Biology subjects

McDougald, D.

Publications and source records attributed to McDougald, D..

7 recordsLinked to original sources

bioRxiv2026

Contact- and diffusion-based allelopathic interaction of a seaweed with coral holobionts

Shifts from coral-dominated to macroalgal-dominated reef systems have become increasingly common in many coastal regions worldwide. Coral-macroalgal interactions have been shown to be generally detrimental to coral health, with macroalgal allelopathic compounds able to exert serious and even lethal effects on coral at various stages of growth and development. Previous studies have shown that the coral-associated microbial communities play important roles in coral health and mitigating external environmental stress, including macroalgal contact stress. However, it remains unclear whether changes in the coral microbiome have an influence on the Symbiodiniaceae community composition, and if such changes subsequently affect coral health. In this study, we examined changes in both the coral microbiome and the Symbiodiniaceae communities of two Singaporean coral species (Pocillopora acuta and Merulina ampliata) when exposed to both direct and water-mediated macroalgal contact with Lobophora sp. This was investigated using 16S rRNA gene amplicon sequencing to characterize the coral microbiome, and ITS2 variable region sequencing to profile the Symbiodiniaceae communities. Although no significant differences were observed for the coral microbiomes and Symbiodiniaceae communities at both alpha-and beta- diversity levels between control and macroalgal contact treated fragments within each coral species, inter-colony variations in responses to macroalgal contact were observed for both the coral microbiome and Symbiodiniaceae communities of M. ampliata. These results suggest that coral colonies vary in the mechanisms that allow mitigation of the effects of macroalgal contact, and in their resilience to macroalgal-induced stress.

ecology↗

bioRxiv2026

Co-dissemination of anti-phage defence systems and multidrug resistance is associated with the seventh-pandemic Vibrio cholerae defensome

Anti-phage defence systems in Vibrio cholerae are increasingly recognised as cargo on mobile genetic elements (MGE) that also carry antimicrobial resistance (AMR) and virulence genes, but a population-scale view of how the V. cholerae defensome partitions between the pandemic O1 clade and the environmental non-O1 reservoir has been missing. We analysed 1,740 RefSeq V. cholerae genomes (773 O1, 967 non-O1) sampled from 1934 to 2022 across 60 countries. The non-O1 reservoir harboured 283 defence subtypes and 55 families absent from any O1 genome. O1 was dominated by abortive infection systems (33.5% vs 14.0% in non-O1; P < 0.001). Defence and prophage burden were inversely related within O1 (R = -0.15) but weakly positive in non-O1, and an 80-year reconstruction revealed mirror trajectories of rising defence diversity and declining prophage burden in O1, coincident with the emergence of SXT/R391 ICE-borne AMR. A bipartite network identified strong defence-AMR associations (Phi up to 0.80), nominating AbiE, AbiJ, dCTPdeaminase, Menshen, Retron-I_A and Lamassu-Fam as candidate co-acquired cargo. UMAP clustering resolved seven distinct defensome lineages, and a Random Forest classifier trained on the defence profile alone predicted-MDR (genotypic MDR) status with pooled cross-validated AUC of 0.96, AUC of 0.92 within O1 only and 0.93 within non-O1 only and generalised across decades (AUC = 0.88) and regions (AUC = 0.92); a five-system signature (AbiE, BREX-I, CBASS-II, dCTPdeaminase, AbiJ) achieved AUC = 0.91. These data implicate the AMR-bearing mobilome rather than phage predation as the principal driver of anti-phage defence evolution in pandemic V. cholerae, and support further evaluation of the defensome as a genomic correlate of multidrug resistance for surveillance use, pending validation in prospectively phenotyped cohorts. Impact statementThe seventh cholera pandemic, ongoing for more than six decades, is driven by a single Vibrio cholerae lineage whose success has been linked to a small set of horizontally acquired mobile genetic elements. Recent work has shown that these elements also carry anti-phage defence systems, but the population-scale picture has been bounded by small genome sets and short clinical sampling windows. We provide a pan-genomic map spanning 1934 to 2022, based on annotation of 1,740 publicly available V. cholerae genomes (with quantitative reconstruction limited to 1970 onwards, where per-window sample sizes support it). We identify the non-O1 environmental reservoir as a substantially larger source of bacterial immune diversity than previously appreciated, document a qualitatively different defence-mechanism balance between pandemic and environmental compartments, and nominate specific candidate defence systems for future mechanistic and long-read characterisation as co-occurring cargo on the SXT/R391 family of integrative conjugative elements. The resource and findings provide an evidence base for V. cholerae genomic surveillance and inform the design of phage-therapy efforts directed at circulating pandemic lineages.

