Biology subjects

Veyrier, F. J.

Publications and source records attributed to Veyrier, F. J..

9 recordsLinked to original sources

bioRxiv2026

Biosurfactant polysaccharide drives dispersal of exopolysaccharide-coated myxospores in Myxococcus xanthus

Bacterial spores are highly resilient cell forms, yet the organization of their protective surface layers in diderm species remains largely unexplored. For the social predatory soil bacterium Myxococcus xanthus, myxospore formation within multicellular fruiting body structures is a key ecological adaptation to surviving conditions of nutrient deprivation. These myxospores were long thought to be outwardly coated with so-called major spore coat (MASC) polysaccharide. Using polysaccharide-deficient mutant strains, electron microscopy, surface hydrophobicity assays, dye binding, and functional swarm complementation, we show that MASC instead forms a protective sub-surface outer-cortex layer, while the exopolysaccharide (EPS) glycocalyx inherited from vegetative cells constitutes the true outermost myxospore coat. EPS mediates inter-myxospore adhesion and supports collective behaviors, whereas secretion of biosurfactant polysaccharide (BPS) reduces myxospore surface stickiness, preventing excessive aggregation. BPS-deficient myxospores form persistent clumps, while EPS-deficient myxospores fail to aggregate or restore EPS-dependent swarm motility of vegetative cells. These results reveal a mechanistic interplay in which MASC serves as a sub-surface protective layer, EPS defines the exterior interface, and BPS tunes surface accessibility to regulate dispersal. Our findings overturn long-standing assumptions about myxospore architecture and illustrate a polysaccharide-driven strategy for controlling aggregation and readiness for germination. More broadly, these results highlight how social diderm bacteria leverage inherited and dynamically remodeled polysaccharide surfaces to coordinate multicellular development, in contrast to the rigid protein-based spore surfaces of Gram-positive species.

microbiology↗

bioRxiv2025

Comparative performance of reference-based metagenomic tools to identify species-level taxa among families of bacteria: benchmarking Mycobacteriaceae and Neisseriaceae

Hypotheses concerning the ecology and evolution of bacteria commonly relate to the presence and abundance of species in various settings and conditions. Shotgun metagenomics may address these hypotheses, which previously relied on PCR or culture. However, the problem of determining the presence/absence of a given species of interest is not trivial, particularly when closely related species are present in the reference database or metagenomic sample. Reference-based methods to detect species-level taxa mostly rely on thresholding of aligned reads or mapped k-mers or derivative metrics like genomic coverage, and create a trade-off between recall/completeness and precision/purity. New methods for species-level profiling (YACHT, metapresence and sylph) have recently been published. Here we test the performance of these methods, along with Kraken2/bracken and MetaPhlAn4, to detect related species of interest using simulated metagenomic samples from genomes in the families Mycobacteriaceae and Neisseriaceae, which contain closely related genomes. Among methods tested, metapresence, when used with an alignment quality filter, and sylph offer the best overall performance. Sylph maintains high precision but requires a depth of coverage greater than approximately 0.1x to reliably detect a genomes presence. Metapresence has a lower limit of detection of hundreds of reads but this is balanced against relatively lower precision. Both methods are relatively robust to the presence of reads from genomes outside the groups of interest. We demonstrate the application of these methods in two real-world datasets: a mycobacterial community in a drinking water system and the community of Neisseriaceae present in the human oral cavity. ImportanceDetecting which bacterial species of interest are present in a given sample is fundamental to studies of microbial ecology and evolution, and to applied microbiology (e.g. clinical diagnostics). Culture-dependent and independent (e.g. PCR) approaches are increasingly complemented by metagenomic approaches, but methods to accurately identify specific low-abundance species-level genomes in a shotgun metagenomic sample are still being refined. Here we comprehensively test YACHT, Kraken2/bracken, metapresence, MetaPhlAn4, and sylph using two simulated datasets of bacterial families, Mycobacteriaceae and Neisseriaceae that contain closely related species. Our simulations exploit natural genomic diversity to create a challenging benchmark. We demonstrate that metapresence and sylph perform best, with the former being well-suited to low-biomass host-associated datasets, and the latter with environmental metagenomic samples. This study is the first extensive benchmark of these methods for this use case, and demonstrates these methods can accurately identify closely related species of interest.

