Biology subjects

Petit, M.-A.

Publications and source records attributed to Petit, M.-A..

15 recordsLinked to original sources

bioRxiv2026

Improving viral protein clustering using both diversified protein profiles and structural information

Viruses are abundant, ancestral and potentially fast-evolving biological entities. As a result, their encoded proteins are diverse and identifying homologous relationships between sequences is as important for phylogeny and functional annotation as it is challenging. Traditional methods group viral proteins by sequence similarity, build HMM profiles for each protein family, and cluster further via profile comparisons. Here, we present an improved framework where HMM sensitivity is boosted by enriching reference virus HMM profiles with tens of millions of metagenomic sequences. This increases diversity within most protein families, raising the diversity index from less than 2 for 92.7% of clusters to a median value of 6. This enrichment of the profiles more than triples the number of homologies detected compared to the raw profiles. First-step clusters are then grouped more effectively using these relationships and further unified via structural predictions and comparisons. The sequence-enrichment strategy excels at linking small proteins, while structures better connect highly structured ones like tail and head proteins. Applied to 1.42 million proteins, our method yields 56,560 families--far fewer than 200,018 (sequence-based) or 135,048 (raw HMM)--revealing that prior approaches vastly overestimated viral protein diversity. The strategy of enriching the diversity of sequences of interest with external sequences, combined with the complementary use of structural information, highlights deep evolutionary links, offering a more accurate picture of viral protein evolution.

bioinformatics↗

bioRxiv2026

DNA-damaging bacteriocins from human Escherichia coli intestinal isolates trigger prophage induction and promote lysogeny.

Lysogens - bacteria harbouring prophages - are prevalent in the human gut microbiota. Nevertheless, factors triggering induction or repression of prophages remain poorly characterized. Here, we studied the involvement of bacteriocins - antibacterials involved in bacteria-bacteria competition - in prophage induction. We screened a collection of 1,768 fecal Escherichia coli isolates for bacteriocin-producing strains and selected 30 to test their capacity to induce a {lambda}-related coliphage. In these, we identified 74 bacteriocin genes and demonstrate that only those coding a DNA-damaging bacteriocin trigger prophage induction. From one strain co-producing an E-type endonuclease colicin and the Mcc1229 microcin, we demonstrate that these colicins induce a broad panel of temperate phage genera. Assessing bacterial competition by pairwise cocultures between an E-type endonuclease-producing strain and a {lambda}-lysogen revealed enhanced prophage induction and increased emergence of new lysogens among the bacteriocin producers. Remarkably, while the {lambda}-lysogen was outcompeted by the E-type endonuclease colicin producer within 6 hours in vitro, both populations were maintained at comparable levels over 10 days in dixenic mice. This work reveals a dual role for DNA-damaging bacteriocins that kill competitors by prophage induction and propagate lysogeny.

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↗

bioRxiv2024

The human blood harbors a phageome which differs in Crohn's disease

Increasing evidence suggests that the human blood hosts microbes including bacteria and eukaryotic viruses, which could have important implications for health. Bacteriophages of the blood are challenging to study and have been overlooked, but could translocate to this environment from different body-sites. We thus developed specific virome protocols and analysis methods to study the viral communities of blood samples obtained from healthy individuals and Crohns disease (CD) patients. We uncovered a diverse viral community in the human blood, dominated by phages infecting Pseudomonadota bacteria. We found that an important fraction of those phages overlaps with the gut virome, consolidating the idea that gut phages can translocate to the blood. Strikingly, viral communities of the blood were different between CD patients and healthy individuals, revealing a new signature of disease. This was not the case for fecal viral communities. Collectively, these results advance our knowledge of the microorganisms present in the human blood and pave the way for further studies of this environment in the context of disease.

microbiology↗

bioRxiv2023

Dynamics of the viral community on the cheese surface during maturation and persistence across production years