microbiology↗

bioRxiv2026

Mixed-species interactions constrain diversification and shape biofilm evolution

Long-term experimental evolution (LTEE) provides a powerful framework for dissecting how ecological interactions shape adaptive trajectories. Here, we evolved Klebsiella pneumoniae, Pseudomonas protegens and Pseudomonas aeruginosa in single- and mixed-species biofilm communities for 24 weeks and tracked changes in population dynamics, phenotypes, and genomes. In mono-species evolution, all three species exhibited similar dynamics of adaptation, with steadily increasing biofilm-associated populations. In contrast, mixed-species communities displayed striking compositional shifts, with P. protegens emerging as the dominant biofilm former and K. pneumoniae dominating the supernatant. Phenotypic assays revealed that all three species showed enhanced biofilm formation, but this increase was consistently greater in isolates from mono-species than mixed species communities, with P. protegens showing the largest gains. Beyond biofilm production, biofilm-associated isolates exhibited greater phenotypic diversification than planktonic isolates, whereas mixed-species interactions constrained diversification. Whole-genome sequencing identified species-specific putative adaptations such as csrD in K. pneumoniae, yfiBNR in P. protegens, and cheA in P. aeruginosa that arose early, persisted, and were enriched in mixed-species isolates. Functional assays confirmed that these mutations were indeed adaptive by enhancing biofilm formation, with yfiBNR mutations in P. protegens increasing cyclic-di-GMP production and producing a competitive advantage that recapitulated its dominance in LTEE biofilms. Our findings show that biofilm evolution fosters phenotypic diversification, whereas interspecific interactions shape adaptive trajectories, with specific mutations acting as keystone drivers of long-term ecological dynamics in multi-species communities.

microbiology↗

bioRxiv2024

A model, mixed-species urinary catheter biofilm derived from spinal cord injury patients

Complex multispecies biofilms consistently colonise the interior of indwelling urinary catheters, causing persistent asymptomatic bacteriuria and frequent symptomatic episodes in long-term catheterized individuals. Simple single-species models often fail to capture the complexities of mixed-species interactions, leading to limited conclusions about microbial behaviour and treatment efficacy. Additionally, using lab-based organisms can obscure the genomic diversity found in real-world infections. The primary objective of this study was to establish a stable and reproducible in vitro biofilm model derived from the multi-species clinical flora associated with catheter-related infections, reflecting the dynamics of in vivo infections. Biofilm samples from clinical catheters of spinal cord injury (SCI) participants were used to establish polymicrobial macro-fluidic models within catheters. Metagenomic techniques using short-read Illumina and long-read Oxford Nanopore sequencing was used to assess the community composition, produce metagenome-assembled genomes (MAGs), analyse strain-level phylogeny diversity and single nucleotide polymorphisms (SNP) of isolates. Antibiotic resistance tests using our models highlighted the drastic differences between planktonic bacteria, single-species, and multispecies biofilms. In silico analysis of antibiotic resistance further revealed a high number of varied resistance genes present in these communities. The models developed and characterised in this study are expected to facilitate more effective strategies to prevent and treat catheter-associated infections.

microbiology↗

bioRxiv2024

Prediction of symptomatic and asymptomatic bacteriuria in spinal cord injury patients using machine learning

