Publications by authors named "Julien Lossouarn"

8 Publications

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Newly identified proviruses in Thermotogota suggest that viruses are the vehicles on the highways of interphylum gene sharing.

Environ Microbiol 2021 11 26;23(11):7105-7120. Epub 2021 Aug 26.

Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.

Phylogenomic analyses of bacteria from the phylum Thermotogota have shown extensive lateral gene transfer 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 bacteria belonging to eight Thermotogota genera and induce viral particle production from one of the proviruses. All except an incomplete provirus from Mesotoga fall into two groups based on sequence similarity, gene synteny and taxonomic classification. Proviruses of Group 1 are found in the genera Geotoga, Kosmotoga, Marinitoga, Thermosipho and Mesoaciditoga and are similar to the previously characterized Marinitoga viruses, while proviruses from Group 2 are distantly related to the Group 1 proviruses, have different genome organization and are found in Petrotoga and Defluviitoga. Genes carried by both groups are closely related to Firmicutes and Firmicutes (pro)viruses in phylogenetic analyses. Moreover, one of the groups show evidence of recent gene exchange and may be capable of infecting cells from both phyla. We hypothesize that viruses are responsible for a large portion of the observed gene flow between Firmicutes and Thermotogota.
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http://dx.doi.org/10.1111/1462-2920.15723DOI Listing
November 2021

PHROG: families of prokaryotic virus proteins clustered using remote homology.

NAR Genom Bioinform 2021 Sep 5;3(3):lqab067. Epub 2021 Aug 5.

Université Clermont Auvergne, CNRS, LMGE, F-63000 Clermont-Ferrand, France.

Viruses are abundant, diverse and ancestral biological entities. Their diversity is high, both in terms of the number of different protein families encountered and in the sequence heterogeneity of each protein family. The recent increase in sequenced viral genomes constitutes a great opportunity to gain new insights into this diversity and consequently urges the development of annotation resources to help functional and comparative analysis. Here, we introduce PHROG (Prokaryotic Virus Remote Homologous Groups), a library of viral protein families generated using a new clustering approach based on remote homology detection by HMM profile-profile comparisons. Considering 17 473 reference (pro)viruses of prokaryotes, 868 340 of the total 938 864 proteins were grouped into 38 880 clusters that proved to be a 2-fold deeper clustering than using a classical strategy based on BLAST-like similarity searches, and yet to remain homogeneous. Manual inspection of similarities to various reference sequence databases led to the annotation of 5108 clusters (containing 50.6 % of the total protein dataset) with 705 different annotation terms, included in 9 functional categories, specifically designed for viruses. Hopefully, PHROG will be a useful tool to better annotate future prokaryotic viral sequences thus helping the scientific community to better understand the evolution and ecology of these entities.
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http://dx.doi.org/10.1093/nargab/lqab067DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8341000PMC
September 2021

Viral metagenomic analysis of the cheese surface: A comparative study of rapid procedures for extracting viral particles.

Food Microbiol 2020 Feb 24;85:103278. Epub 2019 Jul 24.

UMR1319 MICALIS, INRA, AgroParisTech, Université Paris-Saclay, Domaine de Vilvert, 78350, Jouy-en-Josas, France.

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 viral 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 first cheese surface virome, using Epoisses cheese as example. This study provides the basis of future investigations regarding the ecological importance of viruses in cheese microbial ecosystems.
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http://dx.doi.org/10.1016/j.fm.2019.103278DOI Listing
February 2020

Countermeasures Defeat a Virulent Bacteriophage.

Viruses 2019 01 10;11(1). Epub 2019 Jan 10.

Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.

is an opportunistic pathogen that has emerged as a major cause of nosocomial infections worldwide. Many clinical strains are indeed resistant to last resort antibiotics and there is consequently a reawakening of interest in exploiting virulent phages to combat them. However, little is still known about phage receptors and phage resistance mechanisms in enterococci. We made use of a prophageless derivative of the well-known clinical strain V583 to isolate a virulent phage belonging to the subfamily and to the P68 genus that we named Idefix. Interestingly, most isolates of tested-including V583-were resistant to this phage and we investigated more deeply into phage resistance mechanisms. We found that V583 prophage 6 was particularly efficient in resisting Idefix infection thanks to a new abortive infection (Abi) mechanism, which we designated Abiα. It corresponded to the Pfam domain family with unknown function DUF4393 and conferred a typical Abi phenotype by causing a premature lysis of infected . The gene is widespread among prophages of enterococci and other Gram-positive bacteria. Furthermore, we identified two genes involved in the synthesis of the side chains of the surface rhamnopolysaccharide that are important for Idefix adsorption. Interestingly, mutants in these genes arose at a frequency of ~10 resistant mutants per generation, conferring a supplemental bacterial line of defense against Idefix.
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http://dx.doi.org/10.3390/v11010048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6356687PMC
January 2019

