Biology subjects

Williams, E.

Publications and source records attributed to Williams, E..

At least 19 recordsLinked to original sources

bioRxiv2026

Separation, isolation, and membrane lipid profiling of selectively vulnerable and resilient neurons

Certain neurons are more susceptible to pathogenic stressors and degenerate, while others remain resilient in neurodegenerative diseases. However, the mechanisms underlying this cell-to-cell heterogeneity in neuronal vulnerability remain unclear, primarily due to challenges in isolating vulnerable and resilient neurons to characterize their properties. In this study, we report the development of a novel cell-labeling method utilizing two cell-impermeable dyes to identify vulnerable and resilient neurons in culture, which are subsequently separated and isolated via fluorescence-activated cell sorting (FACS). As a proof-of-concept of a mechanistic study, we conducted lipidomic analysis to determine whether the lipid composition of membranes differs between vulnerable and resilient neurons to oxidative stress. This simple but unique method sets the groundwork for investigating the molecular underpinnings of selective neuronal vulnerability, which could inform new diagnostic strategies and therapeutic targets for neurodegenerative diseases.

neuroscience↗

bioRxiv2026

Genetic Variation, Iron Status, and FGF23 Signaling Converge to Regulate Renal Calcium Buffering in Sickle Cell Disease

Sickle cell disease (SCD) causes heterogeneous mineral imbalances including variable degrees of hypocalcemia. The kidney controls systemic calcium by reabsorbing calcium from the glomerular filtrate via paracellular transport and transcellular transport in the nephron tubules, yet it is unknown whether these processes are modulated by genetic or environmental factors or disrupted in SCD. Using SCD mouse models and single-cell multiomics, we identify the distal convoluted tubule (DCT) as the nephron segment most susceptible to calcium reabsorption dysfunction in SCD, mainly via reduction of calcium buffer protein calbindin 1 (CALB1). We show that CALB1 and its encoding mRNA are decreased in DCT cells in SCD, alongside decreased Klotho (KL)-dependent fibroblast growth factor (FGF) 23 signaling and intracellular calcium signaling. Dietary iron restriction reduces CALB1, KL, and calcium exporter SLC8A1 levels in SCD kidneys. Loss of CALB1 shifts DCT cells toward energy-inefficient glycolysis with the metabolite 2,3-diphosphoglycerate impairing KL-dependent FGF23 signaling to create a feed-forward loop suppressing calcium reabsorption. Analysis of gene expression and protein quantitative trait loci data from kidneys of genetically diverse mice revealed that Calb1 expression levels are highly heritable and co-regulated with Slc8a1, identifying a genetic axis that dictates differential capacities for calcium buffering and trafficking toward blood in the kidney. Together, these findings support a model in which genetic variation, dietary iron status, and FGF23 signaling converge on DCT calcium buffering to reduce renal calcium reabsorption in the SCD kidney. This points to personalized, genotype- and iron-dependent strategies for managing mineral metabolism in SCD patients.

physiology↗

bioRxiv2026

Characterisation and manufacture of a Neisseria gonorrhoeae challenge agent for use in an oropharyngeal controlled human infection model

BackgroundDespite the importance of oropharyngeal gonorrhoea in transmission, suboptimal antimicrobial responses and propensity for horizontal transfer of antimicrobial resistance at this site, it remains understudied. An oropharyngeal N. gonorrhoeae controlled human infection model (CHIM) represents a promising tool to study infection and undertake translational research. MethodsA panel of five contemporary N. gonorrhoeae isolates were subject to detailed characterisation to assess antimicrobial susceptibility, in vitro infectivity, cytotoxicity and serum sensitivity to inform challenge agent selection. A method for challenge agent manufacture, including release testing, was developed and validated. FindingsAll candidate isolates were able to infect the surface of pharyngeal and cervical cells in vitro. One isolate displayed an invasive phenotype, induced higher inflammatory cytokine production and displayed elevated serum resistance and was excluded. The remaining four isolates were minimally inflammatory, did not induce cytotoxicity and were susceptible to serum killing. Three of the four isolates grew in a defined liquid medium. Together these results led to the selection of a contemporary N. gonorrhoeae isolate suitable for use in CHIM. A challenge agent manufacture workflow was established and shown to reliably and reproducibly generate doses suitable for direct inoculation in an oropharyngeal CHIM. ConclusionPhenotypic characterization of candidate N. gonorrhoeae challenge agents led to the successful identification of a contemporary isolate suitable for implementation in a novel oropharyngeal gonorrhoea CHIM. We demonstrate the feasibility of a challenge inoculum manufacturing process that aligns with international best practice guidelines.