bioinformatics↗

bioRxiv2024

Phenotypic plasticity in bacterial elongation among closely related species

Cell elongation is a fundamental component of the bacterial cell cycle and has been studied over many decades, in part owing to its mechanisms being a target of numerous antibiotic classes. While several distinct modes of cell elongation have been described, these studies have largely relied on a handful of model bacterial species. Therefore, we have a limited view of the diversity of cell elongation approaches that are employed by bacteria, and how these vary in response to evolutionary and environmental influences. Here, by employing fluorescent D-amino acids (FDAAs) to track the spatiotemporal dynamics of elongation, we reveal previously unsuspected diversity of elongation modes among closely related species of the Caulobacteraceae, with species-specific combinations of dispersed, midcell and polar elongation that can be either unidirectional or bidirectional. Using genetic, cell biology, and phylogenetic approaches, we demonstrate that evolution of unidirectional-midcell elongation is accompanied by changes in the localization pattern of the peptidoglycan synthase PBP2 and infer that elongation complexes display a high degree of phenotypic plasticity, both among the Caulobacteraceae and more widely among the Alphaproteobacteria. Demonstration that even closely related bacterial species employ highly distinct mechanisms of cell elongation reshapes our understanding of the evolution and regulation of bacterial cell growth, with broad implications for bacterial morphology, adaptation, and antibiotic resistance.

microbiology↗

bioRxiv2024

Evolutionary insights into the emergence of virulent Leptospira spirochetes

Pathogenic Leptospira are spirochete bacteria which cause leptospirosis, a re-emerging zoonotic disease of global importance. Here, we use a recently described lineage of environmental-adapted leptospires, which are evolutionarily the closest relatives of the highly virulent Leptospira species, to explore the key phenotypic traits and genetic determinants of Leptospira virulence. Through a comprehensive approach integrating phylogenomic comparisons with in vitro and in vivo phenotyping studies, we show that the evolution towards pathogenicity is associated with both a decrease of the ability to survive in the environment and the acquisition of strategies that enable successful host colonization. This includes the evasion of the human complement system and the adaptations to avoid activation of the innate immune cells. Moreover, our analysis reveals specific genetic determinants that have undergone positive selection during the course of evolution in Leptospira, contributing directly to virulence and host adaptation as demonstrated by gain-of-function and knock-down studies. Taken together, our findings define a new vision on Leptospira pathogenicity, identifying virulence attributes associated with clinically relevant species, and provide insights into the evolution and emergence of these life-threatening pathogens. AUTHOR SUMMARYLeptospira is a highly heterogeneous bacterial genus and leptospires are ubiquitous bacteria found as free-living saprophytes or as pathogens that can cause disseminated infections, from asymptomatic carriage in rats to lethal acute infection in both humans and animals. Leptospirosis is thus causing over one million cases and nearly 60,000 deaths annually. Despite leptospirosis being a re-emerging zoonosis, little is known about the ability of the etiologic agent to adapt to different hosts and cause disease. Here, combining genome analysis and phenotyping studies of representative species and mutant strains, we show that only a small group of species have the ability to evade the host immune system and cause disease. In addition, our findings provide key insight into the emergence of pathogens from a saprophytic ancestor through events of gene gain and genome reduction.

microbiology↗

bioRxiv2023

Pan-species transcriptomic analysis reveals a constitutive adaptation against oxidative stress for the highly virulent Leptospira species.

Different environments exert selective pressures on bacterial populations, favoring individuals with particular genetic traits that are well-suited for survival in those conditions. Evolutionary mechanisms such as natural selection have, therefore, shaped bacterial populations over time selecting, in a stepwise manner, the fittest bacteria that gave rise to the modern lineages that exist today. Advances in genomic sequencing, computational analysis, and experimental techniques continue to enhance our understanding of bacterial evolution and its implications. Nevertheless, these are often limited to genomic comparisons of closely related species. In the present study, we introduce Annotator-RNAtor, a graphical user interface (GUI) method for performing pan-species transcriptomic analysis and studying intragenus evolution. The pipeline uses third-party software to infer homologous genes in various species and highlight differences in the expression of the core-genes. To illustrate the methodology and demonstrate its usefulness, we focus on the emergence of the highly virulent Leptospira subclade known as P1+, which includes the causative agents of leptospirosis. Here, we expand on the genomic study through the comparison of transcriptomes between species from P1+ and their related P1-counterparts (low-virulent pathogens). In doing so, we shed light on differentially expressed pathways and focused on describing a specific example of adaptation based on a differential expression of PerRA-controlled genes. We showed that P1+ species exhibit higher expression of the katE gene, a well-known virulence determinant in pathogenic Leptospira species correlated with greater tolerance to peroxide. Switching PerRA alleles between P1+ and P1-species demonstrated that the lower repression of katE and greater tolerance to peroxide in P1+ species was solely controlled by PerRA and partly caused by a PerRA amino-acid permutation. Overall, these results demonstrate the strategic fit of the methodology and its ability to decipher adaptive transcriptomic changes, not observable by comparative genome analysis, that may have been crucial for the emergence of these pathogens. Author summaryNatural selection is one of the central mechanisms of the bacterial evolution. Speciation events and adaptation occurs such as mutations, deletions and horizontal gene transfers to enhance our understanding of evolution. Nevertheless, these are often limited to genomic comparisons between species. Here, we are developed a graphical user interface method, named Annotator-RNAtor, to perform pan-species transcriptomic analysis and studying intragenus evolution. To illustrate the methodology, we focus on the emergence of the virulent Leptospira species, causative agents of leptospirosis. We shed light on a differential regulation of several PerRA-controlled genes in P1+ Leptospira subclade (highly virulent pathogens) compared to P1-Leptospira subclade (low virulent pathogens). P1+ species exhibit higher expression of the catalase-encoding gene katE, than P1-species, correlating with a greater ability to withstand peroxide. Additionally, we demonstrate that the difference in katE expression is mediated only by PerRA and the residue 89 of the PerRA protein participates on this regulation. These findings highlight the importance to decipher adaptative transcriptomic changes to fully understand the emergence of pathogenic species.

