Biology subjects

Riou, M.

Publications and source records attributed to Riou, M..

5 recordsLinked to original sources

bioRxiv2026

TRIDENT (Taxonomic Resolution and IDentification using Environmental dNa Traces): An Optimized Algorithm for Vertebrate Taxonomic Assignments in eDNA Metabarcoding, Integrating Molecular, Taxonomic, and Ecological Criteria

Environmental DNA (eDNA) metabarcoding has become a powerful approach for large-scale biodiversity assessment, yet taxonomic assignment remains one of its most critical error-prone steps. Current bioinformatic pipelines rely on molecular similarity searches against reference databases, but assignment accuracy is constrained not only by short marker length and database incompleteness, but also by fundamental limitations, including recent species radiations, incomplete lineage sorting, introgression, NUMTs, and the imperfect correspondence between genetic variation and species boundaries. Here, we present TRIDENT (Taxonomic Resolution and IDentification using Environmental dNa Traces), an automated and simple protocol designed to improve taxonomic assignments in eDNA metabarcoding. Initially developed for marine vertebrates, TRIDENT may be used with any barcode and integrates three complementary sources of evidence: molecular similarity (NCBI/GenBank and BOLD), curated taxonomic information (WoRMS), and ecological plausibility derived from biogeographic occurrence data (GBIF). The workflow sequentially constructs candidate taxon lists based on sequence similarity, expands them through taxonomic hierarchies, and filters them using spatial occurrence constraints. It further identifies possible taxa lacking reference barcodes and evaluates their plausibility through CO1-based similarity if data exist in BOLD. TRIDENT has been implemented as a source-available Python tool and tested using empirical eDNA datasets from marine vertebrates as well as simulated communities. Results demonstrate that the tool produces taxonomic assignments consistent with expert manual curation while substantially reducing processing time and attention errors caused by manual processing of large datasets. By combining molecular, taxonomic, and ecological criteria within a single framework, TRIDENT improves transparency and reproducibility and provides a robust and flexible solution strengthening confidence in taxonomic identifications in eDNA-based biodiversity assessments.

Molecular Biology↗

bioRxiv2026

Multiscale oocyst wall mechanics govern coccidian resistance

Coccidian parasites spread through oocysts, environmental transmission stages that must survive harsh conditions yet rupture on cue inside the host to release infectious sporozoites. How the oocyst wall reconciles these opposing demands is unknown. Using single-oocyst microindentation, quantitative imaging and infection assays in Eimeria acervulina and Eimeria tenella, we show that the bilayered wall is functionally partitioned: the chemically fragile outer layer is mechanically dispensable, while the inner layer bears the mechanical load and remains impermeable to macromolecules and limiting osmotic exchange even after the outer layer is stripped. Oocysts behave as pressurised shells that fail preferentially at the anterior pole, a fixed mechanical weak point that channels sporocyst release regardless of where force is applied. Wall structure, autofluorescence, mechanics and infectivity prove dissociable: bleach removes the outer layer without weakening the wall or fully abolishing infectivity, whereas heat weakens the wall and abolishes infectivity while leaving the bilayered structure intact. These findings define a mechanical logic for coccidian oocyst resistance, disinfection and controlled excystation, and identify the inner wall as the critical target for inactivating environmentally transmitted parasites.

microbiology↗

bioRxiv2025

Flagellin aerosol administration improves the efficacy of antibiotic treatment in Actinobacillus pleuropneumoniae infected pigs

Swine infections with Actinobacillus pleuropneumoniae (App), the causative agent of porcine pleuropneumonia, lead to significant production losses. Surviving pigs may harbor antibiotic-resistant bacteria, highlighting the need for alternatives to reduce antimicrobial use. Stimulation of respiratory innate immunity via Toll-like receptor 5 (TLR5) agonists such as FLAMOD (a recombinant flagellin), has emerged as a promising strategy for combating bacterial lung infections. In a recent study, aerosolized administration of FLAMOD was found to elicit respiratory immune responses in pigs. This study assessed FLAMODs protective effects against App, either as a prophylactic intervention or as an adjunct to antibiotic therapy. Prophylactic administration of aerosolized FLAMOD via nebulization before App challenge failed to confer protection. However, in a therapeutic setting, where pigs were infected with App and treated with either a subtherapeutic dose of penicillin G (PenG) alone or a combination of PenG and aerosolized FLAMOD. Notably, the FLAMOD and PenG combination significantly improved bacterial clearance from the lungs. Moreover, FLAMOD-PenG treated pigs exhibited a trend toward increased weight gain and fewer lung lesions compared to those receiving PenG alone. These findings provide proof for the concept that FLAMOD enhances antibiotic efficacy, potentially lowering the required antibiotic dose and contributing to antimicrobial resistance mitigation in pigs.

