Biology subjects

Cote, J.-P.

Publications and source records attributed to Cote, J.-P..

7 recordsLinked to original sources

bioRxiv2026

Highly effective modulator therapy hinders the emergence of hyperbiofilm variants of Pseudomonas aeruginosa PA14 grown in a cystic fibrosis lung model

Pseudomonas aeruginosa is an opportunistic pathogen that often adopts persistent phenotypes -- such as biofilm formation-- that are associated with chronic infections including those observed in the cystic fibrosis (CF) lung Recently, highly effective modulator therapy (HEMT) such as elexacaftor/tezacaftor/ivacaftor (ETI) has significantly improved the quality of life of people with CF (pwCF). Yet a potential direct impact of ETI on the physiology of P. aeruginosa during growth to a remodeled CF lung environment has remained unexplored. To address this, we conducted an experimental evolution using P. aeruginosa PA14 grown in CF-like conditions in the presence or absence of ETI. We observed a marked reduction in biofilm formation and in the number of small colony variants (SCVs) for P. aeruginosa populations evolved under ETI treatment. Also, sequencing of specific evolved clones exhibiting distinct morphotypes revealed two major observations: (i) P. aeruginosa-evolved communities exposed to ETI retained a wild type-like morphotype and, (ii) P. aeruginosa populations evolved in the absence of ETI adopted a SCV-like phenotype with mutations acquired in the Wsp chemosensory pathway. Furthermore, analysis of evolved populations revealed that ETI treatment likely modulates c-di-GMP pools by driving mutations in an enzyme catalyzing the degradation of this second messenger. Overall, our work suggests that ETI has the potential to hinder the acute to chronic biofilm transition of P. aeruginosa thereby limiting the emergence of variants typically associated with long-term CF lung colonization.

microbiology↗

bioRxiv2026

High-throughput dual bioreporter screening reveals distributed regulation of biofilm matrix components in Staphylococcus aureus

Staphylococcus aureus biofilm formation is a key factor enabling persistent infections. However, the lack of efficient high-throughput tools previously limited systematic study of its regulatory mechanisms. Here, we used high-efficiency transduction to construct two luminescent bioreporter libraries, each probing a distinct biofilm regulatory pathway. Derived from the Nebraska Transposon Mutant Library, these libraries enabled rapid, quantitative screening of biofilm-associated gene expression in a high-throughput format. Our screens revealed a surprising lack of overlap in the regulation of the two biofilm components investigated: adhesin synthesis and extracellular DNA production. However, we identified mntR as a key gene involved in the expression of both biofilm components and confirmed the previously reported role of yjbH. Cross-lineage validation showed that these regulators retain conserved significance across multiple S. aureus backgrounds, although their phenotypic effects varied across strains. Collectively, this work provides a versatile, high-throughput framework to dissect the regulatory networks underlying complex phenotypes in S. aureus. ImportanceBiofilm formation is a major contributor to the persistence and treatment failure of Staphylococcus aureus infections, yet its regulatory network remains incompletely understood. We developed a high-throughput bioreporter platform that enables genome-wide screening of biofilm-associated gene expression across nearly 2,000 transposon mutants. Using this approach, we show that key biofilm processes, adhesion and extracellular DNA release, are controlled by largely distinct regulatory networks, and we identify mntR as a previously unrecognized regulator shared by both pathways. Beyond these biological insights, our work provides a versatile and readily adaptable strategy for dissecting complex regulatory systems in S. aureus and other bacterial species.

microbiology↗

bioRxiv2026

Aggregation-mediated microcolony shields bacteria from contact-dependent competition and maintains phenotypic heterogeneity

Bacteria are adaptable microorganisms capable of surviving in a wide variety of environments. One common strategy for persistence and attachment to surfaces is the formation of microcolonies, often controlled by cell surfaces structures that mediate adhesion such as fimbriae. In this study, we show that type 1 fimbriae, and other adhesins structures such as autotransporter adhesins, trigger microcolony formation which confer resistance against a broad range of short-range contact-dependent weapons (e.g. T6SS, T4SS, CDI) but not against long-range diffusible weapons (e.g. diffusible toxins like colicins). Interestingly, we identify "sheltered" bacteria within microcolonies that benefit from collective protection without expressing the adhesive structure. Our findings demonstrate that adhesive structures not only improve survival in hostile environments by promoting microcolony formation but also maintain phenotypic heterogeneity within the microcolony, highlighting the importance of social behavior in bacterial adaptation to changing environments.

microbiology↗

bioRxiv2025

Comparative Analysis of Gene Importance in Escherichia coli Across Growth Conditions

As the ability to synthesize complete genomes becomes increasingly accessible, the question of what should compose those sequences is becoming more prevalent. However, identifying genes essential for the survival of an organism is challenging, as gene essentiality is a nuanced concept that heavily depends on context. In this study, we identified growth medium-specific important genes by performing transposon mutagenesis in Escherichia coli BW25113 and sequencing mutant populations at multiple time points in three growth media. Our analysis revealed a core set of 412 important genes shared across all conditions, along with distinct medium-specific gene sets of varying sizes. By analyzing temporal variations in read counts for each gene, we identified additional sets of genes whose inactivation causes a lighter impact on fitness. We used this dataset to define medium-specific gene modules required to sustain robust growth under each condition. Our study underscores the context-dependent nature of gene essentiality and marks a step toward refining the concept from a universal list to a more nuanced, condition-specific framework, which will be invaluable for future genome design efforts. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=159 SRC="FIGDIR/small/679994v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@1a6863corg.highwire.dtl.DTLVardef@1b6e594org.highwire.dtl.DTLVardef@9a879dorg.highwire.dtl.DTLVardef@13d5df5_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2023

