Biology subjects

GHIGO, J.-M.

Publications and source records attributed to GHIGO, J.-M..

14 recordsLinked to original sources

bioRxiv2026

Global analysis of trimeric autotransporters reveals phylogenetically restricted secretion mechanism adaptations

Autotransporters are important diderm bacterial cell-surface proteins and are virulence factors enabling surface attachment and adhesion to other bacteria. These proteins are composed of a signal peptide, a {beta}-barrel that serves as an anchor in the outer membrane, and an extracellular passenger domain responsible for adhesion. Autotransporters rely on BamA for their insertion in the outer membrane (OM), but specific helper proteins, such as TpgA and SadB have been described to promote the surface exposure of trimeric autotransporters (TAAs), a specialized subclass of autotransporters forming homotrimer adhesins. To identify domains or proteins that could help TAAs secretion, we analyzed a recent dataset of all trimeric autotransporters found across the bacterial tree of life. While we did not find additional potential helper proteins for OM translocation, we found that the extended signal peptide (ESPR), sometimes found in TAAs, is associated with longer adhesins both for TAAs and type Va autotransporter adhesins. ESPRs are found in all bacteria but Fusobacteriia and Alphaproteobacteria. We also identified in Burkholderia, Veillonellales and Pasteurellales a DUF2827 domain proteins as potential glycosyltransferases constantly associated with TAAs. Finally, e describe the existence of extra periplasmic domains in some TAAs, featuring either a coiled-coil domain or a peptidoglycan-binding domain. Our research show that there is a strong phylogenetic separation between Terrabacteria, almost invariably displaying additional periplasmic domains, and Gracilicutes (represented by Proteobacteria) where they are largely absent. This suggests that the presence these domains might be correlated with specific Terrabacteria OM features. Using the diderm Firmicute Veillonella parvula as a model, we demonstrate that the absence of periplasmic domains in TAAs leads to a significant protein degradation, yet they are not essential for adhesin trimerization or secretion. Additionnaly, we show that the SLH domains of V. parvula TAAs excludes them from the septum during division, but that this exclusion is not crucial for adhesin function or stability in the tested conditions. Altogether, these results illuminate the genetic flexibility and modularity of autotransporters, enhancing our understanding of this important class of adhesins in diderm bacteria.

microbiology↗

bioRxiv2025

A Chryseobacterium massiliae pore-forming MACPF domain protein mediates intra and interspecies competition against Bacteroides

Microbiota play crucial roles in host health, including protection against pathogens through competitive interactions between commensal and pathogenic bacteria that are mediated by direct contact or secreted factors. We previously demonstrated that Chryseobacterium massiliae, a zebrafish commensal, protects larvae against infection by Flavobacterium covae (formerly F. columnare). Here, we investigated whether interference interactions contribute to this protective effect. We found that C. massiliae culture supernatant inhibits F. covae growth and a transposon mutagenesis screen identified mutants lacking this activity. All identified mutants carried insertions in a gene encoding a protein homologous to Bacteroidales BSAP pore-forming toxins, characterized by a Membrane Attack Complex/Perforin (MACPF) domain. We showed that this protein, which we named CSAP-1 (for Chryseobacterium Secreted Antimicrobial Protein) displays bactericidal, pore-forming activity that lyses F. covae cells. Unlike BSAP proteins from Bacteroides spp., CSAP-1 displays broader antagonistic activity, targeting multiple species across the Flavobacterium and Chryseobacterium genera - thus mediating interspecies and intergenus inhibition within Bacteroidetes. Although CSAP-1 is not essential for the in vivo protective effect of C. massiliae, administration of purified CSAP-1 alone confers significant protection to zebrafish larvae against sensitive F. covae infection. This study therefore identifies CSAP-1 as the first MACPF protein from C. massiliae with broad-spectrum inhibitory activity against members of the order Flavobacteriales. These findings highlight CSAP-1 as a promising candidate for the development of novel antimicrobial strategies and warrant further mechanistic investigation.

microbiology↗

bioRxiv2024

Identification of V. parvula and S. gordonii adhesins mediating co-aggregation and its impact on physiology and mixed biofilm structure

