Biology subjects

Slack, E.

Publications and source records attributed to Slack, E..

At least 19 recordsLinked to original sources

bioRxiv2026

Gut microbiota within-host evolution enforces colonization resistance against enteric infection

Limited resource availability in the gut promotes competitive interactions between bacteria, which drive adaptive within-host evolution (1-3). While adaptive evolution of bacterial communities has been increasingly studied in the recent years (4-7), its functional implications for host physiology remain unknown. Here, we show that within-host evolution of the human commensal Enterococcus faecalis boosts colonization resistance to enteric Salmonella enterica serovar Typhimurium (S. Typhimurium) infection. During gut colonization, E. faecalis evolves the ability to metabolize fructoselysine, an abundant Amadori rearrangement product generated by thermal food processing. The depletion of this diet-derived nutrient prevents S. Typhimurium colonization by restricting an essential resource. This protective mechanism was conserved across independent mouse colonies and arises via diverse evolutionary trajectories, including nucleotide polymorphisms, gene amplifications, and a horizontal gene transfer event. Additionally, analysis of E. faecalis isolates from human infants revealed that adaptation to fructoselysine availability occurs in a diet-dependent manner. Isolates from infants fed with fructoselysine-rich formula were able to utilize fructoselysine, whereas those from infants fed with fructoselysine-poor breast milk were not. Conclusively, our results identify an inherent microbiome-driven self-healing mechanism, wherein bacterial evolution restores colonization resistance against enteric pathogens through evolved nutrient depletion. Understanding these evolutionary dynamics will inform microbiome-targeted approaches to prevent and treat infectious diseases by harnessing adaptive bacterial metabolism.

microbiology↗

bioRxiv2025

Real-time volatilomics reveals microbiota and pathogen fingerprints in the honey bee

Understanding the complex relationship between gut microbiota and their hosts often relies on invasive sampling techniques. Honey bees provide a tractable model for host-microbe studies. Here we establish single-bee volatilomics using secondary electrospray ionization (SESI-HRMS) to examine volatile organic compounds released to the air around an individual live honey bee. Specifically, we focused on primary gut microbiota metabolites present in gnotobiotic bees. Our findings reveal distinct volatilome profiles in honey bees that depend on their gut bacterial colonization state. We cross-validated our findings using an established metabolomics technique, LC-HRMS, to compare and contrast the metabolites detectable with each mass spectrometry-based method. Finally, we assessed the ability of SESI-HRMS to detect colonization with the bee pathogen S. marcescens. By comparing the volatile signature of this bacterium grown in liquid culture with that of infected honey bee headspace, we identified overlapping compounds, including butane-2,3-diol, that were absent in uninfected bees. SESI-HRMS volatilomics, paired with LC-HRMS, therefore has potential to identify non-invasive biomarkers of bee microbiome composition and infection at the level of individual insects. These biomarkers represent practical targets for the development of simple, field-ready diagnostic tools for monitoring pollinator health.

microbiology↗

bioRxiv2025

Transcriptomic profiles of single-copy marker genes enable predicting bacterial growth states in microbial communities

Studying microbial community dynamics is fundamental to better understand ecosystem stability, resilience and environmental change. Community composition changes with the growth of individual members, yet current methods to estimate microbial growth in communities face substantial limitations. For example, genome sequence-based estimates of maximum growth rates may not reflect growth patterns in the natural environment well, and metagenomic in situ growth prediction requires the availability of reference genomes and shows limited accuracy for slow-growing bacteria. Gene expression data provide an information-rich readout of community activity that could reflect growth, however, cross-species comparisons in community settings remain challenging. An approach using expression signatures of universal, single-copy marker genes provides independence from reference genomes and may thereby enable comparability across species. Here, we present a transcriptomic, marker gene-based growth classifier that predicts the growth states of bacterial strains from different phyla cultivated in diverse conditions. We demonstrate its application in vivo in gnotobiotic mice carrying the same bacterial strains, and in a more complex synthetic community, where predicted growth states align with reported growth inhibition induced by systemic inflammatory response. This approach offers a new method for predicting bacterial growth states across species, with potential for broad application in the study of microbial growth dynamics at the whole community level.