microbiology↗

bioRxiv2026

Label-free GAG disaccharide analysis by HILIC-MS/MS for studying diverse biological sample types

The extracellular matrix (ECM) and cell surface glycocalyx are key components of biology and play crucial roles in development and tissue function, as well as disease. Proteoglycans, and their glycosaminoglycan (GAG) side chains, are critical components of the ECM and the glycocalyx. GAGs can bind to many different proteins, such as chemokines, and form hydrated barriers around cells. Existing and new methods are helping us to uncover more about the roles of GAGs in biology. Here, we expand on existing technologies and provide streamlined, standardised and well-documented methods that can be easily adopted in standard analytical facilities. We provide extensive detailed step-by-step guides describing sample disruption, GAG disaccharide preparation from biological tissues and their analysis by HILIC-MS/MS. In addition, we demonstrate utility of this method when using a range of different samples as biological sources. This method will sit alongside existing and new techniques to help improve access to GAG analysis, and thereby further the field of understanding GAG function in complex biological contexts.

biochemistry↗

bioRxiv2026

SMEW: An interactive multi-scale toolkit for cross-condition and network-based analysis of spatial metabolomics data

Spatial metabolomics, measured through mass spectrometry imaging (MSI), provides high-throughput, spatially resolved information on metabolite distributions within tissues, including endogenous metabolites and exogenous compounds. This offers a direct readout of cellular biochemical activity and phenotypes, not fully captured by transcriptomics or proteomic profiling. However, inferring biologically meaningful patterns from noisy, high-dimensional MSI data, particularly across multiple samples and complex experimental designs, remains challenging, and often requires substantial programming expertise. Here we introduce SMEW (Spatial Metabolomics Enhanced Workflow), a flexible, interactive and shareable Shiny-based platform designed to enable code-free downstream analysis of spatial metabolomics MSI data. SMEW provides a unified environment for hierarchical analysis across bulk-, region- and pixel-level resolutions, allowing comparisons between experimental conditions like disease or treatment groups while highlighting coherent metabolic patterns and linking these patterns to biological pathways. The workflow leverages local spatial covariation to robustly summarise MSI data through dimensionality reduction, clustering and identification of spatially variable metabolites. In addition, metabolite co-localisation and covariation network analysis, together with spatially resolved pathway enrichment facilitate the biological interpretation of cross-condition datasets within a single integrated interface. SMEW is applicable across MSI technologies and mass resolutions, as illustrated through case studies on DESI and MALDI-ToF datasets from lung, liver, and kidney. By complementing existing MSI processing and visualisation tools with an accessible, multi-sample, and biologically interpretable analysis framework, SMEW enables functional, flexible, rigorous and intuitive exploration of spatial metabolomics datasets. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=84 SRC="FIGDIR/small/721059v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@1e2abaeorg.highwire.dtl.DTLVardef@753ee9org.highwire.dtl.DTLVardef@1756fc1org.highwire.dtl.DTLVardef@fbedc7_HPS_FORMAT_FIGEXP M_FIG C_FIG Key PointsO_LISMEW provides a flexible, interactive and shareable Shiny-based platform designed to enable code-free downstream analysis of spatial metabolomics MSI data C_LIO_LIThe SMEW framework enables hierarchical analysis at bulk-, region- and pixel levels within a unified framework without relying on extensive programming expertise C_LIO_LIThe pipeline integrates spatially aware clustering, pathway analysis and identification of metabolite co-localisation modules C_LIO_LIThe workflow facilitates flexible comparison of multi-sample experimental conditions through multivariate modelling, differential testing and covariation networks to study treatment- and disease-associated metabolite dynamics C_LIO_LISMEW has been applied to interrogate diverse biological questions, including characterising disease-associated remodelling in a mouse bleomycin model of pulmonary fibrosis, exploring the therapeutic index of antisense oligonucleotides in the liver and assessing metabolic heterogeneity in a small molecule-treated mouse renal tumour model C_LI