The dental plaque is a polymicrobial community where biofilm formation and co-aggregation, the ability to bind to other bacteria, play a major role in the construction of an organized consortium. One of its prominent members is the anaerobic diderm Veillonella parvula, considered as a bridging species, which growth depends on lactate produced by oral Streptococci. Understanding how V. parvula co-aggregates and the impact of aggregation has long been hampered due to the lack of appropriate genetic tools. Here we studied co-aggregation of the naturally competent strain V. parvula SKV38 with various oral bacteria and its effect on cell physiology. We show that V. parvula requires different trimeric autotransporters of the type V secretion system to adhere to oral Streptococci and Actinomyces. In addition, we describe a novel adhesin of Streptococcus gordonii, VisA (SGO_2004), as the protein responsible for co-aggregation with V. parvula. Finally, we show that co-aggregation does not impact cell-cell communication, which is mainly driven by environmental sensing, but plays an important role in the architecture and species distribution within the biofilm.

microbiology↗

bioRxiv2023

Bile-induced biofilm formation in Bacteroides thetaiotaomicron requires magnesium efflux by an RND pump

Bacteroides thetaiotaomicron is a prominent member of the human gut microbiota contributing to nutrient exchange, gut function, and maturation of the hosts immune system. This obligate anaerobe symbiont can adopt a biofilm lifestyle and it was recently shown that B. thetaiotaomicron biofilm formation is promoted by the presence of bile, a process also requiring a B. thetaiotaomicron extracellular DNase, which is not, however, regulated by bile. Here we showed that bile induces the expression of several Resistance-Nodulation-Division (RND) efflux pumps and that inhibiting their activity with a global competitive efflux inhibitor impaired bile-dependent biofilm formation. We then showed that, among the bile-induced RND-efflux pumps, only the tripartite BT3337-BT3338-BT3339 pump, re-named BipABC (for Bile Induced Pump A (BT3337), B (BT3338) and C (BT3339), is required for biofilm formation. We demonstrated that BipABC is involved in the efflux of magnesium to the biofilm extracellular matrix, which leads to a decrease of eDNA concentration. The release of magnesium in the biofilm matrix also impacts biofilm structure, potentially by modifying the electrostatic repulsion forces within the matrix, reducing interbacterial distance and allowing bacteria to interact more closely and form denser biofilms. Our study therefore identifies a new molecular determinant of B. thetaiotaomicron biofilm formation in response to bile salts and provides a better understanding on how an intestinal chemical cue regulates biofilm formation in a major gut symbiont. IMPORTANCEBacteroides thetaiotaomicron is a prominent member of the human gut microbiota able to degrade dietary and host polysaccharides, altogether contributing to nutrient exchange, gut function, and maturation of the hosts immune system. This obligate anaerobe symbiont can adopt a biofilm community lifestyle, providing protection against environmental factors that might, in turn, protect the host from dysbiosis and dysbiosis-related diseases. It was recently shown that B. thetaiotaomicron exposure to intestinal bile promotes biofilm formation. Here we reveal that a specific B. thetaiotaomicron membrane efflux pump is induced in response to bile, leading to the release of magnesium ions, potentially reducing electrostatic repulsion forces between components of the biofilm matrix. This leads to a reduction of interbacterial distance and strengthens the biofilm structure. Our study therefore provides a better understanding of how bile promotes biofilm formation in a major gut symbiont, potentially promoting microbiota resilience to stress and dysbiosis events.

microbiology↗

bioRxiv2023

Bridges instead of boats? The Mla system of diderm Firmicute Veillonella parvula reveals an ancestral transenvelope core of phospholipid trafficking

Despite extensive characterisation of envelope biogenesis systems in diderm bacteria, glycerophospholipid (GPL) trafficking remains poorly understood, and has only been studied in a handful of model species. Within the Proteobacteria, the maintenance of lipid asymmetry (Mla) system facilitates retrograde GPL trafficking via six proteins, MlaA-F. GPLs are extracted from the outer leaflet of the outer membrane by the lipoprotein MlaA which associates with porin trimers, then shipped through the periplasmic space by the chaperone MlaC, which finally delivers GPLs to the inner membrane complex formed by MlaBDEF. Here, we investigate GPL trafficking in Veillonella parvula, a diderm member of the Firmicutes which encodes an Mla system devoid of MlaA and MlaC. V. parvula {Delta}mla mutants display phenotypes characteristic of disrupted lipid asymmetry such as hypervesiculation and detergent hypersensitivity, and lipid content analysis from outer membrane vesicles reveals an enrichment for the major lipid component phosphatidylethanolamine. Interestingly, suppressor analysis identifies mutations in tamB that rescue detergent hypersensitivity and hypervesiculation of {Delta}mla strains, supporting the involvement of these two systems in antagonistic GPL trafficking functions across diverse bacterial lineages. A combination of structural modeling and subcellular localisation assays shows that MlaDVp is longer than in classical diderm models and forms a transenvelope bridge, encoding both an inner membrane-localised MCE domain and an outer membrane {beta}-barrel. These results strongly suggest that V. parvula possesses a minimal Mla system for GPL trafficking, replacing the need for chaperones and outer membrane lipoproteins by directly connecting the two membranes. Finally, phylogenomic analysis indicates that this MlaEFD self-contained architecture is widely distributed in diderm bacteria and most likely represents the ancestral functional core of the Mla system, which subsequently increased in complexity in Proteobacteria and closely related phyla following the emergence of MlaABC. Our work broadens the diversity of current models of GPL trafficking in diderm bacteria, challenging the paradigm set by classical models and shedding light on the evolution of a crucial system in the biogenesis and maintenance of the bacterial outer membrane.