The surface of smear-ripened cheeses constitutes a dynamic microbial ecosystem resulting from the successive development of different microbial groups such as lactic acid bacteria, fungi and ripening bacteria. Recent studies indicate that a viral community, mainly composed of bacteriophages, also represents a common and substantial part of the cheese microbiome. However, the composition of this community, its temporal variations and associations between bacteriophages and their hosts remain poorly characterized. Here, we studied a French smear-ripened cheese by both viral metagenomics and 16S metabarcoding approaches to assess both the succession of phages and bacterial communities on the cheese surface during cheese ripening, and their temporal variations in ready-to-eat cheeses over the years of production. We observed a clear transition of the phage community structure during ripening with a decreased relative abundance of viral species (vOTUs) associated with Lactococcus phages, which were replaced by vOTUs associated with phages infecting ripening bacteria such as Brevibacterium, Glutamicibacter, Pseudoalteromonas and Vibrio. The dynamics of the phage community was strongly associated with bacterial successions observed on the cheese surface. Finally, while some variations in the distribution of phages were observed in ready-to-eat cheeses produced at different dates spanning more than 4 years of production, the most abundant phages were detected throughout. This result revealed the long-term persistence of the dominant phages in the cheese production environment. Together, these findings offer novel perspectives on the ecology of bacteriophages in smear-ripened cheese and emphasize the significance of incorporating bacteriophages in the microbial ecology studies of fermented foods. IMPORTANCEThe succession of diverse microbial populations is critical for ensuring the production of high-quality cheese. We observed a temporal succession of phages on the surface of a smear-ripened cheese, with new phage communities showing up at the time when ripening bacteria start covering this surface. Interestingly, the final phage community of this cheese is also consistent over large periods of time, as the same bacteriophages were found in cheese products from the same manufacturer made over 4-years. This research highlights the importance of considering these bacteriophages when studying the microbial life of fermented foods like cheese.

microbiology↗

bioRxiv2023

The influence of early life exposures on the infant gut virome

Large cohort studies have contributed significantly to our understanding of the factors that influence the development of the bacterial component of the gut microbiome (GM) during the first years of life. However, the factors that shape the colonization by other important GM members such as the viral fraction remain more elusive. Most gut viruses are bacteriophages (phages), i.e., viruses attacking bacteria in a host specific manner, and to a lesser extent, but also widely present, eukaryotic viruses, including viruses attacking human cells. Here, we utilize the deeply phenotyped COPSAC2010 birth cohort consisting of 700 infants to investigate how social, pre-, peri- and postnatal factors may influence the gut virome composition at one year of age, where fecal virome data was available from 645 infants. Among the different exposures studied, having older siblings and living in an urban vs. rural area had the strongest impact on gut virome composition. Differential abundance analysis from a total of 16,118 viral operational taxonomic units (vOTUs) (mainly phages, but also 6.1% eukaryotic viruses) identified 2,105 vOTUs varying with environmental exposures, of which 5.9% were eukaryotic viruses and the rest was phages. Bacterial hosts for these phages were mainly predicted to be within the Bacteroidaceae, Prevotellaceae, and Ruminococcaceae families, as determined by CRISPR spacer matches. Spearman correlation coefficients indicated strong co-abundance trends of vOTUs and their targeted bacterial host, which underlined the predicted phage-host connections. Further, our findings show that some gut viruses encode important metabolic functions and how the abundance of genes encoding these functions is influenced by environmental exposures. Genes that were significantly associated with early life exposures were found in a total of 42 vOTUs. 18 of these vOTUs had their life styles predicted, with 17 of them having a temperate lifestyle. These 42 vOTUs carried genes coding for enzymes involved in alanine, aspartate and glutamate metabolism, glycolysis-gluconeogenesis, as well as fatty acid biosynthesis. The latter implies that these phages could be involved in the utilization and degradation of major dietary components and affect infant health by influencing the metabolic capacity of their bacterial host. Given the importance of the GM in early life for maturation of the immune system and maintenance of metabolic health, these findings provide a valuable source of information for understanding early life factors that predispose for autoimmune and metabolic disorders.

microbiology↗

bioRxiv2022

An alternative method to multiple displacement amplification for preparing virome DNA in a way adapted for the sequencing of both double-strand and single-strand DNA viruses