bioinformatics↗

bioRxiv2026

Multi-omic profiling of human and mouse dorsal root ganglia enables targeted gene delivery to nociceptors

Chronic pain conditions are often driven by hyperexcitability of nociceptors, the peripheral sensory neurons that detect noxious stimuli. Recent single-cell transcriptomic studies have begun to clarify the molecular identity of distinct peripheral sensory neuron subtypes, but tools that restrict transgene expression to nociceptors while sparing other dorsal root ganglion (DRG) subtypes remain limited. Here, we combined single-nucleus multi-omic profiling of human and mouse DRG with in vivo AAV enhancer screening to identify cis-regulatory elements that drive biased AAV expression in mouse DRG nociceptors and human iPSC-derived nociceptors. We then validated that an enhancer AAV designed to express Kir2.1 preferentially in nociceptors reduces DRG neuronal excitability. Leveraging these multi-omic datasets, we trained a sequence-based model to decode the cis-regulatory logic of nociceptors, enabling both the prioritization of native candidate elements and the design of synthetic enhancers with a range of nociceptor targeting properties. Together, these cross-species multi-omic resources define conserved DRG regulatory programs and provide a viral toolkit for pain research with potential translational applications for patients with refractory pain.

neuroscience↗

bioRxiv2026

Ageing impacts extracellular matrix turnover and remodelling in the kidney

At least 10% of the global population is impacted by chronic kidney disease (CKD) and ageing is a key risk factor. CKD is characterised by the build-up of extracellular matrix and a loss of functional nephrons. However, the mechanisms that maintain matrix homeostasis across the physiological lifespan remain elusive. Using {superscript 1}3C-lysine metabolic labelling, we quantified kidney matrix protein turnover in healthy mice at four timepoints (8, 22, 52, and 78 weeks). We found that basement membrane components, including collagen IV, laminin-521, nidogens and perlecan, were more long-lived over age, with collagen IV half-lives extending from weeks in young kidneys to years in aged kidneys, suggesting a reduced capacity for basement membrane renewal. The half-lives of fibrillar collagens I and III also increased over age up to forty-fold, which is consistent with minimal degradation. In contrast, collagen XV retained rapid turnover despite increased abundance, indicating a persistent role in tissue remodelling. Using peptide location fingerprinting to predict structural alterations and proteolytic processing we identified age-dependent meprin oligomerisation and altered nidogen-laminin interaction states. We predicted structural alterations within assembly domains of collagen VI and reduced accessibility of integrin-binding regions, suggesting altered microfibril organisation and cell-surface binding. Collagen XV had predicted structural changes across the NC1 domain encoding the matrikine restin, consistent with altered protease accessibility and matrikine release during ageing. These findings indicate that age-related kidney fibrosis is primarily caused by impaired matrix degradation, with protease accessibility and altered matrix interactions likely playing key roles in this remodeling process.

systems biology↗

bioRxiv2025

Tracking GAD-specific T-cell expansions in Type 1 diabetes by intradermal GAD-Alum challenge