immunology↗

bioRxiv2021

Integrative biology defines novel biomarkers of resistance to strongylid infection in horses

The widespread failure of anthelmintic drugs against nematodes of veterinary interest requires novel control strategies. Selective treatment of the most susceptible individuals could reduce drug selection pressure but requires appropriate biomarkers of the intrinsic susceptibility potential. To date, this has been missing in livestock species. Here, we selected Welsh ponies with divergent intrinsic susceptibility to cyathostomin infection and found that their potential was sustained across a 10-year time window. Using this unique set of individuals, we monitored variations in their blood cell populations, plasma metabolites and faecal microbiota over a grazing season to isolate core differences between their respective responses under worm-free or natural infection conditions. Our analyses identified the concomitant rise in plasmatic phenylalanine level and faecal Prevotella abundance and the reduction in circulating monocyte counts as biomarkers of the need for drug treatment. This biological signal was replicated in other independent populations. We also unravelled an immunometabolic network encompassing plasmatic beta-hydroxybutyrate level, short-chain fatty acid producing bacteria and circulating neutrophils that forms the discriminant baseline between susceptible and resistant individuals. Altogether our observations open new perspectives on the susceptibility of equids to cyathostomin infection and leave scope for both new biomarkers of infection and nutritional intervention.

systems biology↗

bioRxiv2017

Metagenomic signature of natural strongyle infection in susceptible and resistant horses

Gastrointestinal strongyles are a major threat to horses' health and welfare. Given that strongyles inhabit the same niche as the gut microbiota, they may interact with each other. These beneficial or detrimental interactions are unknown in horses and could partly explain contrasted susceptibility to infection between individuals. To address these questions, an experimental pasture trial with 20 worm-free female Welsh ponies (10 susceptible (S) and 10 resistant (R) to parasite infection) was implemented for five months. Fecal egg counts (FEC), hematological and biochemical data, body weight and gut microbiota composition were studied in each individual after 0, 24, 43, 92 and 132 grazing days.\n\nThe predicted R ponies exhibited lower FEC after 92 and 132 grazing days, and showed higher levels of circulating monocytes and eosinophils, while S ponies developed lymphocytosis by the end of the trial. Although the overall microbiota diversity remained similar between the two groups, R and S ponies exhibited sustained differential abundances in Clostridium XIVa, Ruminococcus, Acetivibrio and unclassified Lachnospiracea at day 0. These bacteria may hence contribute to the intrinsic pony resistance towards strongyle infection. Moreover, Paludibacter, Campylobacter, Bacillus, Pseudomonas, Clostridium III, Acetivibrio, members of the unclassified Eubacteriaceae and Ruminococcaceae and fungi loads were increased in infected S ponies, suggesting that strongyle and fungi may contribute to each others success in the ecological niche of the equine intestines. In contrast, butyrate-producing bacteria such as Ruminococcus, Clostridium XIVa and members of the Lachnospiraceae family decreased in S relative to R ponies. Additionally, these gut microbiota alterations induced changes in several immunological pathways in S ponies, including pathogen sensing, lipid metabolism, and activation of signal transduction that are critical for the regulation of immune system and energy homeostasis. These observations shed light on a putative implication of the gut microbiota in the intrinsic resistance to strongyle infection.\n\nOverall, this longitudinal study provides a foundation to better understand the mechanisms that underpin the relationship between host susceptibility to strongyle infection, immune response and gut microbiota under natural conditions in horses and should contribute to the development of novel biomarkers of strongyle susceptibility and provide additional control options.

systems biology↗