Biology subjects

Lamy-Besnier, Q.

Publications and source records attributed to Lamy-Besnier, Q..

9 recordsLinked to original sources

bioRxiv2026

Gnotobiotic OMM12 mice support sustained Clostridioides difficile colonization without antibiotic pretreatment

Antibiotic-induced disruption of the intestinal microbiota predispose individuals to Clostridioides difficile infection (CDI). Although several animal models reproduce acute CDI, sustained colonization in the presence of a defined resident microbiota remains challenging to study. Here, we show that gnotobiotic OMM12 mice support sustained colonization for at least 20 days following oral challenge with either the reference CD630{Delta}erm strain or the clinical R20291 (RT027) strain, without prior antibiotic treatment. Early infection induced transient weight loss, rapid intestinal inflammation and transient shifts in the relative abundance of resident bacterial species. By day 20, inflammatory markers had largely resolved, and the resident microbiota had shifted back towards its baseline composition, despite continued detection of C. difficile vegetative cells, spores and toxins. Early bacterial community perturbations were not accompanied by detectable changes in the resident prophage induction. Moreover, whole-genome sequencing of C. difficile clones recovered at day 20 showed no detectable gut-specific genomic adaptation relative to the inoculum. Similar colonization kinetics and clinical outcomes were observed across independent experiments conducted over five years, supporting the consistent reproducibility of this model. Together, OMM12 mice provide a defined, antibiotic-free and experimentally tractable framework to investigate host-microbiota-pathogen interactions during sustained C. difficile colonization and a robust platform for therapeutic development.

microbiology↗

bioRxiv2025

Bacteriophage PAK_P3 genome structuration and dynamics during infection of Pseudomonas aeruginosa reveal specific interactions patterns

Bacteriophages, or phages, are highly abundant and diverse genomic entities that play an important role in microbial ecology, evolution, and horizontal gene transfer. While the dynamic changes in genome organization in cellular organisms have been well described, the 3D folding of phage genomes during the infection of their host is extremely limited. Understanding how phage genomes fold, invade and rearrange the genome of their host to functionally organize the optimal expression of their genes remains unknown. Here, we explore the spatial dynamics of the virulent double-stranded DNA phage PAK_P3 during infection of its host Pseudomonas aeruginosa and reveal how its genome rapidly decondenses to adopt a specific 3D organization that reflects its transcriptional program. Concomitantly, the host genome decondenses as gene expression wanes and transcription induced domains vanish. We also uncover specific and discrete bridging of the host and the phage genomes, showing how the phage genome exploits the spatial genome architecture of its host to succeed in its infection cycle. Our data highlights an unprecedented level of genome folding and gene expression regulation during a viral infection.

microbiology↗

bioRxiv2025

Third-generation cephalosporin antibiotics induce phage bursts in the human gut microbiome.

The use of antibiotics disrupts the gut microbiota, potentially leading to long-term health issues and the spread of resistance. To investigate the impact of antibiotics on phage populations, we followed 22 healthy individuals two weeks before and up to six months after a three-day course of 3rd-generation cephalosporins. The populations of phages very rarely encoded antibiotic resistance genes and were mostly temperate including many phage-plasmids. Gut phages remained individual-specific even after microbiome perturbation by antibiotics. Yet, we found a 20% decline in phage diversity the day after treatment, alongside blooms of a few (mostly virulent) phages. We suggest that these temporary dominant phages contribute to the recovery of gut bacterial diversity through kill-the-winner dynamics. This is supported by the finding that several phages targeted Parabacteroides distasonis, a bacterium thriving after cephalosporin treatment, and which only proliferated when these phages were absent.Our findings suggest that phages play a crucial role in the gut microbiotas response to antibiotics by contributing to the restoration of microbial balance and diversity. HighlightsO_LIIn healthy individuals, cephalosporin antibiotics cause an approx. 20% decline in gut phage richness that is restored after 30 days C_LIO_LIHuman gut phage communities are specific of each individual, which is retained post-antibiotic treatment C_LIO_LIAntibiotic perturbation causes an increase in the number of dominant virulent phages supporting kill-the-winner dynamics as mechanisms for shaping bacterial diversity C_LIO_LIDominance of Parabacteroides distasonis (after cephalosporin treatment) is likely disrupted through its specific phages C_LI eTOCAntibiotic-induced disruption of the gut microbiome leads to a transient loss of microbiome diversity (bacterial and viral) and causes blooms of bacteria and their viruses. Our analysis suggests that these viruses prey on dominant bacteria, prevent their dominance, and contribute to the recovery of microbiome balance. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=96 SRC="FIGDIR/small/636470v2_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@98c366org.highwire.dtl.DTLVardef@1446921org.highwire.dtl.DTLVardef@51f941org.highwire.dtl.DTLVardef@1c328ed_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2024