microbiology↗

bioRxiv2022

Adaptive radioresistance of Enterohemorrhagic Escherichia coli O157:H7 results in genomic loss of shiga toxin-encoding prophages

Enterohemorragic Escherichia coli (EHEC) O157:H7 is a foodborne pathogen producing shiga toxins (Stx1 and Stx2), can cause hemorrhagic diarrhea, and life-threatening infections. O157:H7 strain EDL933 carries prophages CP-933V and BP-933W that encode shiga toxin genes (stx1 and stx2 respectively). The aim of this work was to investigate the mechanisms of adaptive resistance of EHEC strain EDL933 to a typically "lethal" dose of {gamma}-irradiation (1.5 kGy). Adaptive selection through six passages of exposure to 1.5 kGy resulted in the loss of CP-933V and BP-933W prophages from the genome and mutations within three genes: wrbA, rpoA, and Wt_02639 (molY). Three selected EHEC clones that became irradiation-adapted to the 1.5 kGy dose (C1, C2 and C3) demonstrated increased resistance to oxidative stress, sensitivity to acid pH, and decreased cytotoxicity to Vero cells. To confirm that loss of prophages plays a role in increased radioresistance, C1 and C2 clones were exposed to bacteriophage containing lysates. Although, phage BP-933W could lysogenize C1, C2, and E.coli K-12 strain MG1655, it was not found to have integrated into the bacterial chromosome in C1-{Phi} and C2-{Phi} lysogens. Interestingly, for the E. coli K-12 lysogen (K12-{Phi}), BP-933W DNA had integrated at the wrbA gene (K12-{Phi}). Both C1-{Phi} and C2-{Phi} lysogens regained sensitivity to oxidative stress, were more effectively killed by a 1.5 kGy {gamma}-irradiation dose and had regained cytotoxicity and acid resistance phenotypes. Further, the K12-{Phi} lysogen became cytotoxic, more sensitive to {gamma}-irradiation and oxidative stress and slightly more acid resistant. ImportanceGamma ({gamma})-irradiation of food products can provide an effective means of eliminating bacterial pathogens such as enterohemorrhagic Escherichia coli (EHEC) O157:H7, a significant foodborne pathogen that can cause severe disease due to the production of Shiga toxins. To decipher the mechanisms of adaptive resistance of the O157:H7 strain EDL933, we evolved clones of this bacterium resistant to a lethal dose of {gamma}-irradiation by repeatedly exposing bacterial cells to irradiation following a growth restoration over six successive passages. Our findings provide evidence that adaptive selection involved modifications in the bacterial genome including deletion of the CP-933V and BP-933W prophages. These mutations in EHAC O157:H7 resulted in loss of stx1, stx2, loss of cytotoxicity to epithelial cells and decreased resistance to acidity, critical virulence determinants of EHEC, concomitant with increased resistance to lethal irradiation and oxidative stress. These findings demonstrate that the potential adaptation of EHEC to high doses of radiation would involve elimination of the Stx encoding phages and likely lead to a substantial attenuation of virulence.

microbiology↗

bioRxiv2020

The oxidative stress response and virulence of pathogenic Leptospira are controlled by the interplay of two peroxide stress regulators