microbiology↗

bioRxiv2025

The natural diversity of E. coli transporter-dependent capsules

Serotyping of bacteria using genomic information (in silico serotyping) has increasingly replaced serology. However, the E. coli capsule serotyping system has been largely abandoned since the 1990s, leaving gaps in our knowledge of capsule genetics, diversity, distribution, and epidemiology. To address this, we established a definitive genotype-serotype map for 35 serologically identified and structurally characterized transporter-dependent capsules. We then surveyed >37,000 E. coli genomes, cataloging 85 transporter-dependent capsule types (K-types), including 55 novel ones. We leveraged this catalog to develop an in silico serotyping tool, kTYPr, and applied it to curated sets of >25,000 E. coli genomes and metagenome-assembled genomes spanning diverse environmental and clinical sources. We found novel K-types enriched in under-sampled environments and associated with E. coli disease. This research expands our understanding of E. coli surface structures, supporting efforts for precision targeting with phage therapy or vaccines.

microbiology↗

bioRxiv2025

Emergent spatial structure in the gut microbiota is driven by bacterial growth and gut contractions

Spatial structure can determine function and evolution of bacterial communities. The gut microbiota is known to be spatially structured longitudinally along the many meters of the gastrointestinal tract, but micro-scale structure in the gut lumen has not been extensively explored. In samples from mice and humans, we show that upper large-intestinal content behaves as a non-Newtonian fluid that changes its viscoelastic properties under the force of gut contractions. This phenomenon is sufficient to explain micro-scale bacterial clustering in the murine cecum, resulting from growth within the gel-like structure of cecum content, and periodic disruption due to peristalsis-driven shear-thinning and clearance. Shear-thinning can also explain the surprising observation that fed beads enter the tip of the mouse cecum by flow along the epithelial cell layer before being mixed into the cecum content. Our study shows mechanistically how spatial structure in the gut emerges through the interplay of microbial and host physiology and highlights the possibility of host control over gut microbiota distribution via gut contractions. One sentence summaryWe show how spatial structure emerges in the gut microbiota through bacterial growth in the matrix of gut content.

systems biology↗

bioRxiv2025

Mucosal B cell memory selection integrates tissue-specific microbial cues via the IgA BCR

B cells engender plasma cells (PCs) and memory B cells (MBCs) to combat recurrent pathogens. While B cell receptor (BCR) affinity dictates fate decisions in clonally-restricted set-ups, the driving factors in more complex systems remain unknown. Here, we show that memory selection during mucosal infection is imprinted by inherent cues from barrier tissues: lungs skew selection towards MBCs while the gut favors PC entry, even in response to the same pathogen. This divergence is linked to differential BCR isotype usage across barrier tissues rather than to affinity. In the gut, the commensal-induced TGF-{beta}-rich milieu promotes B cell class-switching to IgA. Consequently, the IgA BCR bias selection towards PCs, a process that is counteracted by its cytosolic tail domain. Overall, mucosal B cell selection integrates tissue-specific cues by strongly relying on BCR isotype usage rather than affinity, with implications for nasal and oral vaccine development. One sentence summaryDivergent B cell memory strategies evolved in lung and gut mucosa to counteract recurrent pathogens.

immunology↗

bioRxiv2025

LC-Inspector: a simple open-source viewer for targeted hyphenated mass spectrometry analysis

The ubiquitousness of hyphenated mass spectrometry techniques across life sciences has made researchers around the world aware of their analytical power. However, the analysis of high-complexity mass spectrometry data remains virtually impossible for non-specialists. LC-Inspector is a standalone graphical user interface application for straightforward analysis of targeted mass spectrometry data, distributed under the MIT license and available free of charge for Windows and MacOS. The user can upload and process the data entirely locally on their machine by specifying the desired mass-to-charge ratios of the targeted compound ions and simply clicking "Process". It allows for the processing of multiple files simultaneously, freely modifying and exporting graphs in real time, and calculating compound concentrations based on calibration standards. We show the versatility and applicability of LC-Inspector to different kinds of mass spectrometry data by analyzing a series of publicly available datasets from various samples recorded on instruments from multiple vendors and by different research teams.

