Biology subjects

Ouellette, M.

Publications and source records attributed to Ouellette, M..

7 recordsLinked to original sources

bioRxiv2026

Culturomics unveils species and expands bacterial and fungal diversity in Inuit oropharyngeal microbiota

Recent advances in high-throughput sequencing and novel culture techniques have revolutionized our understanding of the human microbiota. However, most studies primarily focused on bacterial communities, often overlooking the fungal component. Building upon our previous metagenomic analysis of the Inuit oropharyngeal microbiome 1, this study used culturomics to provide a more comprehensive view of both bacterial and fungal communities. We analyzed oropharyngeal swabs from the Qanuilirpitaa? 2017 Inuit Health Survey 2, demonstrating the complementarity of metagenomic and culturomic approaches. Our findings highlight the importance of culturomics in revealing low-abundance microorganisms, particularly fungi, which are often underrepresented in metagenomics data. Moreover, we designed an approach to isolate previously uncultivated species. We described two Pauljensenia sp., and provided insights into the phylogenetic relationship between Schaalia and Pauljensenia genera. This study underscores the necessity of a holistic approach to microbiome research, combining multiple techniques to fully elucidate microbial diversity in unique populations like the Inuit.

microbiology↗

bioRxiv2024

Identification and mitigation of blood's interference with the antimicrobial activity of AgNbO3 particles

The detrimental impact of blood on the antimicrobial activity of AgNbO3 particles was identified and investigated. It was observed that the impact is more severe in the case of lysed blood and also operates in the case of commonly used silver salt, AgNO3. The inhibition was shown to be due to hemoglobin, but unrelated to the heme moiety. In an attempt to find additives to mitigate the inhibitory effect of hemoglobin, iron ions and the chelating agent, K2EDTA, were selected as promising candidates. Including iron on the particles was shown to have a marginal effect, but supplying the medium with K2EDTA, an agent preventing clotting of blood samples, fully countered the deleterious impact of hemoglobin on AgNbO3 activity. These findings may be relevant for adapting the silver compounds to applications such as wound dressings, where silvers antimicrobial action would have to take place in a medium containing blood.

microbiology↗

bioRxiv2024

Bacterial growth dynamics on a surface having a particulate antimicrobial agent

The morphological dynamics of microbial cell proliferation on an antimicrobial surface at an early growth stage was studied with Escherichia coli on the surface of a gel supplied with nanostructured AgNbO3 antimicrobial particles. We demonstrated an inhibitory surface concentration, analogous to minimum inhibitory concentration, beyond which the growth of colonies and formation of biofilm are inhibited. In contrast, at lower concentrations, colonies circumvent the antimicrobial activity of the particles and grow with a short lag time of a few hours. The applicability of these findings, in terms of estimating inhibitory surface concentration, was tested in the case of antimicrobial polymethyl methacrylate (PMMA) bone cement.

bioengineering↗

bioRxiv2023

Streptococcus pyogenes Cas9 ribonucleoprotein delivery for efficient, rapid and marker-free gene editing in Trypanosoma and Leishmania

Kinetoplastids are unicellular eukaryotic flagellated parasites found in a wide range of hosts within the animal and plant kingdoms. They are known to be responsible in humans for African sleeping sickness (Trypanosoma brucei), Chagas disease (Trypanosoma cruzi), and various forms of leishmaniasis (Leishmania spp.), as well as several animal diseases with important economic impact (African trypanosomes, including T. congolense). Understanding the biology of these parasites necessarily implies the ability to manipulate their genomes. In this study, we demonstrate that transfection of a ribonucleoprotein complex, composed of recombinant Streptococcus pyogenes Cas9 (SpCas9) and an in vitro-synthesized guide RNA, results in rapid and efficient genetic modifications of trypanosomatids, in marker-free conditions. This approach was successfully developed to inactivate, delete and mutate candidate genes in various stages of the life cycle of T. brucei and T. congolense, and Leishmania promastigotes. The functionality of SpCas9 in these parasites now provides, to the research community working on these parasites, a rapid and efficient method of genome editing, without requiring plasmid construction and selection by antibiotics. Importantly, this approach is adaptable to any wild-type parasite, including field isolates.

