Biology subjects

Bedhomme, S.

Publications and source records attributed to Bedhomme, S..

6 recordsLinked to original sources

bioRxiv2026

Experimental evolution at high temperature in a Lepidopteran host of an entomopathogenic nematode and its associated microbiota

Entomopathogenic Nematodes (EPNs) have a great potential to control various insect crop pests, but their ability to perform their entire life-cycle in insects depends on environmental conditions. The insect killing ability of the endosymbiotic bacterial species (i.e., Xenorhabdus) located in the EPNs' gut (Steinernema) has been described for years. More recently, experimental data have suggested that other bacteria species of the nematode microbiota may also contribute to the parasitic success of the EPNs. EPNs and their associated bacteria should therefore be considered as holobionts. Global change, among its many predicted consequences, is expected to increase temperatures which may impair the parasitic success of these EPNs in the insect. Furthermore, higher environmental temperatures could modify the composition of the EPN-associated microbiota and could therefore also contribute to parasitic impairement. Using a S. carpocapsae strain originating from a French orchard, we investigated these hypotheses by experimentally evolving independent EPNs lineages in vivo in the lepidopteran species Galleria mellonella, at elevated and control temperatures. Several life-history traits of the evolved lineages were measured (insect killing ability, EPN emergence rate, EPN reproduction rate), and the bacterial microbiota of the evolved lineages was characterized by a metabarcoding approach. The EPNs' lineages evolved at higher temperature showed impaired emergence rate and their reproduction rate was lower, when compared to lineages evolved at control temperature. The bacterial microbiota composition of these lineages was modified, with particular enrichment in bacteria of the genera Alcaligenes and Pseudomonas. Our results provide new evidence that modification of the environment (here, the abiotic parameter temperature) during several successive generations can modify the parasitic success of EPNs, concomitantly to a change in the microbiota composition. A better understanding of the life-history traits of these EPNs should help improve the biocontrol efficiency in a context of global warming.

microbiology↗

bioRxiv2026

The attachment rate of Vibrio anguillarum strains to microplastics strongly varies with abiotic and biotic factors

Microplastics (MPs), resulting from plastic objects and waste degradation, are increasingly abundant, particularly in marine environments. They exhibit a hydrophobic surface on which biofilms form easily. Metagenomic analyses of these biofilms have revealed that they often contain bacterial species potentially pathogenic to humans or animals. For this reason, MPs are suspected to present a risk for public health by acting as a vector for pathogenic bacteria species. To better understand this hazard, we studied different factors potentially affecting the bacterial attachment rate to MPs. Focusing on the fish pathogen Vibrio anguillarum, a collection of 16 strains was assembled and GFP-labelled. Their attachment rates were measured using fluorescence microscopy on three types of MPs (milled polypropylene and polyethylene terephthalate particles and commercially available polystyrene beads). A strong effect of the particle type was found, likely linked to both the chemical composition of the particles and the surface characteristics, with higher attachment rates on rough particles. Our results also revealed a strong intra-specific variation in attachment rate, highlighting the need of testing several strains of the same species to assess attachment rate and related hazards. Finally, it was observed that when a biofilm already formed on the MPs (by field-incubation of the MPs along the Mediterranean French coast), differences in attachment rates between particle types were erased. It was concluded that the attachment rate of V. anguillarum depends on a combination of biotic and abiotic factors, which makes risk assessment of MPs as vectors of pathogenic bacteria species a very complex task.

microbiology↗

bioRxiv2025

Environmental complexity constrains evolutionary adaptation across taxa

Complex environments combining multiple stressors are the new norm worldwide. Adaptive evolution will be critical to population persistence under these combined challenges, but how environmental complexity affects the pace of evolution remains poorly understood. Using a meta-experimental evolution approach, we exposed 14 species, from bacteria to unicellular eukaryotes and plants, to single stressors and their pairwise combinations for multiple generations, while keeping the overall stress level comparable. Populations evolving under combined stressors tended to have lower fitness increase in the selective environments, higher fitness reductions in the control environment, and shallower relation between initial maladaptation and fitness gain, than under single stressors. However, these responses varied with species and stressor type. Accounting for such constraints on evolutionary dynamics should prove crucial for the management of biodiversity. Significance StatementA pressing challenges for modern science and society in the face of ongoing global change is understanding what limits the capacity of living organisms to adapt to complex environments combining multiple stressors. To answer to this question, we conducted a large-scale meta-experimental evolution design across a diversity of organisms, exposing them for multiple generations to either single or combined-stress treatments. Combined stressors led to less adaptive fitness gain than single stressors, and imposed additional costs through reduced fitness in non-stressful conditions. This unique combination of meta-experimental approach with a careful distinction between environmental complexity and overall stress allowed us to gain robust quantitative evidence on how environmental complexity can impact the pace of evolution.