Metabolic connections between folate and peptidoglycan pathways in Pseudomonas aeruginosa inform rational design of a dual-action inhibitor

Peptidoglycan is an important bacterial macromolecule that confers cell shape and structural integrity, and a key antibiotic target. The synthesis and turnover of peptidoglycan are carefully coordinated with other cellular processes and pathways. Although there are established connections between peptidoglycan and DNA replication or outer membrane biosynthesis, connections between peptidoglycan and folate metabolism are comparatively unexplored. Folate is an essential cofactor for bacterial growth and required for the synthesis of many important metabolites. Here we show that inhibition of folate synthesis in the important Gram-negative pathogen Pseudomonas aeruginosa has downstream effects on peptidoglycan metabolism and integrity. Folate inhibitors reduced expression of the AmpC {beta}-lactamase through perturbation of peptidoglycan recycling, potentiating the activity of {beta}-lactams normally cleaved by that resistance enzyme. Folate inhibitors also synergized with fosfomycin, which inhibits MurA - the first committed step in peptidoglycan synthesis - resulting in dose-dependent formation of round cells that underwent explosive lysis.The insights from this work were used to design a dual-active inhibitor that overcomes NDM-1-mediated meropenem resistance and synergizes with the folate inhibitor, trimethoprim. This work shows that folate and peptidoglycan metabolism are intimately connected and offers new opportunities to exploit this relationship in strategies to overcome antibiotic resistance in Gram-negative pathogens.

microbiology↗

bioRxiv2023

Probiotic Lactobacillus strains decrease the susceptibility of Salmonella Typhimurium to the last resort antibiotic azithromycin.

Bacteria are involved in numerous interactions during infection and among host-associated microbial populations. Salmonella enterica serovar Typhimurium is a foodborne pathogen of great importance as well as a model organism to study interactions within a microbial community. In this study, we found that S. Typhimurium becomes tolerant to azithromycin when co-cultured with strains of Lactobacillus. Similarly, acidified media, from cell-free supernatant of Lactobacillus cultures for instance, also induced the tolerance of S. Typhimurium to azithromycin. The addition of membrane disruptors restored the normal sensitivity to azithromycin in acidified media, but not when Lactobacillus was present. These results suggested that the acidification of the media led to modification in envelope homeostasis, but that a different mechanism promoted the tolerance to azithromycin in the presence of Lactobacillus strains. To further understand how Lactobacillus strains modify the sensitivity of S. Typhimurium to azithromycin, a high-throughput assay was carried using the single gene deletion collection of the S. Typhimurium (1) in coculture with L. rhamnosus and (2) in sterile acidic conditions (pH 5.5 media only). As expected, both screens identified genes involved in envelope homeostasis and membrane permeability. Our results also suggest that changes in the metabolism of S. Typhimurium induce the tolerance observed in the presence of L. rhamnosus. Our results thus highlight two different mechanisms by which Lactobacillus strains induce tolerance of S. Typhimurium to antibiotics. ImportanceThis study provides valuable insights into the intricate interactions between bacteria during infections and within host-associated microbial communities. Specifically, it sheds light on the significant role of Lactobacillus strains in inducing antibiotic tolerance in Salmonella enterica serovar Typhimurium, a critical foodborne pathogen and model organism for microbial community studies. The findings not only uncover the mechanisms underlying this antibiotic tolerance but also reveal two distinct pathways through which Lactobacillus strains might influence Salmonellas response to antibiotics. Understanding these mechanisms has the potential to enhance our knowledge of bacterial infections and may have implications for the development of strategies to combat antibiotic resistance in pathogens like Salmonella. Furthermore, our results underscore the necessity to explore beyond the direct antimicrobial effects of antibiotics, emphasizing the broader microbial community context.

microbiology↗

bioRxiv2022

Central metabolism is a key player in E. coli biofilm stimulation by sub-MIC antibiotics

Exposure of Escherichia coli to sub-inhibitory antibiotics stimulates biofilm formation through poorly characterized mechanisms. Using a high-throughput Congo Red binding assay to report on biofilm matrix production, we screened [~]4000 E. coli K12 deletion mutants for deficiencies in this biofilm stimulation response. Mutants lacking acnA, nuoE, or lpdA failed to respond to sub-MIC novobiocin, implicating central metabolism and aerobic respiration in biofilm stimulation. These genes are members of the ArcA/B regulon - controlled by a respiration-sensitive two-component system. Mutants of arcA and arcB had a pre-activated phenotype, where biofilm formation was already high relative to wild type in vehicle control conditions and failed to increase further with the addition of sub-MIC antibiotics. Supporting a role for respiratory stress, the biofilm stimulation response was inhibited when nitrate was provided as an alternative electron acceptor. Deletion of genes encoding the nitrate respiratory machinery abolished its effects, and nitrate respiration increased during growth with sub-MIC antibiotics. In probing the generalizability of biofilm stimulation, we found that the stimulation response to translation inhibitors was minimally affected by nitrate supplementation. Finally, using a metabolism-sensitive dye, we showed spatial co-localization of increased respiration with sub-MIC bactericidal antibiotics. By characterizing the biofilm stimulation response to sub-MIC antibiotics at a systems level, we identified multiple avenues for design of therapeutics that impair bacterial stress management.

microbiology↗