microbiology↗

bioRxiv2020

Nutrient supplementation experiments on saltern microbial communities support utilization of DNA as a source of phosphorus

All environments including hypersaline ones harbor measurable concentrations of dissolved extracellular DNA (eDNA) that can be utilized by microbes as a nutrient. However, it remains poorly understood which eDNA components are used, and who in a community utilizes it. For this study, we incubated a saltern microbial community with combinations of carbon, nitrogen, phosphorus, and DNA, and tracked the community response in each microcosm treatment via 16S rRNA and rpoB gene sequencing. We show that microbial communities used DNA only as a phosphorus source, and provision of other sources of carbon and nitrogen was needed to exhibit a substantial growth. The taxonomic composition of eDNA in the water column changed with the availability of inorganic phosphorus or supplied DNA, hinting at preferential uptake of eDNA from specific organismal sources. Especially favored for growth was eDNA from the most abundant taxa, suggesting some haloarchaea prefer eDNA from closely related taxa. Additionally, microcosms composition shifted substantially depending on the provided nutrient combinations. These shifts allowed us to predict supplemented nutrients from microbial composition with high accuracy, suggesting that nutrient availability in an environment could be assessed from a taxonomic survey of its microbial community.

microbiology↗

bioRxiv2020

The Impact of Restriction-Modification Systems on Mating in Haloferax volcanii

Halobacteria have been observed to be highly recombinogenic, frequently exchanging genetic material. Several barriers to mating in the Halobacteria have been examined, such as CRISPR-Cas, glycosylation, and archaeosortases, but these are low barriers that do not drastically reduce the recombination frequency. Another potential barrier could be restriction-modification (RM) systems, which cleave DNA that is not properly methylated, thus limiting the exchange of genetic material between cells which do not have compatible RM systems. In order to examine the role of RM systems on limiting recombination in the Halobacteria, the impact of RM systems on cell-to-cell mating in Haloferax volcanii, a well-characterized method of genetic exchange and recombination in a halobacterial species, was examined. Strains which possessed all naturally-occurring RM system genes in H. volcanii (RM+) and strains without these RM systems ({Delta}RM) were mated together to compare the efficiency of gene transfer between RM-compatible strains and RM-incompatible strains. The results indicated that mating RM-incompatible strains together resulted in a decrease in gene transfer efficiency compared to mating RM-compatible strains together, suggesting that RM systems limit mating in H. volcanii, but do not act as absolute barriers to recombination. Therefore, RM systems are low barriers to recombination in the Halobacteria, with RM-incompatible strains exchanging genetic material at a lower frequency than those with compatible RM systems, similar to other low recombination barriers in the Halobacteria.

evolutionary biology↗

bioRxiv2019

The Patchy Distribution of Restriction-Modification System Genes and the Conservation of Orphan Methyltransferases in Halobacteria.

Restriction-modification (RM) systems in Bacteria are implicated in multiple biological roles ranging from defense against parasitic genetic elements, to selfish addiction cassettes, and barriers to gene transfer and lineage homogenization. In Bacteria, DNA-methylation without cognate restriction also plays important roles in DNA replication, mismatch repair, protein expression, and in in biasing DNA uptake. Little is known about archaeal RM systems and DNA methylation. To elucidate further understanding for the role of RM systems and DNA methylation in Archaea, we undertook a survey of the presence of RM system genes and related genes, including orphan DNA methylases, in the halophilic archaeal class Halobacteria. Our results reveal that some orphan DNA methyltransferase genes were highly conserved among lineages indicating an important functional constraint, whereas RM systems demonstrated patchy patterns of presence and absence. This irregular distribution is due to frequent horizontal gene transfer and gene loss, a finding suggesting that the evolution and life cycle of RM systems may be best described as that of a selfish genetic element. A putative target motif (CTAG) of one of the orphan methylases was underrepresented in all of the analyzed genomes, whereas another motif (GATC) was overrepresented in most of the haloarchaeal genomes, particularly in those that encoded the cognate orphan methylase.

genomics↗