microbiology↗

bioRxiv2023

Anti-diarrheal drug loperamide induces dysbiosis in zebrafish microbiota via bacterial inhibition

BackgroundPerturbations of animal-associated microbiomes from chemical stress can affect host physiology and health. While dysbiosis induced by antibiotic treatments and disease are well known, chemical, non-antibiotic drugs have recently been shown to induce changes in microbiome composition, warranting further exploration. Loperamide is an opioid-receptor agonist drug widely prescribed drug for treating acute diarrhea in humans. Loperamide is also used as a tool to study the impact of bowel dysfunction in animal models by inducing constipation, but its effect on host-associated microbiota is poorly characterized. ResultsWe used conventional and gnotobiotic larval zebrafish models to show that in addition to host-specific effects, loperamide also has anti-bacterial activities that directly induce changes in microbiota diversity. This dysbiosis is due to changes in bacterial colonization, since germ-free zebrafish mono-reconventionalized with bacterial strains sensitive to loperamide are colonized up to 100-fold lower when treated with loperamide. Consistently, the bacterial diversity of gnotobiotic zebrafish colonized by a mix of representative bacterial strains is affected by loperamide treatment. ConclusionOur results demonstrate that loperamide, in addition to host effects, also induces dysbiosis in a vertebrate model, highlighting that established treatments can have underlooked secondary effects on microbiota structure and function. This study further provides a insights for future studies exploring how common medications directly induce changes in host-associated microbiota. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=103 SRC="FIGDIR/small/537295v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@11c5492org.highwire.dtl.DTLVardef@f44f40org.highwire.dtl.DTLVardef@17eff8corg.highwire.dtl.DTLVardef@bb691a_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2022

Bacterial capsular polysaccharides with antibiofilm activity share common biophysical and electrokinetic properties

Bacterial biofilms are surface-attached communities that are difficult to eradicate due to a high tolerance to antimicrobial agents. The use of non-biocidal surface-active compounds to prevent the initial adhesion and aggregation of bacterial pathogens is a promising alternative to antibiotic treatments and several antibiofilm compounds have been identified, including some capsular polysaccharides released by various bacteria. However, the lack of chemical and mechanistic understanding of the activity of these high-molecular-weight polymers limits their use for control of biofilm formation. Here, we screened a collection of 32 purified capsular polysaccharides and identified seven new compounds with non-biocidal activity against biofilms formed by Escherichia coli and/or Staphylococcus aureus. We analyzed the polysaccharide mobility under applied electric field conditions and showed that active and inactive polysaccharide polymers display distinct electrokinetic properties and that all active macromolecules shared high intrinsic viscosity features. Based on these characteristics, we identified two additional antibiofilm capsular polysaccharides with high density of electrostatic charges and their permeability to fluid flow. Our study therefore provides insights into key biophysical properties discriminating active from inactive polysaccharides. This characterization of a specific electrokinetic signature for polysaccharides displaying antibiofilm activity opens new perspectives to identify or engineer non-biocidal surface-active macromolecules to control biofilm formation in medical and industrial settings. Significance statementSome bacteria produce non-biocidal capsular polysaccharides that reduce the adhesion of bacterial pathogens to surfaces. Due to a lack of molecular and structural definition, the basis of their antiadhesion activity is unknown, thus hindering their prophylactic use for biofilm control. Here, we identified nine new active compounds and compared their composition, structure and biophysical properties with other inactive capsular polysaccharides. Despite the absence of specific molecular motif, we demonstrate that all active polysaccharides share common electrokinetic properties that distinguish them from inactive polymers. This characterization of the biophysical properties of antibiofilm bacterial polysaccharide provides key insights to engineer non-biocidal and bio-inspired surface-active compounds to control bacterial adhesion in medical and industrial settings.

microbiology↗

bioRxiv2021

Selection for non-specific adhesion is a driver of FimH evolution increasing Escherichia coli biofilm capacity

