A5076348377- Microbial Community Ecology and Physiology
- Gut microbiota and health
- Genomics and Phylogenetic Studies
- Marine and coastal plant biology
- Plant Pathogens and Fungal Diseases
- Mycorrhizal Fungi and Plant Interactions
- Environmental DNA in Biodiversity Studies
- Marine Biology and Ecology Research
- Plant Virus Research Studies
- Plant-Microbe Interactions and Immunity
- Neuroendocrine regulation and behavior
- Clostridium difficile and Clostridium perfringens research
- Plant Pathogenic Bacteria Studies
- Microbial metabolism and enzyme function
- Echinoderm biology and ecology
- Gastrointestinal motility and disorders
- Coral and Marine Ecosystems Studies
- Biosensors and Analytical Detection
- Peatlands and Wetlands Ecology
- Arsenic contamination and mitigation
- Plant and Fungal Interactions Research
- Stress Responses and Cortisol
- Polar Research and Ecology
- Yeasts and Rust Fungi Studies
- Protist diversity and phylogeny
University of Waterloo
2013-2024
Wilfrid Laurier University
2011
Western University
2006
ABSTRACT Microbial communities host unparalleled taxonomic diversity. Adequate characterization of environmental and host-associated samples remains a challenge for microbiologists, despite the advent 16S rRNA gene sequencing. In order to increase depth sampling diverse bacterial communities, we developed method sequencing assembling millions paired-end reads from (spanning V3 region; ∼200 nucleotides) by using an Illumina genome analyzer. To confirm reproducibility identify suitable...
Fecal microbiota transplants from patients with irritable bowel syndrome and anxiety alter gut function behavior in germ-free mice.
We present bacterial biogeography as sampled from the human gastrointestinal tract of four healthy subjects. This study generated >32 million paired-end sequences 16S rRNA genes (V3 region) representing >95,000 unique operational taxonomic units (OTUs; 97% similarity clusters), with >99% Good's coverage for all samples. The highest OTU richness and phylogenetic diversity was found in mouth microbial communities multiple biopsy sites within colon were highly similar individuals largely...
The red algal order Bangiales has been revised as a result of detailed regional studies and the development expert local knowledge floras, followed by collaborative global analyses based on wide taxon sampling molecular analyses. Combined nuclear SSU rRNA gene plastid RUBISCO LSU ( rbc L) for 157 taxa have conducted. Fifteen genera Bangiales, seven filamentous eight foliose, are recognized. This classification includes five newly described two resurrected genera. revision constitutes major...
ABSTRACT Massively parallel sequencing of 16S rRNA genes enables the comparison terrestrial, aquatic, and host-associated microbial communities with sufficient depth for robust assessments both alpha beta diversity. Establishing standardized protocols analysis is dependent on increasing reproducibility PCR-based molecular surveys by minimizing sources methodological bias. In this study, we tested effects template concentration, pooling PCR amplicons, sample preparation/interlane associated...
Soil pH is an important determinant of microbial community composition and diversity, yet few studies have characterized the specific effects on individual bacterial taxa within communities, both abundant rare. We collected composite soil samples over 2 years from experimentally maintained gradient ranging 4.5 to 7.5 Craibstone Experimental Farm (Craibstone, Scotland). Extracted nucleic acids were by group-specific denaturing gel electrophoresis next-generation sequencing 16S rRNA genes....
Cobalamin (vitamin B12) is a complex metabolite and essential cofactor required by many branches of life, including most eukaryotic phytoplankton. Algae other cobalamin auxotrophs rely on environmental supplied from relatively small set cobalamin-producing prokaryotic taxa. Although several Bacteria have been implicated in biosynthesis associated with algal symbiosis, the involvement Archaea production poorly understood, especially respect to Thaumarchaeota. Based detection synthesis genes...
Tomato Brown Rugose Fruit Virus (ToBRFV) is a plant pathogen that infects important Solanaceae crop species and can dramatically reduce tomato yields. The ToBRFV has rapidly spread around the globe due to its ability escape detection by antiviral host genes which confer resistance other tobamoviruses in plants. development of robust reproducible methods for detecting viruses environment aids tracking reduction transmission. We detected municipal wastewater influent (WWI) samples, likely...
ABSTRACT We analyzed the communities of soil basidiomycetes in agroecosystems that differ tillage history at Kellogg Biological Station Long-Term Ecological Research site near Battle Creek, Michigan. The approach combined DNA extraction through a bead-beating method modified to increase recovery fungal DNA, PCR amplification with basidiomycete-specific primers, cloning and restriction fragment length polymorphism screening mixed products, sequencing unique clones. Much greater diversity was...
