Biology subjects

Rondeau-Leclaire, J.

Publications and source records attributed to Rondeau-Leclaire, J..

5 recordsLinked to original sources

bioRxiv2026

Taxonomic profilers and their influence on metagenomic diversity analyses

Estimating taxonomic profiles is a central task in microbiome research. Several bioinformatic tools have been developed for this purpose, differing in algorithmic strategy, reference database flexibility, sensitivity parameters, and the type of abundance they estimate. As a result, taxonomic profiles carry an unwanted methodological signal whose driving characteristics remains understudied. While benchmarks have evaluated the performance of some of these tools, they rely on simulated data; little work has been done to compare them using real metagenomes in the presence of noise and uncharacterised diversity. Overall, the impact of taxonomic profiler choice and parameterisation on scientific conclusions remains poorly understood. First, we provide a much-needed characterisation of four taxonomic profilers to help researchers better understand the available bioinformatic tools and inform their methodological choices. Then, we leverage 1,211 shotgun metagenomes from eight datasets to compare these taxonomic profilers across 13 methodological designs. Based on diversity indices, we found substantial variability in estimated taxonomic composition depending on methodological features such as reference database and algorithmic strategy. Alpha diversity analysis was substantially sensitive totool choice (particularly among k-mer-based tools) and reference database. Beta diversity showed sensitivity to both database and parameter choices, yet this variability barely affected statistical inference. Our findings highlight the sensitivity of taxonomic diversity analyses to taxonomic profiling methodology and the importance for researchers to consider assessing the robustness of their results to choice of tool, parameter, and reference database. Crucially, differences in sample diversity across methodologies are symptomatic of differences in estimated taxonomic composition, which can affect any analysis based on taxonomic abundances. Overall, this study underscores the importance of tool selection and parametrisation, and of conducting sensitivity analyses to support robust and reliable scientific conclusions. AUTHOR SUMMARYMicrobiome research relies on bioinformatic tools to determine which microbes are present in a sample and estimate their relative abundances, a process known as taxonomic profiling. Because this task requires comparing tens of millions of DNA sequences against thousands of microbial genomes, a wide range of computational strategies have been developed to make profiling accurate and efficient. As a result, many taxonomic profilers are now available, yet do not provide the same results. Although previous studies have evaluated their precision and sensitivity, less attention has been given to how the choice of profiler may influence the scientific conclusions drawn from microbiome data. Here, we selected four widely used taxonomic profilers to examine whether researchers would reach the same biological conclusions when comparing microbiomes across groups of samples, such as healthy and diseased individuals. We show that different profilers can lead to different biological conclusions and identify key tool characteristics that contribute to these discrepancies. Moreover, we provide a comparative overview of these four profilers, offering practical guidance for researchers seeking to choose the most appropriate tool for their study. These findings highlight the importance of software choice in microbiome research and support more transparent and reproducible data analysis practices.

bioinformatics↗

bioRxiv2026

Montreal Urban Observatory: research platform to monitor urban forest ecosystems for global change adaptation and health

As urban populations grow, cities are increasingly seen not only as drivers of climate change but also as critical arenas for implementing mitigation and adaptation strategies. Urban forests and green infrastructure play a vital role in shaping environmental quality and human health, yet access to these benefits remains inequitable. The Montreal Urban Observatory was designed to investigate the complex relationships among biodiversity, ecosystem functioning, and human health. Twenty-five permanent plots were established across the Island of Montreal, strategically located along gradients in vegetation cover, population density, and mean household income. Interdisciplinary research within the Observatory focuses on themes including urban forest structure and function, abiotic conditions, biodiversity, ecological interactions, natures contributions to people, related human health outcomes, and developing novel methodological approaches. The Observatory supports long-term, cross-scale monitoring and fosters collaborative research on urban social-ecological systems, thus contributing to global initiatives to enhance urban sustainability and equity through nature-based solutions. Early results confirm the relevance of the main gradients for several organisms and response variables, from microbes to trees and abiotic factors. For example, sampling all trees, public and private, within a radius of 200m centered on each plot revealed significant differences in the diversity and structure of private and public trees, including an overwhelming dominance of Thuya occidentalis not captured in commonly used public tree inventories.