Background: Bulk microbiome, as well as virome-enriched shotgun sequencing only reveals the double-stranded DNA (dsDNA) content of a given sample, unless specific treatments are applied. However, genomes of viruses often consist of a circular single-stranded DNA (ssDNA) molecule. Pre- treatment and amplification of DNA using the multiple displacement amplification (MDA) method enables conversion of ssDNA to dsDNA, but this process can lead to over-representation of these circular ssDNA genomes. A more recent alternative permits to bypass the amplification step, as library adapters are ligated to sheared and denatured DNA, after an end-modification step (xGen kit). However, the sonication step might shear ssDNA more efficiently than dsDNA, therefore introducing another bias in virome sequencing. These limitations prompted us to explore an alternative method of DNA preparation for sequencing mixed ssDNA and dsDNA viromes. Results: Using a synthetic mix of viral particles, we made use of the T7 DNA polymerase (T7pol) to convert viral circular ssDNA molecules to dsDNA, while preventing over-replication of such molecules, as is the case with the Phi29 DNA polymerase. Our findings indicate that using T7pol and a mix of degenerated primers to convert ssDNA to dsDNA prior library preparation is a good alternative to the currently used methods. It better represents the original synthetic mixtures compared to MDA or direct application of the xGen kit. Furthermore, when applied to two complex virome samples, the T7pol treatment improved both the richness and abundance in the Microviridae fraction. Conclusion: We conclude that T7pol pretreatment is preferable to MDA for the shotgun sequencing of viromes, which is easy to implement and inexpensive.

genomics↗

bioRxiv2022

Prophage taming by the adherent-invasive Escherichia coli LF82 upon macrophage infection

Adherent-invasive Escherichia coli (AIEC) strains are frequently recovered from stools of patients with dysbiotic microbiota. They have remarkable properties of adherence to the intestinal epithelium, and survive better than other E. coli in macrophages. The best studied of these AIEC is probably strain LF82, which was isolated from a Crohns disease patient. This strain contains five complete prophages, which have not been studied until now. We undertook their analysis, both in vitro and inside macrophages, and show that all of them form virions. The Gally prophage is by far the most active, generating spontaneously over 108 viral particles per mL of culture supernatants in vitro, more than 100-fold higher than the other phages. Gally is over-induced after a genotoxic stress generated by ciprofloxacin and trimethoprim. However, upon macrophage infection, Gally virion production is decreased by more than 20-fold, and the transcription profile of the prophage indicates that part of the structural module is specifically repressed while the replication module is overexpressed compared to unstressed culture conditions. We conclude that strain LF82 has evolved an efficient way to "tame" its most active prophage upon macrophage infection, which may participate to its good survival in macrophages. The results are discussed in light of the active lysogeny process. AUTHOR SUMMARYProphages are bacterial viruses stably integrated into their host, to which they can provide new functions, thus increasing their fitness in the environment. Thereby, they can participate to the virulence of bacterial pathogens. However, prophages are double-edged swords that can be awakened in response to genotoxic stresses, resulting in the death of their bacterial host. This raises the question of the effect of this type of stress in the natural environments where their bacterial hosts exert their virulence. In this study, we characterized the five active prophages present in Escherichia coli LF82, a strain belonging to the intestinal microbiota and suspected to be involved in Crohns disease via its ability to invade macrophages, a highly genotoxic environment. We show that LF82 inhibits the awakening of its prophages in macrophages, allowing it to survive there. Moreover, deletion of its most active prophage does not affect the viability of LF82 in this environment. These results show that LF82 has tamed its prophages in macrophages and also suggest that if they convey fitness advantages, they probably do so in environments differing from macrophages, and which remain to be discovered.

microbiology↗

bioRxiv2022

Streptococcus pyogenes Φ1207.3 is a temperate bacteriophage carrying the macrolide efflux gene pair mef(A)-msr(D) and capable to lysogenise different Streptococci

