Biology subjects

Findlay, B.

Publications and source records attributed to Findlay, B..

8 recordsLinked to original sources

bioRxiv2026

LC-MS Metabolomics Reveals No Significant Impact of Microbial Inoculation with Bacillus velezensis and Lachnum sp. on Cranberry Metabolome

Sustainable agriculture has driven the increased exploration of microbial inoculants as a promising strategy to promote plant growth, improve crop yield, and stimulate secondary metabolism to enhance crop nutritional quality. However, the influence of microbial inoculation on the cranberry fruit metabolome under field conditions remains poorly understood. This study investigated the effects of inoculating cranberry (Vaccinium macrocarpon) plants with Bacillus velezensis EB37 and Lachnum sp. EC5, applied individually and in combination, on cranberry fruit phytochemistry. Over two harvest years (2019 and 2021), cranberries were collected from treated and control plots and analysed using untargeted and targeted HPLC-MS-based metabolomics. Untargeted metabolomic analysis revealed no significant treatment-associated differences in the cranberry fruit metabolome. Instead, samples clustered strongly by harvest year, indicating that annual environmental variation had a greater influence on metabolite composition than microbial inoculation. Targeted quantification of six representative phenolic compounds (chlorogenic acid, catechin, p-coumaric acid, phloridzin, myricetin, and quercetin) likewise showed no significant differences between treated and untreated cranberries. These findings indicate that microbial inoculation alone does not substantially alter the cranberry fruit metabolome, including major phenolic compounds, under field conditions. This study underscores how multiple factors, such as environmental conditions, can affect the outcome of microbial inoculation under field conditions and suggests that additional interventions may be required to achieve microbiome-based improvements in cranberry fruit quality.

plant biology↗

bioRxiv2025

Pantetheinamides that inhibit the growth of intracellular Salmonella Typhimurium

The metabolic adaptability of intracellular pathogens, such as the Gram-negative Salmonella enterica serovar Typhimurium (STm), enables their survival in nutrient-restricted host environments, while also presenting an opportunity for selective antimicrobial targeting. Herein, we report the synthesis and screening of a small pantetheinamide library aimed at inhibiting the proliferation of STm within macrophages. Two lead compounds exhibited selective activity against intracellular STm and reduced bacterial burden in a murine colitis model. Mechanistic studies suggest their primary mode of action to be the inhibition of coenzyme A (CoA) biosynthesis via the PanD-PanZ regulatory complex, which is absent in host cells. Importantly, resistance pressure to our compound was shown to be significantly stronger in nutrient-limited media compared to nutrient-rich media, supporting the targeting of nutrient stress as a strategy to delay resistance. This work highlights the value of inhibiting pathogen-specific metabolic vulnerabilities in combination with host defence mechanisms to develop novel antimicrobials.

microbiology↗

bioRxiv2025

Large scale laboratory evolution uncovers clinically relevant collateral antibiotic sensitivity

The increasing prevalence of antibiotic resistance is a critical challenge, necessitating the development of strategies to mitigate the evolution of resistance. Collateral sensitivity (CS)-based sequential therapies have been proposed to mitigate resistance evolution. However, the evolutionary repeatability of CS across different experimental conditions and its clinical relevance remain underexplored, hindering its potential for translation into clinical practice. Here, we evolve 20-24 lineages of E. coli against tigecycline (TIG) and piperacillin (PIP), antibiotics suggested to produce CS, through three separate laboratory adaptive evolution (ALE) platforms to test for the robustness of CS interactions and the effect of the choice of ALE on CS evolution. We generate over 130 resistant mutants and 540 resistance and collateral sensitivity measurements to identify a CS relationship between TIG and polymyxin B (POL) that is highly repeatable across all the ALEs tested, suggesting that this CS interaction is preserved across different evolution microenvironments. We determine the mechanism of this novel CS by showing that cells resistant to TIG deactivate the Lon protease and overproduce negatively charged exopolysaccharides, which in turn attracts the polycationic POL and renders cells hypersensitive to the drug. We find that this CS relationship is present in a clinical dataset of over 750 uropathogenic MDR E. coli isolates, and show that the soft agar gradient evolution (SAGE) platform best predicts collateral effects (CS, neutrality or cross resistance) in this dataset. Our study provides a framework for identifying robust CS with clinical implications that can reduce the emergence of resistance to our existing antibiotics.

microbiology↗

bioRxiv2025

Tripartite loops reverse antibiotic resistance

Antibiotic resistance threatens to undo many of the advancements of modern medicine. A slow antibiotic development pipeline makes it impossible to outpace bacterial evolution, making alternative strategies essential to combat resistance. In this study, we introduce cyclic antibiotic regimens composed of three drugs or "tripartite loops" to contain resistance within a closed drug cycle. We show that as bacteria sequentially evolve resistance to the drugs in a loop, they continually trade their past resistance for fitness gains, reverting back to sensitivity. Through fitness and genomic analyses, we find that tripartite loops guide bacterial strains towards evolutionary paths that mitigate fitness costs and reverse resistance to component drugs in the loops and drive levels of resensitization not achievable through previously suggested pairwise regimens. These findings open the door to sequential antibiotic regimens with high resensitization frequencies which will improve the longevity of existing antibiotics even in the face of antibiotic resistance. TOC O_FIG O_LINKSMALLFIG WIDTH=188 HEIGHT=200 SRC="FIGDIR/small/631305v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@1d67a3corg.highwire.dtl.DTLVardef@1f315c7org.highwire.dtl.DTLVardef@1aee0eorg.highwire.dtl.DTLVardef@2e892_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2024