Anaerobic ammonium-oxidizing (anammox) bacteria perform an important step in the global nitrogen cycle: anaerobic oxidation of ammonium and reduction nitrite to form dinitrogen gas (N(2)). Anammox organisms appear be widely distributed natural artificial environments. However, their roles groundwater attenuation remain unclear only limited biomarker-based data confirmed presence prior this study. We used complementary molecular isotope-based methods assess anammox diversity activity...
The domestication of the laboratory mouse has influenced composition its native gut microbiome, which is now known to differ from that wild ancestor. However, limited exploration rodent microbiome beyond model species Mus musculus made it difficult interpret variation in a broader phylogenetic context. Here, we analyse 120 de novo and 469 public metagenomically-sequenced faecal caecal samples 16 hosts representing wild, captive lifestyles. Distinct bacterial communities were observed between...
Although high-throughput sequencing of small subunit rRNA genes has revolutionized our understanding microbial ecosystems, these technologies generate data at depths that benefit from automated analysis. Here we present AXIOME (Automation, eXtension, and Integration Of Microbial Ecology), a highly flexible extensible management tool for popular ecology analysis packages promotes reproducibility customization in research.AXIOME streamlines manages (SSU) marker QIIME mothur. also implements...
Abstract Detection of SARS-CoV-2 in wastewater is an important strategy for community level surveillance. Variants concern (VOCs) can be detected the samples using next generation sequencing, however it challenging to determine relative abundance different VOCs since reads cannot assembled into complete genomes. Here, we present Alcov (abundance learning variants), a tool that uses mutation frequencies sequencing data predict distribution VOC lineages sample. We used distributions from three...
Despite progress understanding microbial communities involved in terrestrial vertebrate decomposition, little is known about the decomposition of aquatic vertebrates from a functional and environmental context. Here, we analyzed temporal changes "necrobiome" rainbow darters, which are common North American fish that sensitive indicators water quality. By combining 16S rRNA gene shotgun metagenomic sequence data four time points, studied progression decomposers both taxonomic perspectives....
Abstract In corn/maize, silks emerging from cobs capture pollen, and transmit resident sperm nuclei to eggs. There are > 20 million per U.S. maize acre. Fungal pathogens invade developing grain using silk channels, including Fusarium graminearum ( Fg , temperate environments) devastating carcinogen-producers (Africa/tropics). contaminates cereal grains with mycotoxins, in particular Deoxynivalenol (DON), known for adverse health effects on humans livestock. Fitness selection should...
Environmental conditions influence species composition, including the microbial communities that associate with benthic organisms such as corals. In this study we identified and compared bacteria three common deep-water corals, Lophelia pertusa, Madrepora oculata Paragorgia arborea, from a reef habitat on mid-Norwegian shelf. The 16S rRNA gene amplicon sequencing data obtained revealed >50% of sequences were represented by only five operational taxonomic units. Three host-specific...
Brevundimonas sp. is a bacteria able to grow in metal(loid) contaminated soil from Puchuncaví Valley, central Chile. This study has isolated bacterial strain capable of growth under high doses arsenic (As) (6000 mg L−1), and draft genome sequence was generated. Additionally, real-time PCR performed examine the effect As on some genes related resistance. Results demonstrated total 3275 predicted annotated with several ars operon, resistance-related genes, metal efflux pumps, detoxifying...
Research on the role of gut microbiota in behavior has grown dramatically. The probiotic L. reuteri can alter social and stress-related behaviors - yet, underlying mechanisms remain largely unknown. Although traditional laboratory rodents provide a foundation for examining gut-brain axis, they do not naturally display wide variety behaviors. Using highly-social, monogamous prairie vole (Microtus ochrogaster), we examined effects administration behaviors, neurochemical marker expression,...
Abstract The red alga Bangia maxima, in addition to its large size (up 35 cm long × 6 mm diameter), was found this study be distinguishable from other species of by the character mature filament apices containing elongate, separated vegetative cells. phylogenetic position B. maxima resolved using both rbcL and nuclear small subunit rRNA (nSSU rRNA) gene sequences genetic variation within a population studied an inter-simple sequence repeat (ISSR) polymerase chain reaction (PCR)-based DNA...
The prairie vole ( Microtus ochrogaster ) is an important model for the study of social monogamy and dual parental care offspring. Characterization specific host species-microbe strain interactions critical understanding effects microbiota on mood behavior. five metagenome-assembled genome sequences reported here represent step in defining microbiome.