Biology subjects

Lossouarn, J.

Publications and source records attributed to Lossouarn, J..

7 recordsLinked to original sources

bioRxiv2026

A novel virus lineage is abundant in metaviromes from Dehalococcoides-containing mixed cultures

Dehalococcoides mccartyi are obligately anaerobic organohalide-respiring bacteria that play important roles in the detoxification of chlorinated pollutants in groundwater and sediments. Despite having small genomes, they host a diverse set of mobile elements. Here we characterize a family of mobile elements, termed integrative and mobilizable element 1 or IME1, comprising 20 from Dehalococcoides and one from Dehalogenimonas alkenigignens. IME1s are 20,930 - 28,058 bp and are found both integrated in the genomes and as circular episomes. Bioinformatic characterization of IME1 encoded proteins revealed a highly conserved structure with 14 hierarchical orthologous groups (HOGs) found in all 21 IME1s. IME1s lack recognizable hallmark proteins of tailed bacterial viruses (or tailed phages) but encode proteins with similarities to those of filamentous bacterial viruses. In particular, one conserved HOG shows sequence similarity to the pI-like ATPase, the only conserved marker protein identified across filamentous bacterial viruses. Additionally, IME1s encode several small proteins with predicted transmembrane domains and signal peptides, another feature used to identify filamentous bacterial viruses. Both features are also found in budding archaeal viruses of various morphotypes. IME1s dominated metaviromes obtained from the Dehalococcoides-containing KB-1 mixed culture and electron micrographs of the corresponding viral fractions revealed abundant filamentous virus-like particles. We therefore propose that the IME1s represent a novel lineage of double stranded budding, likely filamentous, viruses. Database searches suggest IME1s are found in Dehalococcodia and other Chlorofexota but are so far restricted to this phylum.

microbiology↗

bioRxiv2025

Complementary killing activities of Pbunavirus LS1 and Bruynoghevirus LUZ24 phages on planktonic and sessile Pseudomonas aeruginosa PAO1 derivatives

Four P. aeruginosa phages active against a representative panel of strains, and with complementary spectra of action were chosen with the goal of using them for phage therapy. Two of them were myoviruses belonging to the Pbunavirus LS1 species, and two were podoviruses belonging to the Bruynoghevirus LUZ24 species. In order to better apprehend the interactions of these phages with their P. aeruginosa host bacteria, we undertook the characterization of their bacterial receptors, using a PAO1 derivative as a recipient strain. Whereas the receptor of the P. LS1 phage Ab27 had already been characterized as the O-antigen chain of the lipopolysaccharides, no information was available at the onset of this work on the receptor used by the phages of the B. LUZ24 species. We show that the surface polysaccharide Psl is this receptor. Psl stands for polysaccharide synthesis locus, and it is an important component of the biofilm matrix in a large panel of P. aeruginosa strains, including PAO1. Remarkably, the B. LUZ24 phages were more active against PAO1 in minimal medium compared to rich medium. Consistently, this was correlated with larger amounts of Psl bound at the bacterial surface during exponential growth in the minimal medium compared to the rich medium. Biofilms formed on a medical intubation device, as well as in in 96-well plates, were degraded to different extent by the two phage species: biofilms grown for 7 hours on tubing device were degraded more efficiently by the B. LUZ24 than the P. LS1 phage, whereas mature biofilms (16 hours) formed in 96-well plates were degraded more rapidly by P. LS1 than by B. LUZ24 phage. The frequency of genetic mutants resisting to each phage were determined in liquid medium by a fluctuation assay and found in the range of 10-5 to 10-6 per generation. Interestingly, most of the P. LS1 resisting mutants were more sensitive to the B. LUZ24 phage. We conclude that the combination of the four selected phages has very promising properties, which should be relevant in the framework of phage therapy.

microbiology↗

bioRxiv2021

Analysis of viromes and microbiomes from pig fecal samples reveals that phages and prophages are not vectors of antibiotic resistance genes

Understanding the transmission of antibiotic resistance genes (ARGs) is critical for human health. For this, it is necessary to identify which type of mobile genetic elements is able to spread them from animal reservoirs into human pathogens. Previous research suggests that in pig feces, ARGs may be encoded by bacteriophages. However, convincing proof for phage-encoded ARGs in pig viromes is still lacking, because of bacterial DNA contaminating issues. We collected 14 pig fecal samples and performed deep sequencing on both highly purified viral fractions and total microbiota, in order to investigate phage and prophage-encoded ARGs. We show that ARGs are absent from the genomes of active, virion-forming phages (below 0.02% of viral contigs from viromes), but present in three prophages, representing 0.02% of the viral contigs identified in the microbial dataset. However, the corresponding phages were not detected in the viromes, and their genetic maps suggest they might be defective. Furthermore, our dataset allows for the first time a comprehensive view of the interplay between prophages and viral particles.

microbiology↗

bioRxiv2020

Viruses of the Thermotogota; the vehicles on the highways of gene sharing.