Streptococcus pyogenes prophage {phi}1207.3 (formerly Tn1207.3) carries the mef(A)-msr(D) efflux resistance genes, responsible for type M macrolide resistance. To investigate if {phi}1207.3 is a functional bacteriophage, we transferred the element from the original S. pyogenes host in a prophage-free and competence-deficient S. pneumoniae strain. Pneumococcal cultures of the {phi}1207.3-carrying lysogen were treated with mitomycin C to assess if {phi}1207.3 enters the lytic cycle. Mitomycin C induced a limited phage burst and a growth impairment resulting in early entrance in the stationary phase. To determine if {phi}1207.3 is able to produce mature phage particles we prepared concentrated supernatants recovered from a mitomycin C induced pneumococcal culture by sequential centrifugation and ultracentrifugation steps. Negative staining Transmission Electron Microscopy (TEM) of supernatants revealed the presence of phage particles with an icosahedral, electron dense capsid and a long, non-contractile tail, typical of a siphovirus. Quantification of {phi}1207.3 was performed by qPCR and semi-quantitatively by TEM. PCR quantified 3.34 x 104 and 6.06 x 104 excised forms of phage genome per ml of supernatant obtained from the untreated and mitomycin C treated cultures, respectively. By TEM, we estimated 3.02 x 103 and 7.68 x 103 phage particles per ml of supernatant. The phage preparations of {phi}1207.3 infected and lysogenised pneumococcal recipient strains at a frequency of 7.5 x 10-6 lysogens/recipient, but did not show sufficient lytic activity to form plaques. Phage lysogenisation efficiently occurred after 30 minutes of contact of the phages with the recipient cells and required a minimum of 103 phage particles. ImportanceBacteriophages play an important role in bacterial physiology and genome evolution. The widespread use of genome sequencing revealed that bacterial genomes can contain several different integrated temperate bacteriophages, which can constitute up to 20% of the genome. Most of these bacteriophages are only predicted in silico and never shown to be functional. In fact, it is often difficult to induce the lytic cycle of temperate bacteriophages. In this work, we show that {phi}1207.3, a peculiar bacteriophage originally from Streptococcus pyogenes, which can lysogenise different Streptococci and carries the macrolide resistance mef(A)-msr(D) gene pair, is capable of producing mature virions, but only at a low level, while not being able to produce plaques. This temperate phage is probably a partially functional phage, which seems to have lost lytic characteristics to specialize into lysogenisation. While we are not used to conceive phages separately from lysis, this behavior could actually be more frequent than expected.

microbiology↗

bioRxiv2022

Comparison of interferometric light microscopy with nanoparticle tracking analysis for the study of extracellular vesicles and bacteriophages

Research on extracellular vesicles (EVs) and bacteriophages (phages) has been steadily expanding over the past decades as many of their roles in medicine, biology, and ecosystems have been unveiled. Such interest has brought about the need for new tools to quantify and determine the sizes of these biological nanoparticles. A new device based on interferometric light microscopy (ILM), the Videodrop, was recently developed for this purpose. Here, we compared this new device to two nanoparticle tracking analysis (NTA) devices, the NanoSight and the ZetaView, for the analysis of EVs and phages. We used EVs isolated from bacteria, fecal samples, bovine milk and human cells, and phages of various sizes and shape, ranging from 30 to 120 nm of diameter. While NTA instruments correctly enumerated most phages, the Videodrop detected only the largest one, indicating a lower sensitivity threshold compared to the NTA devices. Nevertheless, the performance of the Videodrop compared favorably to that of the NTA devices for the determination of the concentration of eukaryotic EV samples. The NanoSight instrument provided the most precise size distributions but the Videodrop was by far the most time-saving device, making it worthy of consideration for studies conducted on a large number of samples.

cell biology↗

bioRxiv2021

Manual resolution of virome dark matter uncovers hundreds of viral families in the infant gut