Bacterial interactions with surfaces rely on the coordinated expression and interplay of surface exposed adhesion factors. However, how bacteria dynamically modulate their vast repertoire of adhesins to achieve surface colonization is not yet well-understood. We used experimental evolution and positive selection for improved adhesion to investigate how an initially poorly adherent Escherichia coli strain increased its adhesion capacities to abiotic surfaces. We showed that all identified evolved clones acquired mutations located almost exclusively in the lectin domain of fimH, the gene coding for the -D-mannose-specific tip adhesin of type 1 fimbriae. While most of these fimH mutants showed reduced mannose- binding ability, they all displayed enhanced binding to abiotic surfaces, indicating a trade-off between FimH-mediated specific and non-specific adhesion properties. Several of the identified mutations were already reported in FimH lectin domain of pathogenic and environmental E. coli, suggesting that, beyond patho-adaptation, FimH microevolution favoring non-specific surface adhesion could constitute a selective advantage for natural E. coli isolates. Consistently, although E. coli deleted for the fim operon still evolves an increased adhesion capacity, mutants selected in the {Delta}fim background are outcompeted by fimH mutants revealing clonal interference for adhesion. Our study therefore provides insights into the plasticity of E. coli adhesion potential and shows that evolution of type 1 fimbriae is a major driver of the adaptation of natural E. coli to colonization.

microbiology↗

bioRxiv2021

Bacteroides thetaiotaomicron uses a widespread extracellular DNase to promote bile-dependent biofilm formation

Bacteroides thetaiotaomicron is a gut symbiont that inhabits the mucus layer and adheres to and metabolizes food particles, contributing to gut physiology and maturation. Whereas adhesion and biofilm formation could be key features for B. thetaiotaomicron stress resistance and gut colonization, little is known about the determinants of B. thetaiotaomicron biofilm formation. We previously showed that the B. thetaiotaomicron reference strain VPI-5482 is a poor in vitro biofilm former. Here we demonstrated that bile, a gut-relevant environmental cue, triggers the formation of biofilm in many B. thetaiotaomicron isolates and common gut Bacteroidales species. We identified the genetic determinants of this bile-dependent biofilm formation and showed that it involves the production of the DNase BT3563, degrading extracellular DNA, in biofilms formed in the presence of bile. Our study therefore identifies a physiologically relevant condition inducing B. thetaiotaomicron biofilm and shows that, in contrast to the biofilm-promoting role played by bacterial eDNA scaffold in Firmicutes and Proteobacteria models, degradation of eDNA by BT3563 DNAse and its widespread homologs is required to achieve B. thetaiotaomicron bile-dependent biofilm formation.

microbiology↗

bioRxiv2020

Lifestyle-specific S-nitrosylation of protein cysteine thiols regulates Escherichia coli biofilm formation and resistance to oxidative stress

Communities of bacteria called biofilms are characterized by reduced diffusion, steep oxygen and redox gradients and specific properties compared to individualized planktonic bacteria. In this study, we investigated whether signaling via nitrosylation of protein cysteine thiols (S-nitrosylation), regulating a wide range of functions in eukaryotes, could also specifically occur in biofilms and contribute to bacterial adaptation to this widespread lifestyle. We used a redox proteomic approach to compare cysteine S-nitrosylation in aerobic and anaerobic biofilm and planktonic Escherichia coli cultures and we identified proteins with biofilm-specific S-nitrosylation status. Using bacterial genetics and various phenotypic screens, we showed that impairing S-nitrosylation in proteins involved in redox homeostasis and amino acid synthesis such as OxyR, KatG and GltD altered important biofilm properties, including motility, biofilm maturation or resistance to oxidative stress. Our study therefore revealed that S-nitrosylation constitutes a physiological basis underlying functions critical for E. coli adaptation to the biofilm environment.

microbiology↗

bioRxiv2020

Gnotobiotic rainbow trout (Oncorhynchus mykiss) model reveals endogenous bacteria that protect against Flavobacterium columnare infection

