Biology subjects

Blasche, S.

Publications and source records attributed to Blasche, S..

11 recordsLinked to original sources

bioRxiv2026

Network-scale disruption of RNA-protein interactions by a bioaccumulating small-molecule drug

Many small-molecule drugs accumulate in both host and gut microbial cells. Yet, the molecular consequences of intracellular drug accumulation are largely unknown. Here we show that the antidepressant duloxetine broadly disrupts RNA-protein interactions revealing a previously unrecognized mode of drug effect. Across phylogenetically diverse bacteria and human intestinal cells, duloxetine consistently reduced RNA-binding capacity, with approximately 80% of RNA-binding proteins responding to duloxetine in bacteria (E. coli IAI1) and human (Caco-2) cells. As a mechanistic example, we show how duloxetine disrupts interactions between the pyrimidine biosynthesis enzyme PyrB and transcripts encoding metabolically linked functions. Biochemical and structural analyses show that duloxetine competes with aspartate, the natural substrate of PyrB, weakening the enzymes binding with 3' UTR-localized stem-loop structures in its RNA partners. Overall, our results uncover the off-target disruption of RNA-protein interactions due to drug accumulation and have implications for understanding molecular basis of variation in drug efficacy and toxicity.

systems biology↗

bioRxiv2026

Oxygen gradients reshape cross-feeding through emergent spatial organization of gut commensal bacteria

Microbial interactions unfold within environments structured by physical transport and chemical gradients. Yet most mechanistic studies rely on well-mixed systems that mask the reciprocal influences of environmental heterogeneity on metabolism and ecology. Here, we investigate how the physical environment modulates the interaction between the gut commensal Bacteroides thetaiotaomicron and Escherichia coli. In anoxic liquid culture, cell-resolved isotope imaging and genetic perturbations reveal exploitative cross-feeding, where E. coli consumes diffusible sugars released by B. thetaiotaomicron during starch degradation. When exposed to intestinal-like oxygen gradients in microfluidics, the interaction is restructured by spatial organization. The species self-organize into complementary niches: E. coli locally depletes sugars and oxygen, thereby expanding the anoxic niche required by B. thetaiotaomicron. A reactive transport model confirms that this organization arises from coupled feedback between physical transport and metabolic reaction rates. Together, our results reveal how physical structure and chemical gradients convert an exploitative cross-feeding interaction into a dynamic niche-construction process that generates emergent spatial organization and stabilizes coexistence.

microbiology↗

bioRxiv2025

Sub-cellular chemical mapping in bacteria using correlated cryogenic electron and mass spectrometry imaging

Electron cryomicroscopy (cryo-EM) allows high-resolution spatial visualization of biological specimens, however, it is challenging to chemically identify densities observed in cryo-EM. To overcome this, we combined cryo-EM with chemical imaging using focused ion beam secondary ion mass spectrometry (FIB-SIMS) for integrated spatio-chemical analysis of untagged specimens. We show that our correlative workflow permits sub-cellular localisation of molecules inside bacterial cells and is compatible with cryogenic light microscopy and FIB-milled lamellae of multicellular specimens. To highlight biological insights enabled by the workflow, we studied the uptake of Bisphenol-AF, a widespread chemical pollutant, by environmental bacteria, revealing the storage of these chemicals within cytosolic phase-separated aggregates in pollutant-exposed cells, where they cannot be removed by the bacterial efflux machinery despite its robust upregulation. These mechanistic insights were directly facilitated by the versatile cryo-EM-FIB-SIMS technique, showing that it is an effective avenue to map elemental and molecular signatures in near-native biological samples, which can be extended in the future for multiple applications in cell biology and imaging.

molecular biology↗

bioRxiv2025

Interspecies interactions drive bacterial proteome reorganisation and emergent metabolism

Species in microbial communities must respond to the presence of others to stave off resource competition or to capitalise on new resources that may become available due to additional metabolic activities. Such metabolic interactions manifest in growth effects such as competitive exclusion or cooperative growth boost. However, intra-cellular molecular changes that underpin these responses are very sparsely studied, preventing mechanistic insights into community function and dynamics. Here, we analyse meta-proteomics and metabolomic responses in 104 pairwise co-cultures of 15 diverse gut bacteria in a nutrient-rich medium. These co-cultures span a diversity of ecological interactions with competition, amensalism and exploitation being prominent, and with around one in five positive interactions. The species in co-cultures feature substantial molecular responses, with typically more than 60% of the proteome changing in response to at least one partner. Even closely related species and ortholog proteins show different expression profiles in response to the same partner indicating functional diversification at both protein and species level. We show that the magnitude of these responses is determined by genome size, species abundance, and pH. Small-molecule transport and carbon metabolism are among the most responsive processes indicating pervasive metabolic interactions. Using metabolomics, we identify likely cross-fed metabolites, emergent polyamine metabolism, and niche partitioning in amino acid utilisation. Overall, our study shows how bacteria respond to the presence of other species through extensive remodelling of their proteome and metabolome.