bioinformatics↗

bioRxiv2025

DMB labelling for detection and analysis of capsular polysaccharides

Bacterial capsules are major virulence factors enabling systemic infection by undermining innate and adaptive immunity. Capsular polysaccharides are also the antigen in some of the most successful antibacterial vaccines - including the pneumococcal, neisserial and Hib conjugate vaccines. However, it remains exceptionally challenging to study capsules, primarily due to their high chemical diversity and the limited methods available for their detection and analysis. We describe a robust biochemical method for detection and analysis of ABC transporter-dependent capsular polysaccharides, a major class of capsules that are associated with extraintestinal pathogenic Escherichia coli (ExPEC). The method involves release and fluorescent tagging of polysaccharides from the cell surface. Anion exchange chromatography of labelled samples reveals the presence, relative abundance, and length-distribution of these diverse polysaccharide antigens. The method provides a modern approach to detecting the capsule phenotype, bridging a critical gap left by the decline of serotyping assays. It will enhance our understanding of fundamental capsule biology and advance the development of capsule-targeting vaccines.

biochemistry↗

bioRxiv2024

Investigating Polyreactivity of CD4+ T Cells to the Intestinal Microbiota

The symbiotic relationship between host and microbiota plays a pivotal role in training and development of the hosts innate and adaptive immune systems. Antigen-specific recognition of microbiota by T cells enforces tolerance at homeostasis. Conversely, dysbiosis--characterized by alterations in microbiota diversity and abundance--leads to imbalanced T cell responses and triggering of inflammatory and autoimmune diseases. Despite their significance, the identities of immunogenic microbial antigens are still largely enigmatic. Here, we leveraged an in-house developed antigen screening platform, the MCR system 1, to delineate CD4+ T cell reactivity against Akkermansia muciniphila (AKK) and Bacteroides thetaiotaomicron (BT), --two prominent members of the gut microbiota. T-cell hybridomas reactive to AKK and BT bacteria showed polyreactivity to select microbiota-derived peptides in MCR co-cultures. We discovered 13 novel antigenic epitopes from AKK and 14 from BT. Steady-state T cells recognized these epitopes in an MHC-restricted fashion. Ex vivo stimulation of peptide-specific T cells revealed induction of type 1 and type 17 immune responses, albeit with non-overlapping specificities, contrary to MCR system results. Our findings further demonstrated that most identified epitopes are broadly conserved within the given phylum and originate from both membrane and intracellular proteins. Our work showcases the potential of the MCR system for identifying immunogenic microbial epitopes, providing a valuable resource. Additionally, it indicates the existence of mucosal T cells with a tropism toward broadly conserved bacterial epitopes. Overall, our study forms the basis for decoding antigen specificity in immune system-bacterial interactions, with applications in understanding both microbiome and pathogenic bacterial immunity.

immunology↗

bioRxiv2024

Quantifying the daily harvest of fermentation products from the human gut microbiota

Fermentation products released by the gut microbiota provide energy and regulatory functions to the host. Yet, little is known about the magnitude of this metabolic flux and its quantitative dependence on diet and microbiome composition. Here, we establish orthogonal approaches to consistently quantify this flux, integrating data on bacterial metabolism, digestive physiology, and metagenomics. From the nutrients fueling microbiota growth, most carbon ends up in fermentation products and is absorbed by the host. This harvest varies strongly with the amount of complex dietary carbohydrates and is largely independent of bacterial mucin and protein utilization. It covers 2-5% of human energy demand for Western, and up to 10% for non-Western diets. Microbiota composition has little impact on the total harvest but determines the amount of specific fermentation products. This consistent quantification of metabolic fluxes by our analysis framework is crucial to elucidate the gut microbiotas mechanistic functions in health and disease.

microbiology↗

bioRxiv2023

Surface crosslinking of virus-like particles increases resistance to proteases, low pH and mechanical stress for mucosal applications

AbstractVirus-like particles (VLPs) are emerging as nano-scaffolds in a variety of biomedical applications including the delivery of vaccine antigens to mucosal surfaces. These soft, colloidal, and proteinaceous structures (capsids) are nevertheless susceptible to mucosal environmental factors which limit their usefulness. We addressed this issue by crosslinking multiple capsid surface reactive residues using polyethylene glycol tethers. Surface crosslinking enhanced the colloidal stability and mechanical strength of VLPs against low pH, proteases, and mechanical agitation, while it did not interfere with function as vaccine. Chemical crosslinking thus offers a viable means to enhance the resilience of VLPs in mucosal applications.

