A5037814785- Gut microbiota and health
- Diet and metabolism studies
- Semiconductor Quantum Structures and Devices
- Advanced Semiconductor Detectors and Materials
- Cannabis and Cannabinoid Research
- Research on Leishmaniasis Studies
- Clostridium difficile and Clostridium perfringens research
- Genomics and Phylogenetic Studies
- Respiratory viral infections research
- Probiotics and Fermented Foods
- Microbial Community Ecology and Physiology
- Dietary Effects on Health
- Trypanosoma species research and implications
- Chalcogenide Semiconductor Thin Films
- ZnO doping and properties
- Antibiotic Resistance in Bacteria
- Enterobacteriaceae and Cronobacter Research
- Gene expression and cancer classification
- solar cell performance optimization
- Diet, Metabolism, and Disease
- Viral gastroenteritis research and epidemiology
- Pneumonia and Respiratory Infections
- Bacterial Infections and Vaccines
- Metabolomics and Mass Spectrometry Studies
- Bacteriophages and microbial interactions
Université Laval
2016-2025
Quebec - Clinical Research Organization in Cancer
2024
Nestlé (Switzerland)
2021
Centre hospitalier de l'Université Laval
2009-2018
Centre hospitalier universitaire de Québec
2005-2017
Wilfrid Laurier University
2008-2012
Universität Greifswald
2011
Universitätsmedizin Greifswald
2011
McGill University
2011
Institut National de Santé Publique du Québec
2010
Abstracta Voluminous parallel sequencing datasets, especially metagenomic experiments, require distributed computing for de novo assembly and taxonomic profiling. Ray Meta is a massively metagenome assembler that coupled with Communities, which profiles microbiomes based on uniquely-colored k-mers. It can accurately assemble profile three billion read experiment representing 1,000 bacterial genomes of uneven proportions in 15 hours 1,024 processor cores, using only 1.5 GB per core. The...
Microbiome studies have demonstrated the high inter-individual diversity of gut microbiota. However, how initial composition microbiome affects impact antibiotics on microbial communities is relatively unexplored. To specifically address this question, we administered a second-generation cephalosporin, cefprozil, to healthy volunteers. Stool samples gathered before antibiotic exposure, at end treatment and 3 months later were analysed using shotgun metagenomic sequencing. On average, 15...
Abstract Background Bioactive lipids produced by human cells or the gut microbiota might play an important role in health and disease. Dietary intakes are key determinants of microbiota, its production short-chain (SCFAs) branched-chain fatty acids (BCFAs), host endocannabinoidome signalling, which all involved metabolic diseases. This hypothesis-driven longitudinal fixed sequence nutritional study, realized healthy participants, was designed to determine if a lead-in diet affects response...
Human metapneumovirus (hMPV) and respiratory syncytial virus (RSV) are leading pediatric pathogens. However, risk factors for severe hMPV disease remain unknown. We comparatively assessed environmental, host, viral determinants RSV infections.We studied a prospective cohort of >1000 children aged <3 years hospitalized in or presenting to clinic acute infection. collected clinical data at enrollment 1-month follow-up tested nasopharyngeal secretions viruses. Disease severity was defined as...
Antimonials remain the first line drug against protozoan parasite Leishmania but their efficacy is threatened by resistance. We carried out a RNA expression profiling analysis comparing an antimony-sensitive and -resistant (Sb2000.1) strain of infantum using whole-genome 70-mer oligonucleotide microarrays. Several genes were differentially expressed between two strains, several which found to be physically linked in genome. MRPA, ATP-binding cassette (ABC) gene known involved antimony...
Abstract Background Drug resistance can be complex, and several mutations responsible for it co-exist in a resistant cell. Transcriptional profiling is ideally suited studying complex genotypes has the potential to lead novel discoveries. We generated full genome 70-mer oligonucleotide microarrays all protein coding genes of human protozoan parasites Leishmania major infantum . These arrays were used monitor gene expression methotrexate parasites. Results eukaryotic organism with minimal...
The Leishmania tarentolae Parrot-TarII strain genome sequence was resolved to an average 16-fold mean coverage by next-generation DNA sequencing technologies. This is the first non-pathogenic humans kinetoplastid protozoan be described thus providing opportunity for comparison with completed genomes of pathogenic species. A high synteny observed between all sequenced limited number chromosomal regions diverged L. and infantum, while remaining syntenic major. Globally, >90% gene content...
Abstract Background Leishmania parasites cause a diverse spectrum of diseases in humans ranging from spontaneously healing skin lesions (e.g., L. major ) to life-threatening visceral infantum ). The high conservation gene content and genome organization between contrasts their distinct pathophysiologies, suggesting that highly regulated hierarchical temporal changes expression may be involved. Results We used multispecies DNA oligonucleotide microarray compare whole-genome patterns...
Gene amplification of specific loci has been described in all kingdoms life. In the protozoan parasite Leishmania, product is usually part extrachromosomal circular or linear amplicons that are formed at level direct inverted repeated sequences. A bioinformatics screen revealed sequences widely distributed Leishmania genome and repeats chromosome-specific, conserved among species, generally present low copy number. Using sensitive PCR assays, we provide evidence continuously being rearranged...
The gut microbiota is a unique ecosystem of microorganisms interacting with the host through several biochemical mechanisms. endocannabinoidome (eCBome), complex signaling system including endocannabinoid system, approximately 50 receptors and metabolic enzymes, more than 20 lipid mediators important physiopathologic functions, modulates gastrointestinal tract function may mediate cell-microbe communications there. Germ-free (GF) mice, which lack an intestinal microbiome so differ...