BackgroundIndividuals with spinal cord injuries (SCI) frequently rely on urinary catheters to drain urine from the bladder, making them susceptible to asymptomatic and symptomatic catheter-associated bacteriuria and urinary tract infections (UTI). Proper identification of these conditions lacks precision, leading to inappropriate antibiotic use which promotes selection for drug-resistant bacteria. Since infection often leads to dysbiosis in the microbiome and correlates with health status, this study aimed to develop a machine learning-based diagnostic framework to predict potential UTI by monitoring urine and/or catheter microbiome data, thereby minimising unnecessary antibiotic use and improving patient health. ResultsMicrobial communities in 609 samples (309 catheter and 300 urine) with asymptomatic and symptomatic bacteriuria status were analysed using 16S rRNA gene sequencing from 27 participants over 18 months. Microbial community compositions were significantly different between asymptomatic and symptomatic bacteriuria, suggesting microbial community signatures have potential application as a diagnostic tool. A significant decrease in local (alpha) diversity was noted in symptomatic bacteriuria compared to the asymptomatic bacteriuria (P < 0.01). Beta diversity measured in weighted unifrac also showed a significant difference (P < 0.05) between groups. Supervised machine learning models trained on amplicon sequence variant (ASVs) counts and bacterial taxonomic abundances (Taxa) to classify symptomatic and asymptomatic bacteriuria with a 10-fold cross-validation approach. Combining urine and catheter microbiome data improved the model performance during cross-validation, yielding a mean area under the receiver operating characteristic curve (AUROC) of 0.91-0.98 (Interquartile range, IQR 0.93-0.96) and 0.78-0.91 (IQR 0.86-0.88) for ASVs and taxonomic features, respectively. ASVs and taxa features achieve a mean AUROC of 0.85-1 (IQR 0.93-0.98) and 0.69-0.99 (IQR 0.78-0.88) in the independent held-out test set, respectively, signifying their potential in differentiating symptomatic and asymptomatic bacteriuria states. ConclusionsOur findings demonstrate that signatures within catheter and urine microbiota could serve as tools to monitor the health status of SCI patients. Establishing an early warning system based on these microbial signatures could equip physicians with alternative management strategies, potentially reducing UTI episodes and associated hospital costs, thus significantly improving patient quality of life while mitigating the impact of drug-resistant UTI.

microbiology↗

bioRxiv2022

Low Level Whole-Brain Radiation Enhances Theranostic Potential Of Single Domain Antibody Fragments For HER2-Positive Brain Metastases