biophysics↗

bioRxiv2023

Salmonella-driven Intestinal Edema in Mice is Characterized by Tensed Fibronectin Fibers

Intestinal edema is a common manifestation of numerous gastrointestinal diseases and is characterized by the accumulation of fluid in the interstitial space of the intestinal wall. Technical advances in laser capture microdissection and low-biomass proteomics now allow us to specifically characterize the intestinal edema proteome. Our data identifies a high abundance of antimicrobial factors, but also highlights major contributions from the blood clotting system, extracellular matrix (ECM) and protease - protease inhibitor networks. The ECM is a complex fibrillar network of macromolecules that provides structural and mechanical support to the intestinal tissue. One abundant component of the ECM observed in the Salmonella-driven intestinal edema is the mechanosensitive glycoprotein fibronectin. Using mechanosensitive staining of fibronectin reveals a solely tensed molecular conformation of fibronectin fibers present in the edema, in contrast to other cecal tissue areas, despite the high abundance of proteases able to cleave fibronectin. Co-staining for fibrin(ogen) indicates the formation of a provisional matrix, similar to what is observed in response to skin injury. The absence of low tensional fibronectin fibers and the additional finding of a high number of protease inhibitors in the edema proteome could indicate a critical role of stretched fibronectin fibers in maintaining tissue integrity in the severely inflamed cecum. Understanding these processes may provide valuable functional diagnostic markers of intestinal disease progression. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/550515v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1318c52org.highwire.dtl.DTLVardef@1f35d21org.highwire.dtl.DTLVardef@67370borg.highwire.dtl.DTLVardef@4ec7e6_HPS_FORMAT_FIGEXP M_FIG C_FIG

pathology↗

bioRxiv2023

Nanoscale clustering by O-antigen-Secretory Immunoglobulin-A binding limits outer membrane diffusion by encaging individual Salmonella cells

Secreted immunoglobulins, predominantly SIgA, influence the colonization and pathogenicity of mucosal bacteria. While part of this effect can be explained by SIgA-mediated bacterial aggregation, we have an incomplete picture of how SIgA binding influences cells independently of aggregation. Here we show that akin to microscale crosslinking of cells, SIgA targeting the Salmonella Typhimurium O-antigen extensively crosslinks the O-antigens on the surface of individual bacterial cells at the nanoscale. This crosslinking results in an essentially immobilized bacterial outer membrane. Membrane immobilization, combined with Bam-complex mediated outer membrane protein insertion results in biased inheritance of IgA-bound O-antigen, concentrating SIgA-bound O-antigen at the oldest poles during cell growth. By combining empirical measurements and simulations, we show that this SIgA-driven biased inheritance increases the rate at which phase-varied daughter cells become IgA-free: a process that can accelerate IgA escape via phase-variation of O-antigen structure. Our results show that O-antigen-crosslinking by SIgA impacts workings of the bacterial outer membrane, helping to mechanistically explain how SIgA may exert aggregation-independent effects on individual microbes colonizing the mucosae.

microbiology↗

bioRxiv2023

Acute targeted induction of gut-microbial metabolism disrupts host circadian rhythm

The gut microbiota and host diurnal rhythm mutually influence each other, and microbiota metabolism has been shown to play a role in regulating host circadian function via secretion of fermentation products. Microbial metabolism is dependent on the availability of nutrients for the microbiota, typically through the hosts food intake, making it challenging to disentangle the effect of host and microbiota metabolism. In this study, we acutely induced gut microbial metabolic activity without inducing host metabolism in mice. We found that increasing microbial metabolism in the gut altered clock gene expression locally. Actuating microbiota metabolism also reduced host food intake beyond the calories provided by the microbiota, suggesting a systemic signaling effect of microbial metabolism on the host.

microbiology↗

bioRxiv2023

A rationally designed inactivated Salmonella Typhimurium vaccine induces strong and long-lasting immune responses in pigs