Identifying and monitoring autoreactive T cells that drive beta cell destruction remains a major obstacle to developing effective immunotherapies for type 1 diabetes (T1D). These cells are extremely rare in peripheral blood and cannot be accessed directly from the pancreas. We used intradermal injection of GAD-Alum to recruit GAD-specific T cells to accessible sites in the skin and skin-draining lymph nodes (LNs), sampled by skin suction blisters and ultrasound-guided LN aspiration. Peripheral blood samples obtained before GAD injection were restimulated with GAD in vitro to detect reactive CD4+ T cells. Re-expression of selected T cell receptors (TCRs) confirmed antigen specificity. Up to 70% of T cells at the skin injection site were clonally-expanded and 4 of 14 (28%) re-expressed TCRs were GAD-reactive. In draining LNs 1 of 14 (4%) clonally-expanded TCRs was GAD-reactive, representing [~]0.08% of all T-cells. GAD-reactive cells across compartments displayed Th1 and Th17-associated transcription signatures. These results demonstrate the intradermal autoantigen challenge, coupled with scRNAseq, enables direct identification and molecular profiling of autoreactive T cells in vivo. This minimally invasive approach provides a powerful platform for tracking antigen-specific specific T cells to monitor disease activity and evaluate immune interventions in T1D.

immunology↗

bioRxiv2025

Complex Assembly and Activity States as Multifaceted Protein Attributes Explaining Phenotypic Variability

Cell function studies primarily focus on measuring overall molecular abundances while often overlooking critical clues--including protein modifications and molecular interaction networks--that critically determine the functional properties of the cell. In prior work, we introduced a suite of methods to reveal context-specific transcription factor-gene regulatory networks, kinase-substrate networks, and protein interaction networks and leveraged them to gain deeper insights into transcriptional regulation and signal transduction. However, the complex interdependencies between these networks are still elusive. To address this challenge, we introduce a multi-omics framework, aimed at harnessing measured or inferred protein activity in context-specific networks, which yields deeper functional insights into mechanisms underlying molecular phenotypes, compared to protein abundance alone. As proof of concept, we utilized progressively differentiated instances of HeLa CCL2 and Kyoto cell lines to explore the role of protein complexes and interactions in cell doubling time and susceptibility to Salmonella Typhimurium infection. Notably, this analysis underscores the pivotal role of protein interaction networks in linking molecular profiles to phenotypic outcomes, thus providing a highly generalizable framework for multi-omics dataset analysis.

systems biology↗

bioRxiv2025

Increased in vivo transduction of AAV-9 cargo in Alport podocytes

Alport syndrome is a rare genetic disorder characterized by progressive kidney disease, hearing loss, and eye abnormalities. Gene therapy for Alport syndrome has not yet been realized due to technical challenges, including effective transduction of target cells. In this study, we established a quantitative testing platform using podocytes in culture, ex vivo glomeruli, and a mouse model of Alport syndrome to evaluate the transduction efficacy of adeno-associated Virus-9 (AAV9) as a gene delivery vehicle. We compared transduction levels of AAV9-GFP vectors between healthy and Alport podocytes in culture, revealing that both cell types exhibited similar transduction rates. We then incubated ex vivo glomeruli with AAV9-GFP and found enhanced transduction in Alport compared to wild type podocytes. Finally in mice following a peripheral intravenous injection of AAV9-GFP we found a striking increase in transduction in Alport podocytes suggesting that the pathological environment may facilitate higher penetration of the vector. These findings underscore the potential of AAV9 for effective gene delivery in the context of Alport syndrome, providing a foundation for future therapeutic strategies aimed at correcting the underlying genetic defects. Plain Language SummaryThis study highlights the clinical significance of AAV9 as a potential gene delivery vehicle for Alport syndrome treatment. Our findings demonstrate that Alport podocytes exhibit enhanced transduction levels in ex vivo and in vivo environments compared to healthy podocytes. This suggests that AAV9 could effectively target podocytes in Alport syndrome, paving the way for innovative gene therapy strategies that may improve patient outcomes and quality of life.