BackgroundSingle-domain antibody fragments (aka VHH, [~]13 kDa) are promising delivery systems for brain tumor theranostics; however, achieving efficient delivery of VHH to intracranial lesions remains challenging due to the tumor-brain barrier. Here, we evaluate low-dose whole-brain irradiation as a strategy to increase the delivery of an anti-HER2 VHH to breast cancer-derived intracranial tumors in mice. MethodsMice with intracranial HER2-positive BT474BrM3 tumors received 10-Gy fractionated cranial irradiation and evaluated using non-invasive imaging methods. The anti-HER2 VHH 5F7 was labeled with 18F, administered intravenously to irradiated mice and controls, and PET/CT imaging was conducted at various intervals after irradiation. Tumor uptake of 18F-labeled 5F7 in irradiated and control mice was compared by PET/CT image analysis and correlated with tumor volumes. In addition, longitudinal dynamic contrast-enhanced MRI (DCE-MRI) was conducted to visualize and quantify the potential effects of radiation on tumor perfusion and permeability. ResultsIncreased 18F-labeled 5F7 intracranial tumor uptake was observed with PET in mice that received cranial irradiation, with maximum tumor accumulation seen approximately 12 days post initial radiation treatment. No radiation-induced changes in HER2 expression were detected by Western blot, flow cytometry, or on tissue sections. DCE-MRI imaging demonstrated transiently increased tumor perfusion and permeability after irradiation, consistent with the higher tumor uptake of 18F-labeled anti-HER2 5F7 in irradiated mice. ConclusionLow-level brain irradiation induces dynamic changes in tumor vasculature that increase the intracranial tumor delivery of an anti-HER2 VHH, which could facilitate the use of labeled sdAb to detect, monitor, and treat HER2-expressing brain metastases. Key pointsO_LILow-level radiation enhances uptake of HER2-specific VHH in intracranial tumors. C_LIO_LIXRT + radiolabeled VHH shows promise as a treatment strategy for breast cancer brain metastases. C_LI Importance of the StudyImproving the detection and treatment of brain metastases (BM) that overexpress human epidermal growth factor receptor type 2 (HER2) is an urgent medical need. Drug delivery to BM is confounded by their tumor vasculature, which is more restrictive than in GBM. Single domain antibody fragments, about one-tenth the size of antibodies, could be promising theranostic vectors for BM provided sufficient BM uptake could be achieved. In this study, we utilized longitudinal PET imaging to demonstrate that low-dose whole-brain irradiation (WBRT) significantly increased 18F-labeled HER2-specific 5F7 VHH uptake in intracranial HER2-positive tumors in mice. Combining low dose WBRT with 5F7 VHH labeled with -or {beta}-particle emitting radionuclides could provide an effective and specific targeted radiotherapeutic strategy for treating patients with HER2-expressing BM.

cancer biology↗

bioRxiv2020

Pseudomonas aeruginosa isolates co-incubated with Acanthamoeba castellanii exhibit phenotypes similar to chronic cystic fibrosis isolates

The opportunistic pathogen, Pseudomonas aeruginosa, is ubiquitous in the environment, and in humans is capable of causing acute and chronic infections. P. aeruginosa, when co-incubated with the bacterivorous amoeba, Acanthamoeba castellanii, for extended periods, produced genetic and phenotypic variants. Sequencing of late-stage amoeba-adapted P. aeruginosa isolates demonstrated single nucleotide polymorphisms within genes that encode known virulence factors, and this correlated with a reduction in expression of virulence traits. Virulence towards the nematode, Caenorhabditis elegans, was attenuated in late-stage amoeba-adapted P. aeruginosa compared to early stage amoeba-adapted and non-adapted counterparts. Late-stage amoeba-adapted P. aeruginosa lost competitive fitness compared to non-adapted counterparts when grown in nutrient rich media. However, non-adapted P. aeruginosa were rapidly cleared by amoeba predation, whereas late-stage amoeba-adapted isolates remained in higher numbers 24 h after ingestion by amoeba. In addition, there was reduced uptake by macrophage of amoeba-adapted isolates and reduced uptake by human neutrophils as well as increased survival in the presence of neutrophils. Our findings indicate that the selection imposed by amoeba on P. aeruginosa resulted in reduced virulence over time. Importantly, the genetic and phenotypic traits possessed by late-stage amoeba-adapted P. aeruginosa are similar to what is observed for isolates obtained from chronic cystic fibrosis infections. This notable overlap in adaptation to different host types suggests similar selection pressures among host cell types. Author SummaryPseudomonas aeruginosa is an opportunistic pathogen that causes both acute infections in plants and animals, including humans and also causes chronic infections in immune compromised and cystic fibrosis patients. This bacterium is commonly found in soils and water where bacteria are constantly under threat of being consumed by the bacterial predators, protozoa. To escape being killed, bacteria have evolved a suite of mechanisms that protect them from being consumed or digested. Here we examined the effect of long-term predation on the genotype and phenotypes expressed by P. aeruginosa. We show that long-term co-incubation with protozoa resulted in mutations in the bacteria that made them less pathogenic. This is particularly interesting as we see similar mutations arise in bacteria associated with chronic infections. Thus, predation by protozoa and long term colonization of the human host may represent similar environments that select for similar losses in gene functions.

microbiology↗