Phylogenomic analyses of bacteria from the phylum Thermotogota have shown extensive lateral gene transfer (LGT) with distantly related organisms, particularly with Firmicutes. One likely mechanism of such DNA transfer is viruses. However, to date only three temperate viruses have been characterized in this phylum, all infecting bacteria from the Marinitoga genus. Here we report 17 proviruses integrated into genomes of eight Thermotogota genera and induce viral particle production from one of the proviruses. The proviruses fall into two groups based on sequence similarity, gene synteny and taxonomic classification. Proviruses of one group are found in six genera and are similar to the previously identified Marinitoga viruses, while proviruses from the second group are only distantly related to the proviruses of the first group, have different genome organization and are found in only two genera. Both groups are closely related to Firmicutes in genomic and phylogenetic analyses, and one of the groups show evidence of very recent LGT and are therefore likely capable of infecting cells from both phyla. We conjecture that viruses are responsible for a large portion of the observed gene flow between Firmicutes and Thermotogota.

evolutionary biology↗

bioRxiv2018

Viral metagenomic analysis of the cheese surface: a comparative study of rapid procedures for extracting virus-like particles

The structure and functioning of microbial communities from fermented foods, including cheese, have been extensively studied during the past decade. However, there is still a lack of information about both the occurrence and the role of viruses in modulating the function of this type of spatially structured and solid ecosystems. Viral metagenomics was recently applied to a wide variety of environmental samples and standardized procedures for recovering virus-like particles from different type of materials has emerged. In this study, we adapted a procedure originally developed to extract viruses from fecal samples, in order to enable efficient virome analysis of cheese surface. We tested and validated the positive impact of both addition of a filtration step prior to virus concentration and substitution of purification by density gradient ultracentrifugation by a simple chloroform treatment to eliminate membrane vesicles. Viral DNA extracted from the several procedures, as well as a vesicle sample, were sequenced using Illumina paired-end MiSeq technology and the subsequent clusters assembled from the virome were analyzed to assess those belonging to putative phages, plasmid-derived DNA, or even from bacterial chromosomal DNA. The best procedure was then chosen, and used to describe the Epoisses cheese virome. This study provides the basis of future investigations regarding the ecological importance of viruses in cheese microbial ecosystems.\n\nIMPORTANCEWhether bacterial viruses (phages) are necessary or not to maintain food ecosystem function is not clear. They could play a negative role by killing cornerstone species that are necessary for fermentation. But they might also be positive players, by preventing the overgrowth of unwanted species (e.g. food spoilers). To assess phages contribution to food ecosystem functioning, it is essential to set up efficient procedures for extracting viral particles in solid food matrix, then selectively sequence their DNA without being contaminated by bacterial DNA, and finally to find strategies to assemble their genome out of metagenomic sequences. This study, using cheese rind surface as a model, describes a comparative analysis of procedures for selectively extracting viral DNA from cheese and to efficiently characterize the genome of dominant phages with cross-sample assembly.

microbiology↗

bioRxiv2018

Thermosipho spp. immune system differences affect variation in genome size and geographical distributions

Thermosipho species inhabit thermal environments such as marine hydrothermal vents, petroleum reservoirs and terrestrial hot springs. A 16S rRNA phylogeny of available Thermosipho spp. sequences suggested habitat specialists adapted to living in hydrothermal vents only, and habitat generalists inhabiting oil reservoirs, hydrothermal vents and hotsprings. Comparative genomics of 15 Thermosipho genomes separated them into three distinct species with different habitat distributions: the widely distributed T. africanus and the more specialized, T. melanesiensis and T. affectus. Moreover, the species can be differentiated on the basis of genome size, genome content and immune system composition. For instance, the T. africanus genomes are largest and contained the most carbohydrate metabolism genes, which could explain why these isolates were obtained from ecologically more divergent habitats. Nonetheless, all the Thermosipho genomes, like other Thermotogae genomes, show evidence of genome streamlining. Genome size differences between the species could further be correlated to differences in defense capacities against foreign DNA, which influence recombination via HGT. The smallest genomes are found in T. affectus that contain both CRISPR-cas Type I and III systems, but no RM system genes. We suggest that this has caused these genomes to be almost devoid of mobile elements, contrasting the two other species genomes that contain a higher abundance of mobile elements combined with different immune system configurations. Taken together, the comparative genomic analyses of Thermosipho spp. revealed genetic variation allowing habitat differentiation within the genus as well as differentiation with respect to invading mobile DNA.

microbiology↗

bioRxiv2017

Habitat generalists or specialists, insights from comparative genomic analyses of Thermosipho lineages

Thermosipho species inhabit various extreme environments such as marine hydrothermal vents, petroleum reservoirs and terrestrial hot springs. A 16S rRNA phylogeny of available Thermosipho spp. sequences suggested habitat specialists adapted to living in hydrothermal vents only, and habitat generalists inhabiting oil reservoirs, hydrothermal vents and hotsprings. Comparative genomics and recombination analysis of the genomes of 15 Thermosipho isolates separated them into three species with different habitat distributions, the widely distributed T. africanus and the more specialized, T. melanesiensis and T. affectus. The three Thermosipho species can also be differentiated on the basis of genome content. For instance the T. africanus genomes had the largest repertoire of carbohydrate metabolism, which could explain why these isolates were obtained from ecologically more divergent habitats. The three species also show different capacities for defense against foreign DNA. T. melanesiensis and T. africanus both had a complete RM system, while this was missing in T. affectus. These observations also correlated with Pacbio sequencing, which revealed a methylated T. melanesiensis BI431 genome, while no methylation was detected among two T. affectus isolates. All the genomes carry CRISPR arrays accompanied by more or less complete CRISPR-cas systems. Interestingly, some isolates of both T. melanesiensis and T. africanus carry integrated prophage elements, with spacers matching these in their CRISPR arrays. Taken together, the comparative genomic analyses of Thermosipho spp. revealed genetic variation allowing habitat differentiation within the genus as well as differentiation with respect to invading mobile DNA that is present in subsurface ecosystems.

microbiology↗