De novo evolution of antibiotic resistance to Oct-TriA1

The rise of antimicrobial resistance as a global health concern has led to a strong interest in compounds able to inhibit the growth of bacteria without detectable levels of resistance evolution. A number of these compounds have been reported in recent years, including the tridecaptins, a small family of lipopeptides typified by the synthetic analogue octyl-tridecaptin A1. Hypothesizing that prior reports of negligible resistance evolution have been due in part to limitations in the laboratory evolution systems used, we have attempted to select for resistant mutants using a soft agar gradient evolution (SAGE) system developed by our lab. Following optimization of the media conditions by incorporation of the anti-synaeresis agent xanthan gum into the agar matrix, we successfully evolved high-level resistance to both octyl-tridecaptin A1 as well as the challenging lipopeptide antibiotic polymyxin B. Decreased tridecaptin susceptibility was linked to mutations in outer membrane proteins ompC, lptD and mlaA, with the effect of these genes confirmed through a mix of allelic replacement and knockout studies. Overall, this work demonstrates the robust evolutionary potential of bacteria, even in the face of challenging antimicrobial agents.

microbiology↗

bioRxiv2024

Backward collateral sensitivity can restore antibiotic susceptibility

The prevalence of antibiotic resistance continues to rise, rendering many valuable drugs ineffective. Antibiotic cycling regimens that incorporate collateral sensitivity (CS), the phenomenon where resistance to one antibiotic leads to hypersensitivity to another, are hypothesized to slow the evolution of antibiotic resistance. However, the repeatability of CS interactions and their ability to drive bacterial extinction and resensitizations remain unclear. In this study, we thoroughly investigate four drug pairs proposed for cycling regimens with experimental evolution. We find that reported pairwise CS interactions are not always robust, and even when they are, forward CS (where resistance to drug A leads to hypersensitivity to drug B) does not reliably reduce resistance or promote bacterial extinction. Instead, we find that if evolution of resistance to drug B in naive cells is associated with CS to drug A, a phenomenon we term backward CS, drug A-resistant cells can be rendered more sensitive to A again when resistance to B develops. We describe the mechanism of resistance disruption via backward CS in an aminoglycoside-{beta}-lactam pair, where perturbation of the electron transport chain to inhibit aminoglycoside entry impairs {beta}-lactam efflux. Overall, we highlight the importance of applying antibiotics in the correct order in cycling regimens and identify robust CS interactions that may be used to design treatment regimens less likely to lead to resistance evolution. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=129 SRC="FIGDIR/small/622341v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@1745531org.highwire.dtl.DTLVardef@85172corg.highwire.dtl.DTLVardef@1b48784org.highwire.dtl.DTLVardef@12d2153_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOTOC GraphicC_FLOATNO C_FIG

evolutionary biology↗

bioRxiv2023

Enhancer Binding Proteins Regulate Natural Product Biosynthesis in Photorhabdus laumondii

Biosynthetic gene clusters are readily transferred between microbes through horizontal gene transfer, but to provide benefit to their host they must be induced to high levels during times of stress. Working with the insect pathogen Photorhabdus laumondii, here we study the effect of plasmid-induced stress on natural product biosynthesis. We find that the expression plasmid pARO190 alone was sufficient to induce production of an array of natural products, and that the induction could be increased with heterologous expression of either bacterial enhancer binding proteins or a random DNA sequence. Overall, this suggests that generalized stress may be an effective way to increase production of natural products in P. laumondii.

microbiology↗

bioRxiv2021

The ubiquitous terpene geosmin is a warning chemical

Known as the smell of earth after rain, geosmin is an odorous terpene detectable by humans at picomolar concentrations. Geosmin production is heavily conserved in actinobacteria, myxobacteria, cyanobacteria, and some fungi, but its biological activity is poorly understood. We theorized that geosmin was an aposematic signal used to indicate the unpalatability of toxin-producing microbes, discouraging predation by eukaryotes. Consistent with this hypothesis we found that geosmin and the related terpene 2-methylisoborneol reduced predation of Streptomyces coelicolor and Myxococcus xanthus by the bacteriophagous Caenorhabditis elegans. Predation was restored by the removal of both terpene biosynthetic pathways or deletion of the C. elegans ASE sensory neuron, and resulted in the death of the nematodes. Geosmin itself was non-toxic. This is the first warning chemical to be identified in bacteria or fungi, and suggests molecular signalling affects microbial predator-prey interactions in a manner similar to the well-studied visual markers of poisonous animal prey.

microbiology↗