The health and environmental risks associated with antibiotic use in aquaculture have promoted bacterial probiotics as an alternative approach to control fish infections in vulnerable larval and juvenile stages. However, evidence-based identification of probiotics is often hindered by the complexity of bacteria-host interactions and host variability in microbiologically uncontrolled conditions. While these difficulties can be partially resolved using gnotobiotic models harboring no or reduced microbiota, most host-microbe interaction studies are carried out in animal models with little relevance for fish farming. Here we studied host-microbiota-pathogen interactions in a germ-free and gnotobiotic model of rainbow trout (Oncorhynchus mykiss), one of the most widely cultured salmonids. We demonstrated that germ-free larvae raised in sterile conditions displayed no significant difference in growth after 35 days compared to conventionally-raised larvae, but were extremely sensitive to infection by Flavobacterium columnare, a common freshwater fish pathogen causing major economic losses worldwide. Furthermore, re-conventionalization with 11 culturable species from the conventional trout microbiota conferred resistance to F. columnare infection. Using mono-re-conventionalized germ-free trout, we identified that this protection is determined by a commensal Flavobacterium strain displaying antibacterial activity against F. columnare. Finally, we demonstrated that use of gnotobiotic trout is a suitable approach for the systematic identification of both endogenous and exogenous probiotic bacterial strains that may protect teleostean hosts against F. columnare and other pathogens. This study establishes a novel and ecologically-relevant gnotobiotic model that will improve the sustainability and health of aquaculture.

microbiology↗

bioRxiv2020

Visualizing the dynamics of exported bacterial proteins with the chemogenetic fluorescent reporter FAST

Bacterial proteins exported to the cell surface play key cellular functions. However, despite the interest to study the localization of surface proteins such as adhesins, transporters or hydrolases, monitoring their dynamics in live imaging remains challenging, due to the limited availability of fluorescent probes remaining functional after secretion. In this work, we used the Escherichia coli intimin and the Listeria monocytogenes InlB invasin as surface exposed scaffolds fused with the recently developed chemogenetic fluorescent reporter protein FAST. Using both membrane permeant (HBR-3,5DM) and non-permeant (HBRAA-3E) fluorogens that fluoresce upon binding to FAST, we demonstrated that fully functional FAST can be exposed at the cell surface and specifically tagged on the external side of the bacterial envelop in both diderm and monoderm bacteria. Our work opens new avenues to study of the organization and dynamics of the bacterial cell surface proteins.

microbiology↗

bioRxiv2020

Mining zebrafish microbiota reveals key community-level resistance against fish pathogen infection

The long-known resistance to pathogens provided by host-associated microbiota fostered the notion that adding protective bacteria could prevent or attenuate infection. However, the identification of endogenous or exogenous bacteria conferring such protection is often hindered by the complexity of host microbial communities. Here, we used zebrafish and the fish pathogen Flavobacterium columnare as a model system to study the determinants of microbiota-associated colonization resistance. We compared infection susceptibility in germ-free, conventional and re-conventionalized larvae and showed that a consortium of 10 culturable bacterial species are sufficient to protect zebrafish. Whereas survival to F. columnare infection does not rely on host innate immunity, we used antibiotic dysbiosis to alter zebrafish microbiota composition, leading to the identification of two different protection strategies. We first identified that the bacterium Chryseobacterium massiliae individually protects both larvae and adult zebrafish. We also showed that an assembly of 9 endogenous zebrafish species that do not otherwise protect individually confer a community-level resistance to infection. Our study therefore provides a rational approach to identify key endogenous protecting bacteria and promising candidates to engineer resilient microbial communities. It also shows how direct experimental analysis of colonization resistance in low-complexity in vivo models can reveal unsuspected ecological strategies at play in microbiota-based protection against pathogens.

microbiology↗

bioRxiv2020

Capsular polysaccharides cross-regulation modulates Bacteroides thetaiotaomicron biofilm formation

Bacteroides thetaiotaomicron is one of the most abundant gut symbiont species, whose contribution to host health through its ability to degrade diet polysaccharides and mature the immune system is under untense scrutiny. By contrast, adhesion and biofilm formation, which are potentially involved in gut colonization, microbiota structure and stability, have hardly been investigated in this intestinal bacterium. To uncover B. thetaiotaomicron biofilm-related functions, we performed a transposon mutagenesis in the poor biofilm-forming reference strain VPI 5482 and showed that capsule 4, one of the eight B. thetaiotaomicron capsules, hinders biofilm formation. We then showed that the production of capsules 1, 2, 3, 5 and 6 also inhibits biofilm formation and that decreased capsulation of the population correlated with increased biofilm formation, suggesting that capsules could be masking adhesive surface structures. We also showed that, by contrast, capsule 8 displayed intrinsic adhesive properties. Finally, we demonstrated that BT2934, the wzx homolog of B. thetaiotaomicron glycosylation locus, competes with capsule production and therefore impacts its adhesion capacity. This study identified regulation of capsular polysaccharides as a major determinant of B. thetaiotaomicron biofilm formation, providing new insights into how modulation of different B. thetaiotaomicron surface structures affect in vitro biofilm formation.

microbiology↗