Salmonella enterica subspecies enterica serovar Typhimurium (S.Tm) poses a considerable threat to public health due to its zoonotic potential. Human infections are mostly foodborne, and pork and pork products are ranked among the top culprits for transmission. In addition, the high percentage of antibiotic resistance, especially in monophasic S.Tm, limits treatment options when needed. Better S.Tm control would therefore be of benefit both for farm animals and for safety of the human food chain. A promising pre-harvest intervention is vaccination. In this study we tested safety and immunogenicity of an oral inactivated S.Tm vaccine, which has been recently shown to generate an "evolutionary trap" and to massively reduce S.Tm colonization and transmission in mice. We show that this vaccine is highly immunogenic and safe in post-weaning pigs and that administration of a single oral dose results in a strong and long-lasting serum IgG response. This has several advantages over existing - mainly live - vaccines against S.Tm, both in improved seroconversion and reduced risk of vaccine-strain persistence and reversion to virulence.

immunology↗

bioRxiv2022

Microbiota colonization tunes the antigen threshold of microbiota-specific T cell activation in the gut

Harnessing the potential of commensal bacteria for immunomodulatory therapy in the gut requires the identification of conditions that modulate immune activation towards incoming colonizing bacteria. In this study, we used the commensal Bacteroides thetaiotaomicron (B.theta) and combined it with B.theta-specific transgenic T cells, in the context of defined colonization of gnotobiotic and immunodeficiency mouse models, to probe the factors modulating bacteria-specific T cell activation against newly colonizing bacteria. After colonizing germ-free (GF) and conventionally raised (SPF) mice with B.theta, we only observed proliferation of B.theta-specific T cells in GF mice. Using simple gnotobiotic communities we could further demonstrate that T-cell activation against newly colonizing gut bacteria is restricted by previous bacteria colonization in GF mice. However, this restriction requires a functional adaptive immune system as Rag1-/- allowed B.theta-specific T cell proliferation even after previous colonization. Interestingly, this phenomenon seems to be dependent on the type of TCR-transgenic model used. B.theta-specific transgenic T cells also proliferated after gut colonization with an E.coli strain carrying the B.theta-specific epitope. However, this was not the case for the SM-1 transgenic T cells as they did not proliferate after similar gut colonization with an E.coli strain expressing the cognate epitope. In summary, we found that activation of T cells towards incoming bacteria in the gut is modulated by the influence of colonizing bacteria on the adaptive immune system of the host.

immunology↗

bioRxiv2022

Combined oral vaccination with niche competition can generate sterilizing immunity against entero-pathogenic bacteria

Colonization of the intestinal lumen precedes invasive infection for a wide range of enteropathogenic and opportunistic pathogenic bacteria. Here we show that combining oral vaccination with engineered or selected niche-competitor strains permits pathogen exclusion and strain replacement in the mouse gut lumen. This approach can be applied both prophylactically to prevent invasion of non-typhoidal Salmonella strains, or therapeutically to displace an established Escherichia coli. Both intact adaptive immunity and metabolic niche competition are necessary for efficient vaccine-enhanced competition. Our findings imply that mucosal antibodies have evolved to work in the context of gut microbial ecology, by influencing the outcome of competition. This has broad implications for the elimination of pathogenic and antibiotic-resistant bacterial reservoirs, and for rational microbiota engineering.

microbiology↗

bioRxiv2022

Fitness advantage of Bacteroides thetaiotaomicron capsular polysaccharide is dependent on the resident microbiota

Many microbiota-based therapeutics rely on our ability to introduce a microbe of choice into an already-colonized intestine. However, we remain largely blind to the quantitative effects of processes determining colonization success. In this study, we used genetically-barcoded Bacteroides thetaiotaomicron (B.theta) strains in combination with mathematical modeling to quantify population bottlenecks experienced by B.theta during gut colonization. Integrating population bottlenecks sizes with careful quantification of net growth rates in vivo and in vitro allows us to build models describing the events during intestinal colonization in the context of gnotobiotic and complex microbiotas. Using these models, we estimated the decrease in niche size for B.theta colonization with increasing microbiota complexity. In addition, our system can be applied to mechanistically dissect colonization defects of mutant strains. As a proof of concept, we demonstrated that the competitive disadvantage of a B.theta mutant lacking capsular polysaccharide is due to a combination of an increased lag-phase before growth initiation in the gut, combined with an increased clearance rate. Crucially, the requirement for the B.theta capsule depended strongly on microbiota composition, suggesting that the dominant role may be protection from bacterial or phage aggression rather than from host-induced bactericidal mechanisms.

microbiology↗