ecology↗

bioRxiv2025

Season and city shape urban bioaerosol composition beyond vegetation and socioeconomic gradients

Urban vegetation varies with socio-economic gradients, as lower-income neighborhoods often host sparser and less diverse green spaces. This disparity may affect respiratory health by influencing exposure to bioaerosols. Understanding the characteristics of this aerobiome could help anticipate risks related to allergies and other respiratory conditions. Here, we hypothesized that urban vegetation cover and socio-economic status shape urban bioaerosols. We sampled bioaerosols at 65 sites across three Canadian cities of varying population size and density using an active air sampler over four months, and characterized their bacterial, fungal, and pollen composition using amplicon sequencing. Seasonal alpha diversity varied significantly for fungi and pollen. Based on beta diversity, sampling period alone explained up to 40% of pollen, 29% of fungal, and 11% of bacterial community composition variation. In contrast, vegetation cover explained only a minor portion of the variance in bioaerosol composition, and median household income, almost none. These findings provide a critical baseline for understanding the urban aerobiome and highlight the need to study how vegetation identity and diversity, rather than cover alone, may shape bioaerosol dynamics in cities. As cities grow and urban greening initiatives expand, demystifying the aerobiome dynamics becomes an urgent public health priority.

microbiology↗

bioRxiv2025

Responses to Agricultural Practices in Apple Orchards: A Field-Based Mycobiome Study of the Phyllosphere

Microbial communities in the phyllosphere are key players in plant health and disease resistance, yet their response to agricultural management strategies remains poorly understood under field conditions. Here, we compare fungal community composition and diversity across conventional and organic apple orchards using ITS amplicon sequencing. Leaf samples were collected from six sites at three distinct time points during the 2023 growing season (in May, July, and August) corresponding approximately to monthly intervals throughout the summer. Flower samples were collected from the same trees in May. Our analyses reveal that agricultural management strategies are significantly associated with fungal community structure, with effects intensifying from May to July. Both types of management strategies showed enrichment for different genera known to include common apple tree pathogens: Alternaria and Podosphaera were associated with conventional sites, while Didymella and Ramularia were associated with organic sites. Although fungal alpha diversity was higher in May at conventional orchards compared to organic orchards, it declined over time at conventional sites while it remained stable at organic sites. Together, these patterns indicate that distinct management interventions impose contrasting selective pressures on the apple tree phyllosphere mycobiome, thus shaping both broad fungal community composition and the dominance dynamics of key fungal taxa. Our findings underscore the ecological relevance and inherent challenges of field-based microbiome research, and provide insights to inform the development of sustainable orchard management strategies grounded in fungal community dynamics.

microbiology↗

bioRxiv2023

Moss species, sections, and land use type drive moss-associated microbial taxonomy and functions in boreal forests

Moss-microbe interactions contribute to ecosystem processes in boreal forests. Yet, how host-specific characteristics and the environment drive the composition and metabolic potential of moss microbiomes is still poorly understood. In this study, we use shotgun metagenomics to identify the taxonomy and metabolic potential of the bacteria of four moss species of the boreal forests of Northern Quebec, Canada. To characterize moss bacterial community composition and diversity, we assembled the genomes of 110 potentially novel bacterial species. Our results highlight that moss genus, species, gametophyte section, and to a lesser extent soil pH and soil temperature, drive moss-associated bacterial community composition and diversity. In the brown gametophyte section, two Stigonema spp. showed partial pathway completeness for photosynthesis and nitrogen fixation, while all brown-associated Hyphomicrobiales had complete assimilatory nitrate reduction pathways and many nearly complete carbon fixation pathways. Several brown-associated species showed partial to complete pathways for coenzyme M and F420 biosynthesis, important for methane metabolism. In addition, green-associated Hyphomicrobiales (Methylobacteria spp.) displayed potential for the anoxygenic photosystem II pathway. Overall, our findings demonstrate how host-specific characteristics and environmental factors shape the composition and metabolic potential of moss bacteria, highlighting their roles in carbon fixation, nitrogen cycling, and methane metabolism in boreal forests.

microbiology↗