cell biology↗

bioRxiv2025

Far-Ultraviolet Light Causes Direct DNA Damage in Human Lung Cells and Tissues

Far-ultraviolet C (Far-UVC) radiation, with a wavelength range from 200 to 235 nm, is germicidal and holds potential for clinical applications. However, its use against deep-seated and internal infections, such as those affecting the lungs, remains less well established. The safety profile of Far-UVC irradiation requires further investigation across different human tissues. In this study, we utilised a krypton-chloride (KrCl) excimer lamp and a pulsed laser system to examine the effects of Far-UVC irradiation on human lung cells in vitro and primary human tracheal tissue. Primary human tracheal tissue and cells exposed to continuous wave (222 nm) and pulsed 206 nm and 222 nm light at doses of 5, 25, and 50 mJ/cm2 exhibited Deoxyribonucleic acid (DNA) damage, including phosphorylation of {gamma}H2AX (Ser139). The continuous wave and pulsed 222 nm irradiation caused the formation of pyrimidine-pyrimidone (6-4) photoproducts. Irradiated human lung cells demonstrated reduced viability in vitro, and increased lactate dehydrogenase release into the culture medium 48 hours post-irradiation. Our findings reveal that even low doses of Far-UVC (206 nm, 222 nm) light can penetrate monolayers of human lung epithelial cells, causing direct DNA damage in the form of (6-4) photoproducts and DNA double-strand breaks, ultimately leading to cell death.

cell biology↗

bioRxiv2025

A multiomic network approach uncovers disease modifying mechanisms of inborn errors of metabolism

For many inborn errors of metabolism (IEM) the understanding of disease mechanisms remains limited in part explaining their unmet medical needs. We hypothesize that the expressivity of IEM disease phenotypes is affected by the activity of specific modifier pathways, which is controlled by rare and common polygenic variation. To identify these modulating pathways, we used RNA sequencing to generate molecular signatures of IEM in disease relevant tissues. We then integrated these disease signatures with multiomic data and gene regulatory networks generated from animal and human populations without overt IEM. We identified and subsequently validated glucocorticoid signaling as a candidate modifier of mitochondrial fatty acid oxidation disorders, and we re-capitulated complement signaling as a modifier of inflammation in Gaucher disease. Our work describes a novel approach that can overcome the rare disease-rare data dilemma, and reveal new IEM pathophysiology and potential drug targets using multiomics data in seemingly healthy populations. Take-home message: Multiomic data and gene regulatory networks derived from animal and human populations without overt IEM can be used to study disease mechanisms in inborn errors of metabolism.

genetics↗

bioRxiv2024

Pathological α-synuclein elicits granulovacuolar degeneration independent of tau

BackgroundPathologic heterogeneity is a hallmark of Lewy body dementia (LBD), yet the impact of Lewy pathology on co-pathologies is poorly understood. Lewy pathology, containing -synuclein, is often associated with regional tau pathology burden in LBD. Similarly, granulovacuolar degeneration bodies (GVBs) have been associated with tau pathology in Alzheimers disease. Interestingly, GVBs have been detected in a broad range of neurodegenerative conditions including both -synucleinopathies and tauopathies. Despite the frequent co-occurrence, little is known about the relationship between -synuclein, tau, and granulovacuolar degeneration. MethodsWe developed a mouse model of limbic-predominant -synucleinopathy by stereotactic injection of -synuclein pre-formed fibrils (PFFs) into the basal forebrain. This model was used to investigate the relationship of -synuclein pathology with tau and GVB formation. ResultsOur model displayed widespread -synuclein pathology with a limbic predominant distribution. Aberrantly phosphorylated tau accumulated in a subset of -synuclein inclusion-bearing neurons, often colocalized with lysosomes. Many of these same neurons also contained CHMP2b- and CK1{delta}-positive granules, established markers of GVBs, which suggests a link between tau accumulation and GVB formation. Despite this observation, GVBs were also detected in tau-deficient mice following PFF-injection, suggesting that pathological -synuclein alone is sufficient to elicit GVB formation. ConclusionsOur findings support that -synuclein pathology can independently elicit granulovacuolar degeneration. The frequent co-accumulation of tau and GVBs suggests a parallel mechanism of cellular dysfunction. The ability of -synuclein pathology to drive GVB formation in the absence of tau highlights the broader relevance of this process to neurodegeneration with relevance to the pathobiology of LBD.