Understanding the relationship between genome of a cell and its phenotype is central problem in precision medicine. Nonetheless, genotype-to-phenotype prediction comes with great challenges for machine learning algorithms that limit their use this setting. The high dimensionality data tends to hinder generalization scalability most algorithms. Additionally, produce models are complex difficult interpret. We alleviate these limitations by proposing strong performance guarantees, based on...
Blueberry consumption can prevent obesity-linked metabolic diseases, and it has been proposed that the polyphenol content of blueberries may contribute to these effects. Polyphenols have shown favorably impact health, but role specific classes whether gut microbiota is linked effects remain unclear. We aimed evaluate whole blueberry powder polyphenols on development obesity insulin resistance determine potential microbes in by using fecal transplantation (FMT). Sixty-eight C57BL/6 male mice...
The gut microbiota modulates response to hormonal treatments in prostate cancer (PCa) patients, but whether it influences PCa progression remains unknown. Here, we show a reduction fecal alpha-diversity correlating with increase tumour burden two distinct groups of hormonotherapy naïve patients and three murine models. Fecal transplantation (FMT) from high volume is sufficient stimulate the growth mouse revealing existence microbiome-cancer crosstalk. Analysis microbial-related pathways mice...
Respiratory virus infections are a major health concern and represent the primary cause of testing consultation hospitalization for young children. We developed compared two assays that allow detection up to 23 different respiratory viruses frequently infect The first method consisted single TaqMan quantitative real-time PCR in 96-well-plate format. second multiplex followed by primer extension microarray hybridization an integrated molecular diagnostic device, Infiniti analyzer. Both our...
Background Drug resistance is a major problem in leishmaniasis chemotherapy. RNA expression profiling using DNA microarrays suitable approach to study simultaneous events leading drug-resistance phenotype. Genomic analysis has been performed primarily with Old World Leishmania species and here we investigate molecular alterations antimony the New L. amazonensis. Methods/Principal Findings We selected populations of amazonensis promastigotes for by step-wise drug pressure. Gene highly...
Summary Antimonials are still the mainstay of treatment against leishmaniasis but drug resistance is increasing. We carried out short read next‐generation sequencing ( NGS ) and comparative genomic hybridization CGH three independent L eishmania major antimony‐resistant mutants. Copy number variations were consistently detected with both . A attribute antimony was a novel terminal deletion variable length (67 kb to 204 kb) polyploid chromosome 31 in Terminal deletions two mutants occurred at...
Abstract The endocannabinoidome encompasses several fatty acid (FA)-derived mediators, including the endocannabinoid anandamide (AEA) and 2-arachidonoyl-glycerol (2-AG), which served as targets for anti-obesity drug development, their congener N -acyl-ethanolamines (NAEs) 2-monoacyl-glycerols (2‑MAGs), are involved in food intake energy metabolism. Body weight fat distribution have been suggested determinants of peripheral levels. We aimed at investigating factors, beyond body composition,...
The intestinal microbiota and the expanded endocannabinoid system, or endocannabinoidome, have both been implicated in diet-induced obesity dysmetabolism. This study aims at identifying potential interactions between these two fundamental systems—which form gut microbiota-endocannabinoidome axis—and their involvement establishment of related metabolic complications. We report here time- segment-specific microbiome disturbances as well modifications circulating endocannabinoidome mediators...
Current hybridization protocols on microarrays are slow and need skilled personnel. Microfluidics is an emerging science that enables the processing of minute volumes liquids to perform chemical, biochemical, or enzymatic analyzes. The merging microfluidics microarray technologies constitutes elegant solution will automate speed up hybridization.We developed a microfluidic flow cell consisting network chambers channels molded into polydimethylsiloxane substrate. substrate was aligned...
ABSTRACT The impact of Clostridium difficile fecal loads on diagnostic test results is poorly understood, but it may have clinical importance. In this study, we investigated the relationship between C. load and four assays: a glutamate dehydrogenase (GDH) enzyme immunoassay (EIA), toxin A/B antigen EIA (ToxAB), cell culture cytotoxicity assay (CCA), PCR targeting tcdB gene. We also compared cycle threshold ( C T ) with quantitative using Spearman's rank correlation coefficient. Finally,...
Whole genome sequencing (WGS) studies can enhance our understanding of the role patients with asymptomatic Clostridium difficile colonization in transmission. Isolates obtained from infection (CDI) and identified a study conducted during 2006–2007 at 6 Canadian hospitals underwent typing by pulsed-field gel electrophoresis, multilocus sequence typing, WGS. incident CDI cases not initial were also sequenced where possible. Ward movement data combined to identify plausible donors for each...
During the summer of 2012, a major Legionella pneumophila serogroup 1 outbreak occurred in Quebec City, Canada, which caused 182 declared cases Legionnaire's disease and included 13 fatalities. isolates from 23 patients as well 32 cooling towers located vicinity were recovered for analysis. In addition, 6 1996 City 4 unrelated to both outbreaks added allow comparison. We characterized using pulsed-field gel electrophoresis, sequence-based typing, whole genome sequencing. The comparison...
Antibiotics profoundly affect the gut microbiome and modulate microbial communities. We recently observed that antimicrobial drugs also impact abundance distribution of antibiotic resistance genes. In this addendum, we reanalyze our ∼1 trillion nucleotide shotgun metagenomic dataset to quantify comprehensive genomic differences at sequence level before after treatment. show 7 day exposure cefprozil leads a statistically significant loss metagenome sequences. Recovery microbiomes 3 months...
Dietary omega-3 polyunsaturated fatty acids (