. Given recent studies demonstrating importance skin microbiome frog innate immune defenses against pathogens, investigating impact species present, thus their potential contribution host defense, will provide better understanding conditions that may alter susceptibility...
Summary Polyhydroxyalkanoates (PHAs) are a family of microbially-made polyesters commercialized as biodegradable plastics. PHA production rates predicted to increase concerns around environmental plastic contamination and limited fossil fuel resources have increased the importance bio-based alternatives. Microbially-produced depolymerases key enzymes mediating biodegradation, but only few been well-characterized screens employing metagenomic sequence data lacking. Here, we used 3,078...
ABSTRACT The oxidation of sulfide-bearing mine tailings catalysed by acidophilic iron and sulfur-oxidizing bacteria releases toxic metals other contaminants into soil groundwater as acid drainage. Understanding the environmental variables that control community structure metabolic activity endogenous microbes living in (especially abiotic stressors low pH high dissolved metal content) is crucial to developing sustainable bioremediation strategies. We determined microbial composition along...
ABSTRACT The oxidation of sulfide-bearing mine tailings catalyzed by acidophilic iron and sulfur-oxidizing bacteria releases toxic metals other contaminants into soil groundwater as acid drainage. Understanding the environmental variables that control community structure metabolic activity microbes indigenous to (especially abiotic stressors low pH high dissolved metal content) is crucial developing sustainable bioremediation strategies. We determined microbial composition along two...
Science benefits from rapid, open data sharing but samples for sequencing are expensive creators to acquire and process. Current guidelines reuse were established two decades ago, when databases several million times smaller, necessitating an update. This article presents a roadmap establish best practices sequence reuse, developed in consultation with consortium of 167 microbiome scientists. It introduces Data Reuse Information tag (DRI) public data, which will be associated at least one...
Abstract Background: Recent work demonstrated that detection of SARS-CoV-2 on the floor long-term care facilities is associated with impending COVID-19 outbreaks. It unknown if similar results will be observed in hospitals. Methods: Floor swabs were prospectively collected weekly from healthcare worker-only areas (eg, staff locker rooms) at two hospitals Ontario, Canada for 39 weeks. processed using quantitative reverse-transcriptase polymerase chain reaction. Results reported as percentage...
Thermal recovery technologies for in-situ bitumen extraction can result in the heating of surrounding aquifers, potentially mobilizing arsenic naturally present sediments to groundwater. The relative toxicity dissolved is related its speciation, with As(V) being less toxic than As(III). Microorganisms have various mechanisms resistance, including efflux and methylation. may also perform reduction/oxidation As(V)/As(III) as part their detoxification and/or metabolic pathways. We characterized...
Abstract Currently described members of Elusimicrobia , a relatively recently defined phylum, are animal-associated and rely on fermentation. However, free-living have been detected in sediments, soils groundwater, raising questions regarding their metabolic capacities evolutionary relationship to species. Here, we analyzed 94 draft-quality, non-redundant genomes, including 30 newly reconstructed from diverse natural environments. Genomes group into 12 clades, 10 which previously lacked...