neuroscience↗

bioRxiv2024

A complete collagen IV fluorophore knock-in toolkit reveals -chain diversity in basement membrane

The type IV collagen triple helix, composed of three -chains, is a core basement membrane (BM) component that assembles into a network within BMs. Endogenous tagging of all -chains with genetically encoded fluorophores has remained elusive, limiting our understanding of this crucial BM component. Through genome editing, we show that the C-termini of the C. elegans type IV collagen -chains EMB-9 and LET-2 can be fused to a variety of fluorophores to create a strain toolkit with wild-type health. Using quantitative imaging, our results suggest a preference for LET-2-LET-2-EMB-9 trimer construction, but also tissue-specific flexibility in trimers assembled driven by differences in -chain expression levels. By tagging emb-9 and let-2 mutants that model human Gould Syndrome, a complex multi-tissue disorder, we further discover defects in extracellular accumulation and turnover that might help explain disease pathology. Together, our findings identify a permissive tagging site that will allow diverse studies on type IV collagen regulation and function in animals. SummarySrinivasan et al., construct a collagen IV fluorophore knock-in toolkit in C. elegans using a newly identified permissive genome editing site and reveal tissue-specific -chain diversity and basement membrane turnover defects in collagen IV mutants modeling human COL4A1/A2 (Gould) syndrome.

developmental biology↗

bioRxiv2024

Bwa, an ortholog of alkaline ceramidase-ACER2, promotes intestinal stem cell proliferation through pro-inflammatory cytokine signaling in Drosophila melanogaster

Sphingolipids, including ceramides, are an important component of high-fat diets. These molecules can regulate fatty acid oxidation and intestinal stem cell proliferation, predisposing the gut to tumorigenesis. However, the molecular mechanisms involved in ceramide metabolism-mediated intestinal stem cell (ISC) proliferation and tumorigenesis are poorly understood. To understand how changes in sphingolipid metabolite flux affect intestinal stem cells, we manipulated the activities of each of the enzymes of the ceramide synthetic pathway using cell type-specific over-expression or depletion of the corresponding mRNAs in each intestinal cell type of the Drosophila midgut. We documented cell-autonomous and non-cell-autonomous effects, including alterations in cell size, number, differentiation, and proliferation. In our screen, the altered expression of several ceramide metabolism enzymes led to changes in ISC proliferation, cell sizes, and overall cellularity. Among other genes, over-expression of ceramidase homolog, Brain washing (bwa) in gut enteroblasts (EB) increased EB cell size and caused a non-cell-autonomous, 7-8-fold increase in ISC proliferation. Our analysis confirmed previous reports that bwa does not have ceramidase activity, and lipidomic studies indicated that bwa increases the saturation status of sphingolipids, free fatty acids, and other lipids. The pro-proliferative effects of bwa could be counter-acted by depleting a serine palmitoyltransferase, Lace, or a sphingosine acyltransferase, Schlank, which are needed for ceramide synthesis, or by co-expressing a ceramide desaturase enzyme, ifc, indicating that increased saturated ceramides were causal for ISC proliferation and the disruption of gut homeostasis. Accumulating saturated sphingolipids and fatty acids induced inflammatory signaling in the gut, and activated ISC proliferation through the pro-inflammatory cytokines, Upd3 and Upd2. We propose that saturated sphingolipids promote ISC proliferation through pro-inflammatory pathways.

