Biology subjects

Fillol-Salom, A.

Publications and source records attributed to Fillol-Salom, A..

6 recordsLinked to original sources

bioRxiv2026

HaloClassifier: integrating coding-signature features and k-mer composition for plasmid-chromosome discrimination in haloarchaeal genomes

Background: Plasmids are key drivers of horizontal gene transfer (HGT), enabling the dissemination of accessory traits that shape microbial adaptation and ecological interactions. In Haloarchaea-dominant members of hypersaline environments-characterizing plasmidomes remains particularly challenging because most available genomes are incomplete, leaving many contigs unassigned to either chromosomal or plasmidic origin. This limitation hampers our ability to reconstruct archaeal plasmid diversity and to evaluate how plasmid-borne genes circulate within Haloarchaea and, potentially, outside this class. Results: Here, we present HaloClassifier, the first machine-learning tool specifically designed to distinguish plasmid- and chromosome-derived contigs in haloarchaeal genomes. Unlike existing bacterial-focused approaches, HaloClassifier uniquely integrates haloarchaeal-specific genomic signatures with coding-derived features-an underused but highly informative class of predictors-and incorporates a variable-selection strategy that substantially reduces model complexity and computational cost while maintaining high predictive accuracy. When trained on simulated contigs generated from complete haloarchaeal genomes, the model achieves 96.61% accuracy on extralarge contigs (40-100 kb), increasing to 98.1% at a 0.6 classification threshold, with only 3.55% of contigs left unclassified. For small contigs (1-5 kb), the model achieves 79.51% accuracy overall and 84.42% at the 0.6 classification threshold, with 17.07% of contigs left unclassified. The model also maintains robust performance in metagenomic datasets. Conclusions: By enabling reliable plasmid identification in fragmented assemblies, HaloClassifier fills a major gap and establishes the foundation for large-scale haloarchaeal plasmidome reconstruction. This framework will support future investigations into gene mobility, ecological adaptation, and the evolutionary dynamics of plasmids and HGT in Haloarchaea.

bioinformatics↗

bioRxiv2026

Integrative mobilizable elements are pervasive throughout Pseudomonadota

Integrative mobilizable elements (IMEs) are mobile genetic elements that reside stably integrated into chromosomes and rely on helper conjugative elements for horizontal transfer. Here, we identify and characterize a widespread family of IMEs, named Pseudomonadota Integrative Mobilizable Elements (PIMEs), which are distributed exclusively in the Pseudomonadota phylum. Genome and phylogenomic analyses reveal [~]1,000 putative PIMEs, comprising at least four distinct PIME subfamilies defined by distinctive genomic organizations and conserved hallmark features. Characterized PIMEs depend on helper conjugative plasmids of the incompatibility group P (IncP) and, upon induction, PIMEs excise, replicate and mobilize intra- and inter-species. Remarkably, the representative PIME and its helper conjugative plasmid engages in cross-complementation, revealing an unrecognized level of functional interplay between hijacker and helper element. We also demonstrate that PIMEs act as reservoirs of known and novel prokaryotic immune systems. Overall, our findings uncover an overlooked and disseminated family of IMEs, which likely plays an important role in bacterial ecology and evolution.

microbiology↗

bioRxiv2025

Chimeric infective particles expand species boundaries in phage inducible chromosomal island mobilization

Some mobile genetic elements spread among unrelated bacterial species through unknown mechanisms. Recently, we discovered that identical capsid-forming phage-inducible chromosomal islands (cf-PICIs), a new family of phage satellites, are present across multiple species and genera, raising questions about their widespread dissemination. Here we have identified and characterized a new biological entity enabling this transfer. Unlike other satellites, cf-PICIs produce their own capsids and package their DNA, relying solely on phage tails for transfer. Remarkably, cf-PICIs release non-infective, tail-less capsids containing their DNA into the environment. These subcellular entities then interact with phage tails from various species, forming chimeric particles that inject DNA into different bacterial species depending on the tail present. Additionally, we elucidated the structure of the tail-less cf-PICIs and the mechanism behind their unique capsid formation. Our findings illuminate novel mechanisms used by satellites to spread in nature, contributing to bacterial evolution and the emergence of new pathogens.

microbiology↗

bioRxiv2022

Identification and characterization of thousands of bacteriophage satellites across bacteria

Bacteriophage-bacteria interactions are affected by phage satellites, elements that exploit phages for transfer between bacterial cells. Satellites can encode defense systems, antibiotic resistance genes, and virulence factors, but their number and diversity are unknown for lack of a tool to identify them. We developed a flexible and updateable program to identify satellites in bacterial genomes - SatelliteFinder - and use it to identify the best described families: P4-like, phage inducible chromosomal islands (PICI), capsid-forming PICI, and phage-inducible chromosomal island-like elements (PLE). We vastly expanded the number of described elements to [~]5000, finding hundreds of bacterial genomes with two different families of satellites, and dozens of Escherichia coli genomes with three. Most satellites were found in Proteobacteria and Firmicutes, but some are in novel taxa such as Actinobacteria. We characterized the gene repertoires of satellites, which are variable in size and composition, and their genomic organization, which is very conserved. With the partial exception of PICI and cfPICI, there are few homologous core genes between families of satellites, and even fewer homologous to phages. Hence, phage satellites are ancient, diverse, and probably evolved multiple times independently. Occasionally, core genes of a given family of satellites are found in another, suggesting gene flow between different satellites. Given the many elements found in spite of our conservative approach, the many bacteria infected by phages that still lack known satellites, and the recent proposals for novel families, we speculate that we are at the beginning of the discovery of massive numbers and types of satellites. SatelliteFinder is accessible for the community as a Galaxy service at https://galaxy.pasteur.fr/root?tool_id=toolshed.pasteur.fr/repos/fmareuil/satellitefinder/SatelliteFinder/0.9

microbiology↗

bioRxiv2022

A widespread family of phage-inducible chromosomal islands only steals bacteriophage tails to spread in nature

Phage satellites interfere with helper phage packaging through the production of small-capsids, where only satellites can be packaged. So far, in all the analysed systems, the satellite-sized capsids are composed of phage proteins. Here we report the first demonstration that a family of phage-inducible chromosomal island (PICIs), a type of satellites, encodes all the proteins required for both the production of the small-sized capsids and the exclusive packaging of the PICIs into these capsids. Therefore, this new family, that we have named cf-PICIs (capsid forming PICIs), only requires phage tails to generate infective PICI particles. Remarkably, the representative cf-PICI reproduces without cost for their helper phages, suggesting that the relationship between these elements is not parasitic but commensalistic. Finally, our phylogenomic studies indicate that cf-PICIs are present both in Gram-positive and Gram-negative bacteria and have evolved at least three times independently to spread widely into the satellite universe.

microbiology↗

bioRxiv2021

The secret life (cycle) of temperate bacteriophages

Lysogenic induction ends the stable association between a bacteriophage and its host, and the transition to the lytic cycle begins with prophage excision followed by DNA replication and packaging (ERP) - a temporal program that is considered universal for most temperate phages. Here we report that the long-standing ERP program is an artefact of the experimentally favoured Salmonella phage P22 tsc229 heat-inducible mutant, and that wildtype P22 actually follows a replication-packaging-excision (RPE) program. We found that unlike P22 tsc229, P22 delayed excision to just before it was detrimental to phage production. Thus, at minimal expense to itself, P22 has tuned the timing of excision to balance propagation with lateral transduction, powering the evolution of its host through gene transfer in the interest of self-preservation. One Sentence SummaryGenetic analyses propose a new life cycle for temperate bacteriophages.

microbiology↗