Differential translocation of bacteriophages across the intestinal barrier in health and Crohn's disease

Impaired intestinal barrier function is a major feature of Crohns disease (CD), leading to exacerbated inflammation in response to the microbiota. In this context, the translocation of intestinal bacteriophages (phages) and their effects on the host have been little investigated. We used phage fluorescence imaging coupled with ex-vivo and in-vitro models that mimic physiological and inflammatory conditions and found that phages can translocate across the intestinal barrier without disrupting its integrity. Although the translocation rate across the intestinal epithelium depended on phage morphology and the condition of the barrier, these factors did not influence the crossing of phage across the vascular endothelium. Virome analysis confirmed that viral sequences shared between blood and stool samples are more abundant in CD patients than healthy subjects, indicating that a barrier defect facilitates phage translocation from the gut to the bloodstream.

cell biology↗

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↗

bioRxiv2022

Chromosome folding and prophage activation reveal gut-specific genome dynamics of bacteria in the OMM12 consortium

Bacteria and their viruses, bacteriophages, are the most abundant entities of the gut microbiota, a complex community of microorganisms associated with human health and disease. In this ecosystem the interactions between these two key components are still largely unknown. In particular, the impact of the gut environment on bacteria and their associated prophages is yet to be deciphered. To gain insight into the activity of lysogenic phages within the context of their host genomes, we performed Hi-C on the 12 strains of the OMM12 synthetic bacterial community stably associated within mice gut (gnotobiotic mouse line OMM12) in both in vitro and in vivo conditions. High-resolution contact maps of the chromosome 3D organization of the bacterial genomes revealed a wide diversity of architectures, differences between environments and an overall stability over time in the gut of mice. The DNA contacts also pointed at 3D signatures of prophages leading to predict 16 of them as functional. We identified circularization signals and observed different 3D patterns depending on the condition. Concurrent virome analysis showed that 11 of these prophages produced viral particles in vivo and/or in vitro, and that OMM12 mice do not carry other intestinal viruses. By predicting functional prophages, the Hi-C approach unlocks the study of phage-bacteria interaction dynamics.

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 spatial heterogeneity of the gut limits bacteriophage predation leading to the coexistence of antagonist populations of bacteria and their viruses

Bacteria and their viruses, bacteriophages (phages), are the most abundant components of the mammalian gut microbiota where these two entities coexist over time. The ecological dynamics underlying the coexistence between these two antagonistic populations in the gut are unknown. We challenged a murine synthetic bacterial community with a set of virulent phages, to study the factors allowing phages-bacteria coexistence in the gut. We found that coexistence was neither dependent on an arms race between bacteria and phages, nor on the ability of phages to extend host range. Instead, our data suggest that some phage-inaccessible sites in the mucosa of the ileum serve as a spatial refuge for bacteria, which from there disseminate in the gut lumen. Luminal phages amplify by infecting luminal bacteria maintaining phage throughout the gut. We conclude that the heterogeneous distribution of microbes in the gut contributes to the long-term coexistence of phages with phage-susceptible bacteria. This observation could explain the persistence in the human gut of intestinal phages, such as the crAssphage, as well as the low efficiency of oral phage therapy against enteric pathogens in animal models and clinical trials.

microbiology↗