evolutionary biology↗

bioRxiv2024

Hurdles to Horizontal Gene Transfer: Synonymous variation determines antibiotic resistance phenotype across species

Evidence that synonymous mutations and synonymous gene variants have fitness effects have accumulated recently. Since horizontal gene transfer represents a change in the genome of expression of the transferred gene, we hypothesized that the codon usage preferences of a horizontally transferred gene could determine the conferred fitness advantage or disadvantage, condition the immediate success of the transfer and in the longer term orient transfers. To test this hypothesis, we characterized resistance levels of synonymous variants of a gentamicin resistance gene, inserted into a broad-host range plasmid and transformed into three different bacterial species Escherichia coli, Acinetobacter baylyi and Pseudomonas aeruginosa. We revealed a strong species effect, explained in part by differences in plasmid copy number between host species. Importantly, the relative levels of resistance conferred by each synonymous variant were not conserved across species, indicating that these phenotypic effects are due to differing compatibility between the transferred variants and the receiver bacterial genomes. This species-variant interaction confirms that the codon composition of a gene can be a determinant of post-horizontal gene transfer success. However, the similarity in codon usage between the synonymous variants and the host genome only explained the phenotypic differences between variants in one species, P. aeruginosa. Further investigations of the effects of local codon usage, translation bottlenecks and internal Shine-Dalgarno sequences did not reveal common universal mechanisms across our three bacterial species and point to multiple paths leading from the synonymous sequence to phenotype and a species-specific sensitivity to these different paths.

evolutionary biology↗

bioRxiv2022

Ecology, more than antibiotics consumption, is the major predictor for the global distribution of aminoglycoside-modifying enzymes

Antibiotics consumption and its abuses have been historically and repeatedly pointed out as the major driver of antibiotic resistance emergence and propagation. However, several examples show that resistance may persist despite substantial reductions in antibiotic use, and that other factors are at stake. Here we study the temporal, spatial, and ecological distribution patterns of aminoglycoside resistance, by screening more than 160,000 publicly available genomes for 27 clusters of genes encoding aminoglycoside-modifying enzymes (AMEGs). We find that AMEGs are ubiquitous: about 25% of sequenced bacteria carry AMEGs. These bacteria were sequenced from all the continents and terrestrial biomes, and belong to a wide number of phyla. By focusing on several European countries between 1997 and 2018, we show that aminoglycoside consumption has little impact on the prevalence of AMEG-carrying bacteria, whereas most variation in prevalence is observed among biomes. We further analyze the resemblance of resistome compositions across biomes: soil, wildlife, and human samples appear to be central to understand the exchanges of AMEGs between different ecological contexts. Moreover, the genomic distribution of AMEGs suggests a selection for widening resistance spectra, mostly driven by mobile genetic elements. Together, these results support the idea that interventional strategies based on reducing antibiotic use should be complemented by a stronger control of exchanges, especially between ecosystems.

genomics↗

bioRxiv2020

PlasForest: a homology-based random forest classifier for plasmid detection in genomic datasets

Plasmids are mobile genetic elements that often carry accessory genes, and are vectors for horizontal transfer between bacterial genomes. The detection of plasmids in large sets of genomes is crucial to analyze their spread and quantify their role in bacteria adaptation and particularly in antibiotic resistance genes propagation. Several bioinformatics methods have been developed to detect plasmids. However, they suffer from low sensitivity (i.e., most plasmids remain undetected) or low precision (i.e., these methods identify chromosomes as plasmids), and are overall not adapted to identify plasmids in whole genomes that are not fully assembled (contigs and scaffolds). Here, we present PlasForest, a homology-based random forest classifier identifying bacterial plasmid sequences in unassembled genomes. This tool is based on the determination of homologies against a database of plasmid sequences, which allow a random forest classifier to discriminate plasmid contigs. Without knowing the taxonomical origin of the samples, PlasForest identifies contigs as plasmids or chromosomes with an accuracy of 98%. Notably, it can detect 96% of plasmid contigs over 50kb with 3.3% of false positives. PlasForest outperforms other currently available tools on test datasets by being both sensitive and precise. We implemented this tool in a user-friendly pipeline that can identify plasmids in large datasets in a reasonable amount of time.

genomics↗