Thermosipho spp. Immune System Differences Affect Variation in Genome Size and Geographical Distributions.

Genome Biol Evol 2018 11 1;10(11):2853-2866. Epub 2018 Nov 1.

Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway.

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 (GS), 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. GS 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.
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http://dx.doi.org/10.1093/gbe/evy202DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211235PMC
November 2018

Draft Genome Sequences of Two Marinitoga camini Isolates Producing Bacterioviruses.

Genome Announc 2016 Nov 10;4(6). Epub 2016 Nov 10.

Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway.

Here, we present the draft genome sequences of two thermophilic Marinitoga strain members of the Thermotogales order, Marinitoga camini DV1155 and Marinitoga camini DV1197. These strains were isolated from deep-sea hydrothermal vents of the Mid-Atlantic Ridge.
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http://dx.doi.org/10.1128/genomeA.01261-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5105104PMC
November 2016

An abyssal mobilome: viruses, plasmids and vesicles from deep-sea hydrothermal vents.

Res Microbiol 2015 Dec 22;166(10):742-52. Epub 2015 Apr 22.

Laboratory of Microbiology of Extreme Environments (LMEE), UMR 6197/UBO/Ifremer/CNRS, IUEM, Place Nicolas Copernic, Technopôle Brest Iroise, 29280, Plouzané, France. Electronic address:

Mobile genetic elements (MGEs) such as viruses, plasmids, vesicles, gene transfer agents (GTAs), transposons and transpovirions, which collectively represent the mobilome, interact with cellular organisms from all three domains of life, including those thriving in the most extreme environments. While efforts have been made to better understand deep-sea vent microbial ecology, our knowledge of the mobilome associated with prokaryotes inhabiting deep-sea hydrothermal vents remains limited. Here we focus on the abyssal mobilome by reviewing accumulating data on viruses, plasmids and vesicles associated with thermophilic and hyperthermophilic Bacteria and Archaea present in deep-sea hydrothermal vents.
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http://dx.doi.org/10.1016/j.resmic.2015.04.001DOI Listing
December 2015

'Ménage à trois': a selfish genetic element uses a virus to propagate within Thermotogales.

Environ Microbiol 2015 Sep 2;17(9):3278-88. Epub 2015 Mar 2.

Université de Bretagne Occidentale (UBO, UEB), Institut Universitaire Européen de la Mer (IUEM) - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), rue Dumont d'Urville, F-29280, Plouzané, France.

Prokaryotic viruses play a major role in the microbial ecology and evolution. However, the virosphere associated with deep-sea hydrothermal ecosystems remains largely unexplored. Numerous instances of lateral gene transfer have contributed to the complex and incongruent evolutionary history of Thermotogales, an order well represented in deep-sea hydrothermal vents. The presence of clustered regularly interspaced short palindromic repeats (CRISPR) loci has been reported in all Thermotogales genomes, suggesting that these bacteria have been exposed to viral infections that could have mediated gene exchange. In this study, we isolated and characterized the first virus infecting bacteria from the order Thermotogales, Marinitoga piezophila virus 1 (MPV1). The host, Marinitoga piezophila is a thermophilic, anaerobic and piezophilic bacterium isolated from a deep-sea hydrothermal chimney. MPV1 is a temperate Siphoviridae-like virus with a 43.7 kb genome. Surprisingly, we found that MPV1 virions carry not only the viral DNA but preferentially package a plasmid of 13.3 kb (pMP1) also carried by M. piezophila. This 'ménage à trois' highlights potential relevance of selfish genetic elements in facilitating lateral gene transfer in the deep-sea biosphere.
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http://dx.doi.org/10.1111/1462-2920.12783DOI Listing
September 2015
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