Pathogenic Leptospira are the causative agents of leptospirosis, the most widespread zoonotic infectious disease. Leptospirosis is a potentially severe and life-threatening emerging disease with highest burden in sub-tropical areas and impoverished populations. Mechanisms allowing pathogenic Leptospira to survive inside a host and induce acute leptospirosis are not fully understood. The ability to resist deadly oxidants produced by the host during infection is pivotal for Leptospira virulence. We have previously shown that genes encoding defenses against oxidants in L. interrogans are repressed by PerRA (encoded by LIMLP_10155), a peroxide stress regulator of the Fur family. In this study, we describe the identification and characterization of another putative PerR-like regulator (LIMLP_05620) in L. interrogans. Protein sequence and phylogenetic analyses indicated that LIMLP_05620 displayed all the canonical PerR amino acid residues and is restricted to pathogenic Leptospira clades. We therefore named this PerR-like regulator PerRB. In L. interrogans, the PerRB regulon is distinct from that of PerRA. While a perRA mutant had a greater tolerance to peroxide, inactivating perRB led to a higher tolerance to superoxide, suggesting that these two regulators have a distinct function in the adaptation of L. interrogans to oxidative stress. The concomitant inactivation of perRA and perRB resulted in a higher tolerance to both peroxide and superoxide and, unlike the single mutants, a double perRAperRB mutant was avirulent. Interestingly, this correlated with major changes in gene and non-coding RNA expression. Notably, several virulence-associated genes (clpB, ligA/B, and lvrAB) were repressed. By obtaining a double mutant in a pathogenic Leptospira strain, our study has uncovered an interplay of two PerRs in the adaptation of Leptospira to oxidative stress with a putative role in virulence and pathogenicity, most likely through the transcriptional control of a complex regulatory network. Author summaryLeptospirosis is a widespread infectious disease responsible for over one million of severe cases and 60 000 fatalities annually worldwide. This neglected and emerging disease has a worldwide distribution, but it mostly affects populations from developing countries in sub-tropical areas. The causative agents of leptospirosis are pathogenic bacterial Leptospira spp. There is a considerable deficit in our knowledge of these atypical bacteria, including their virulence mechanisms. In addition to the Leptospira PerRA regulator that represses defenses against peroxide, we have identified and characterized a second PerR regulator in pathogenic Leptospira species (PerRB) that participates in Leptospira tolerance to superoxide. Phenotypic and transcriptomic analyses of single PerRA and PerRB mutants suggest that the two PerRs fulfill distinct functions in the adaptation to oxidative stress. Concomitant inactivation of PerRA and PerRB resulted in a higher tolerance to both peroxide and superoxide. Moreover, the perRAperRB mutant lost its virulence. Major changes in gene expression, including a decreased expression of several virulence factors, were observed in the double perRAperRB mutant. Our study suggests that PerRA and PerRB cooperate to orchestrate a complex regulatory network involved in Leptospira virulence.

microbiology↗

bioRxiv2020

Bacterial glycocalyx integrity drives multicellular swarm biofilm dynamism

Bacterial surface exopolysaccharide (EPS) layers are key determinants of biofilm establishment and maintenance, leading to the formation of higher-order 3D structures conferring numerous survival benefits to a cell community. In addition to a specific EPS glycocalyx, we recently revealed that the social {delta}-proteobacterium Myxococcus xanthus secretes a novel biosurfactant polysaccharide (BPS), with both EPS and BPS polymers required for type IV pilus (T4P)-dependent swarm expansion via spatio-specific biofilm expression profiles. Thus the synergy between EPS and BPS secretion somehow modulates the multicellular lifecycle of M. xanthus. Herein, we demonstrate that BPS secretion functionally-activates the EPS glycocalyx via its destabilization, fundamentally altering the characteristics of the cell surface. This impacts motility behaviours at the single-cell level as well as the aggregative capacity of cells in groups via EPS fibril formation and T4P assembly. These changes modulate structuration of swarm biofilms via cell layering, likely contributing to the formation of internal swarm polysaccharide architecture. Together, these data reveal the manner by which the interplay between two secreted polymers induces single-cell changes that modulate swarm biofilm communities.

microbiology↗

bioRxiv2019

Genome sequencing and functional characterization of a Dictyopanus pusillus fungal extract offers a promising alternative for lignocellulose pretreatment of oil palm residues

The pretreatment of biomass is a critical requirement of bio-renewable fuel production from lignocellulose. Although current processes primarily involve chemical and physical approaches, the biological breakdown of lignin using enzymes and microorganisms is quickly becoming an interesting eco-friendly alternative to classical processes. As a result, bioprospection of wild fungi from naturally occurring lignin-rich sources remains a suitable method to uncover and isolate new species exhibiting ligninolytic activity. In this study, wild species of white rot fungi were collected from Colombian forests based on their natural wood decay ability and high capacity to secrete oxidoreductases with high affinity for phenolic polymers such as lignin. Based on high activity obtained from solid-state fermentation using a lignocellulose source from oil palm as matrix, we describe the isolation and whole-genome sequencing of Dictyopanus pusillus, a wild basidiomycete fungus exhibiting ABTS oxidation as an indication of laccase activity. Functional characterization of a crude enzymatic extract identified laccase activity as the main enzymatic contributor to fungal extracts, an observation supported by the identification of 13 putative genes encoding for homologous laccases in the genome. To the best of our knowledge, this represents the first report of an enzymatic extract exhibiting laccase activity in the Dictyopanus genera, offering means to exploit this species and its enzymes for the delignification process of lignocellulosic by-products from oil palm.

bioengineering↗