microbiology↗

bioRxiv2025

Impact of low-calorie sweeteners on gut bacteria is modulated by common xenobiotics

The gut microbiota is implicated in adverse effects associated with low-calorie sweeteners. Yet, the direct impact of sweeteners on gut bacteria remains largely uncharacterized. Here we report interactions between 25 phylogenetically diverse gut bacterial strains and 39 commercially used sweeteners. We tested these sweeteners individually and in combination with four commonly co-consumed compounds, viz., advantame, caffeine, vanillin, and duloxetine. Three quarters of the tested sweeteners individually impacted growth of at least one bacterial strain. Further, over 100 interactions were found between sweeteners and the four co-consumed compounds. Isosteviol, a commonly used sweetener, and duloxetine, an antidepressant, synergistically inhibited Roseburia intestinalis, a bacterium previously linked to glucose homeostasis, and Parabacteroides merdae, a prevalent commensal linked to healthy microbiota. Proteomic, metabolomic, and genetic analyses indicate altered small molecule transport underpinning this sweetener-drug synergy. The isosteviol-duloxetine combination also modulated metabolism of a synthetic gut bacterial community leading to increased toxicity to HeLa cells and altered secretion of inflammation modulatory cytokines IL-6 and IL-8 by Caco-2 cells. Together, our data bring forward the prevalence of interactions between low-calorie sweeteners and common xenobiotics.

microbiology↗

bioRxiv2024

Extensive PFAS accumulation by human gut bacteria

Per- and polyfluoroalkyl Substances (PFAS) - the so-called forever chemicals - are a major cause of environmental and health concern due to their toxicity and long-term persistence1,2. Yet, no efficient mechanisms for their removal have been identified. Here we report bioaccumulation of PFAS by several gut bacterial species over a wide range of concentrations from nanomolar up to 500 M. For bioaccumulating Bacteroides uniformis, a highly prevalent species, we estimate intracellular PFAS concentration in the mM range - above that of most native metabolites. Despite this high bioaccumulation, B. uniformis cells could grow appreciably up to 250 M perfluorononanoic acid (PFNA) exposure. Escherichia coli, which accumulated PFAS to a much lesser extent, substantially increased PFAS bioaccumulation when lacking TolC efflux pump indicating trans-membrane transport in PFAS bioaccumulation. Electron microscopy and cryogenic Focused Ion Beam-Secondary Ion Mass-spectrometry revealed distinct morphological changes and intracellular localisation of PFNA aggregates. Bioaccumulation of PFAS and transmembrane transport is also evident in proteomics, metabolomics, thermal proteome profiling, and mutations following adaptive laboratory evolution. In an in vivo context, mice colonized with human gut bacteria showed, compared to germ-free controls or those colonized with low-bioaccumulating bacteria, higher PFNA levels in excreted feces. As the gut microbiota is a critical interface between exposure and human body, our results have implications for understanding and utilizing microbial contribution to PFAS clearance.

microbiology↗

bioRxiv2024

Off-purpose activity of industrial and agricultural chemicals against human gut bacteria

Contamination by industrial and agricultural chemicals like pesticides are a cause of great concern due to the risk to human and environmental health. While these chemicals are often considered to have restricted activity and are labelled as such, there are concerns over a broader toxicity range. Here we report the impact of 1076 pollutants spanning diverse chemistries and indicated applications on 22 prevalent commensal gut bacteria. Our systematic investigation uncovered 588 interactions involving 168 chemicals, the majority of which were not previously reported to have antibacterial properties. Fungicides and industrial chemicals showed the largest impact with circa 30% exhibiting anti-commensal properties. We find that the sensitivity to chemical pollutants across species surprisingly correlates with that to human-targeted drugs, suggesting common susceptibility mechanisms. Using a genome-wide chemical-genetic screen, we identified membrane transport and fatty acid metabolism as major modulators of the off-target toxicity of chemicals. Mutants exhibiting chemical resistance include those defective in producing human-health-relevant metabolites like branched short-chain fatty acids, indicating that chronic exposure could lead to selection against production of beneficial metabolites. Toxicokinetic modelling suggested gut bacteria could be used as more sensitive in vitro toxicity indicators for chemicals of concern than animal models. Together, our data uncovers the off-target activity of industrial and agricultural chemicals with widespread exposure against human gut bacteria. Impact on the structure and function of the microbiota should therefore be considered in assessing chemical safety.