cell biology↗

bioRxiv2024

Discovery of potent SARS-CoV-2 nsp3 macrodomain inhibitors uncovers lack of translation to cellular antiviral response

A strategy for pandemic preparedness is the development of antivirals against a wide set of viral targets with complementary mechanisms of action. SARS-CoV-2 nsp3-mac1 is a viral macrodomain with ADP-ribosylhydrolase activity, which counteracts host immune response. Targeting the virus immunomodulatory functionality offers a differentiated strategy to inhibit SARS-CoV-2 compared to approved therapeutics, which target viral replication directly. Here we report a fragment-based lead generation campaign guided by computational approaches. We discover tool compounds which inhibit nsp3-mac1 activity at low nanomolar concentrations, and with responsive structure-activity relationships, high selectivity, and drug-like properties. Using our inhibitors, we show that inhibition of nsp3-mac1 increases ADP-ribosylation, but surprisingly does not translate to demonstrable antiviral activity in cell culture and iPSC-derived pneumocyte models. Further, no synergistic activity is observed in combination with interferon gamma, a main protease inhibitor, nor a papain-like protease inhibitor. Our results question the extent to which targeting modulation of innate immunity-driven ADP-ribosylation can influence SARS-CoV-2 replication. Moreover, these findings suggest that nsp3-mac1 might not be a suitable target for antiviral therapeutics development.

microbiology↗

bioRxiv2024

Adversarial learning enables unbiased organism-wide cross-species alignment of single-cell RNA data

Todays single-cell RNA (scRNA) datasets remain siloed, due to significant challenges associated with their integration at scale. Moreover, most scRNA analysis tools that operate at scale leverage supervised techniques that are insufficient for cell-type identification and discovery. Here, we demonstrate that the alignment of scRNA data using unsupervised models is accurate at an organism-wide scale and between species. To do this, we show adversarial training of a deep-learning model we term batch-adversarial single-cell variational inference (BA-scVI) can be employed to align standardized benchmark datasets comprising dozens of scRNA studies spanning tissues in humans and mice. In the aligned space, we analyze cell types that span tissues in both species and find prevalent complement expressing macrophages and fibroblasts. We provide access to the tools presented via an online interface for atlas exploration and reference-based drag-and-drop alignment of new data.

genetics↗

bioRxiv2024

A Strain of Streptococcus mitis Inhibits Biofilm Formation of Caries Pathogens via Abundant Hydrogen Peroxide Production

Commensal oral streptococci that colonize supragingival biofilms deploy mechanisms to combat competitors within their niche. Here, we determined that Streptococcus mitis more effectively inhibited biofilm formation of Streptococcus mutans within a seven species panel. This phenotype was common amongst all assayed isolates of S. mutans, but was specific to a single strain of S. mitis, ATCC 49456. The growth inhibitory factor was not effectively carried in spent supernatants of S. mitis. However, we documented ATCC 49456 to accumulate 4-5 times more hydrogen peroxide (H2O2) than other species tested, and 5-18 times more than other S. mitis strains assayed. The S. mutans biofilm formation inhibitory phenotype was reduced when grown in media containing catalase or with a S. mitis mutant of pyruvate oxidase (spxB; pox), confirming that SpxB-dependent H2O2 production was the main antagonistic factor. Addition of S. mitis within hours after S. mutans inoculation was effective at reducing biofilm biomass, but not for 24 h pre-formed biofilms. Transcriptome analysis revealed responses for both S. mitis and S. mutans, with several S. mutans differentially expressed genes following a gene expression pattern previously described, while others being unique to the interaction with S. mitis. Finally, we show that S. mitis also affected coculture biofilm formation of several other commensal streptococci. Our study shows that strains with abundant H2O2 production are effective at inhibiting initial growth of caries pathogens like S. mutans, but are less effective at disrupting pre-formed biofilms and have the potential to influence the stability of other oral commensal strains.

microbiology↗