The gut microbiome (GM) is shaped through infancy and plays a major role in determining susceptibility to chronic inflammatory diseases later in life. Bacteriophages (phages) are known to modulate bacterial populations in numerous ecosystems, including the gut. However, virome data is difficult to analyse because it mostly consists of unknown viruses, i.e. viral dark matter. Here, we manually resolved the viral dark matter in the largest human virome study published to date. Fecal viromes from a cohort of 647 infants at 1 year of age were deeply sequenced and analysed through successive rounds of clustering and curation. We uncovered more than ten thousand viral species distributed over 248 viral families falling within 17 viral order-level clades. Most of the defined viral families and orders were novel and belonged to the Caudoviricetes viral class. Bacterial hosts were predicted for 79% of the viral species using CRISPR spacers, including those in metagenomes from the same fecal samples. While Bacteroides-infecting Crassphages were present, novel viral families were more predominant, including phages infecting Clostridiales and Bifidobacterium. Phage lifestyles were determined for more than three thousand caudoviral species. Lifestyles were homogeneous at the family level for 149 Caudoviricetes families, including 32 families that were found to be virulent, while 117 were temperate. Virulent phage families were more abundant but temperate ones were more diverse and widespread. Together, the viral families found in this study represent a major expansion of existing bacteriophage taxonomy.

microbiology↗

bioRxiv2021

Prophages in the infant gut are largely induced, and may be functionally relevant to their hosts.

BackgroundBacteriophages are the most abundant biological entity on the planet, and are key components of any ecosystem they are present in. The gut virome is increasingly being implicated in disease states although these studies largely focus on lytic phages in adults. Here we identify prophages from a large infant cohort and investigate their potential functions. ResultsWe identified 10645 vOTUs from 662 metagenomes. No core virome was found: the most prevalent vOTU was identified in 70% of the samples. The most abundant and prevalent group of phages are a novel group closely related to Bacteroides phage Hanky p00. Functional annotation of this group revealed the presence of genes in the dDTP-L-rhamnose pathway, possibly involved in the production of capsular polysaccharides. We also found an abundance of diversity generating retroelements in the phages. Additionally, paired virome data allowed us to show that the majority of prophages are induced in at least one sample and that this is not affected by the use of antibiotics in the 4 weeks prior to sampling. ConclusionsProphages in the infant gut are largely unique to the individual and not shared. Most of them appear to be induced and so may be key drivers in shaping the bacterial microbiome. The most abundant group of phages are novel, and possess elements that may allow them to maintain differentially susceptible subpopulations of their host bacterium; whilst also containing diversity generating retroelements that could expand their host range. Prophages are important components of the infant gut that may have far reaching influences on the composition and function of the microbiome.

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↗

bioRxiv2019

The enemy from within: a prophage of Roseburia intestinalis systematically turns lytic in the mouse gut, driving bacterial adaptation by CRISPR spacer acquisition

Despite an overall stability in time of the human gut microbiota at the phylum level, strong temporal variations in species abundance have been observed. We are far from a clear understanding of what promotes or disrupts the stability of microbiome communities. Environmental factors, like food or antibiotic use, modify the gut microbiota composition, but their overall impacts remain relatively low. Phages, the viruses that infect bacteria, might constitute important factors explaining temporal variations in species abundance. Gut bacteria harbour numerous prophages, or dormant viruses. A breakdown of prophage dormancy can evolve through the selection of ultravirulent phage mutants, potentially leading to important bacterial death. Whether such phenomenon occurs in the mammals microbiota has been largely unexplored.\n\nHere we studied temperate phage-bacteria coevolution in gnotoxenic mice colonised with Escherichia coli and Roseburia intestinalis, a dominant symbiont of the human gut microbiota. We show that R. intestinalis harbors two active prophages, Jekyll and Shimadzu, and observed the systematic evolution of ultravirulent Shimadzu phage mutants, leading to a collapse of R. intestinalis population. In a second step, phage infection drove the fast evolution of host phage-resistance mainly through phage-derived spacer acquisition in a Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) array. Alternatively, phage resistance was conferred by a prophage originating from an ultravirulent phage with a restored ability to lysogenize.\n\nOur results demonstrate that prophages are the potential source of ultravirulent phages that can successfully infect most of the susceptible bacteria. This suggests that prophages can play important roles in the short-term temporal variations observed in the composition of the gut microbiota.

microbiology↗

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↗