microbiology↗

bioRxiv2024

Emergent survival and extinction of species within gut bacterial communities

Synthetic communities can help uncover metabolic forces shaping microbial ecosystems. Yet, in case of the gut microbiota, culturing in undefined media has prevented detection of metabolic dependencies. Here we show, using chemically defined media, how species survival is jointly determined by supplied resources and community metabolism. We used 63 representative gut bacterial strains and varied inoculum compositions to assemble stable communities in 14 defined media. Over 95% of the species showed markedly improved or diminished performance relative to monoculture in at least one condition, including 153 cases (21%) of emergent survival, i.e., species incapable of surviving on their own but thriving in a community, and 252 (35%) community-driven extinctions. Through single species additions and exclusions, metabolomic analysis, and ecological modelling, we demonstrate how inter-species dependencies - especially in poor media - are mediated by biotic nutrient supply. Our results highlight communal metabolic dividend as a key biotic force promoting emergent survival and diversity.

microbiology↗

bioRxiv2023

Gut microbiome remains stable following COVID-19 vaccination in healthy and immuno-compromised individuals

The bidirectional interaction between the immune system and the gut microbiota is a key contributor to various host physiological functions. Immune-associated diseases such as cancer and autoimmunity, as well as the efficacy of immunomodulatory therapies, have been linked to microbiome variation. While COVID-19 infection has been shown to cause microbial dysbiosis, it remains understudied whether the inflammatory response associated with vaccination also impacts the microbiota. Here, we investigate the temporal impact of COVID-19 vaccination on the gut microbiome in healthy and immuno-compromised individuals; the latter included patients with primary immunodeficiency and cancer patients on immunomodulating therapies. We find that the gut microbiome remained remarkably stable post-vaccination irrespective of diverse immune status, vaccine response, and microbial composition spanned by the cohort. The stability is evident at all evaluated levels including diversity, phylum, species, and functional capacity. Our results indicate the resilience of the gut microbiome to host immune changes triggered by COVID-19 vaccination and suggest minimal, if any, impact on microbiome-mediated processes. These findings encourage vaccine acceptance, particularly when contrasted with the significant microbiome shifts observed during COVID-19 infection.

microbiology↗

bioRxiv2023

Consistency across multi-omics layers in a drug-perturbed gut microbial community

Multi-omics analyses are increasingly employed in microbiome studies to obtain a holistic view of molecular changes occurring within microbial communities exposed to different conditions. However, it is not always clear to what extent each omics data type contributes to our understanding of the community dynamics and whether they are concordant with each other. Here we map the molecular response of a synthetic community of 32 human gut bacteria to three non-antibiotic drugs by using five omics layers, namely 16S rRNA gene profiling, metagenomics, metatranscriptomics, metaproteomics, and metabolomics. Using this controlled setting, we find that all omics methods with species resolution in their readouts are highly consistent in estimating relative species abundances across conditions. Furthermore, different omics methods complement each other in their ability to capture functional changes in response to the drug perturbations. For example, while nearly all omics data types captured that the antipsychotic drug chlorpromazine selectively inhibits Bacteroidota representatives in the community, the metatranscriptome and metaproteome suggested that the drug induces stress responses related to protein quality control and metabolomics revealed a decrease in polysaccharide uptake, likely caused by Bacteroidota depletion. Taken together, our study provides insights into how multi-omics datasets can be utilised to reveal complex molecular responses to external perturbations in microbial communities.

microbiology↗

bioRxiv2019

Emergence of stable coexistence in a complex microbial community through metabolic cooperation and spatio-temporal niche partitioning

Microbial communities in nature often feature complex compositional dynamics yet also stable coexistence of diverse species. The mechanistic underpinnings of such dynamic stability remain unclear as system-wide studies have been limited to small engineered communities or synthetic assemblies. Here we show how kefir, a natural milk-fermenting community, realizes stable coexistence through spatio-temporal orchestration of species and metabolite dynamics. During milk fermentation, kefir grains (a polysaccharide matrix synthesized by kefir microbes) grow in mass but remain unchanged in composition. In contrast, the milk is colonized in a dynamic fashion with early members opening metabolic niches for the followers. Through large-scale mapping of metabolic preferences and inter-species interactions, we show how microbes poorly suited for milk survive in, and even dominate, the community through metabolic cooperation and uneven partitioning between the grain and the liquid phase. Overall, our findings reveal how spatio-temporal dynamics promote stable coexistence and have implications for deciphering and modulating complex microbial ecosystems.

microbiology↗