Biology subjects

Wolff, R.

Publications and source records attributed to Wolff, R..

9 recordsLinked to original sources

bioRxiv2026

Growth capacity and mortality burden shape microbial persistence under osmotic stress in Bacteroides thetaiotaomicron

Microbial persistence in the gut is central to sustaining beneficial host-microbiota interactions; however, characterizing determinants of persistence in vivo can be challenging due to the complexity of native microbial communities interacting with the host. Here, we used a defined microbial consortium to demonstrate that intrinsic in vitro growth capacity becomes increasingly predictive of in vivo relative abundance as intestinal osmolality increases. In Bacteroides thetaiotaomicron, in vivo abundance was higher than predicted from growth capacity alone, indicating that additional physiological factors contribute to persistence. We identify mortality as one such determinant: adaptation to prolonged osmotic stress markedly reduced cell loss without enhancing growth capacity. This adaptive phenotype was associated with rapid and reversible phase variation in cell surface-associated PUL78/80 rather than fixed de novo mutations, with the PUL78/80-OFF state becoming progressively enriched among surviving cells as mortality increased. Our findings demonstrate that in addition to growth capacity, reduced cell loss can provide a distinct route to microbial persistence during environmental perturbation.

microbiology↗

bioRxiv2025

The Preclinical Animal Network (PCAN): Integrative high-throughput phenotyping of standardized mouse models for Prader-Willi syndrome

The Preclinical Animal Network (PCAN) is a collaborative resource established to advance translational research and therapeutic development for Prader-Willi syndrome (PWS), a rare neurodevelopmental disorder caused by loss of paternally expressed genes on chromosome 15q11-q13. PCAN integrates standardized, high-throughput phenotyping of approximately 1,000 mice across six engineered lines carrying paternal deletions of Ndn, Magel2, Snord116, Ipw, and multigenic loci. Using validated experimental pipelines spanning metabolic, behavioral, and developmental domains, we captured comprehensive phenotypic profiles by applying a statistical variance-decomposition framework to partition genetic and environmental contributions. This analysis provides robust genotype-phenotype maps, revealing shared and model-specific phenotypic effects while accounting for key confounding factors. The PCAN resource provides a framework for evaluating PWS-relevant phenotypes and benchmarking therapeutic strategies. By providing open access to its mouse models, datasets and analytical resources, PCAN enables the research community to apply standardized, reproducible workflows and accelerate the development of targeted, mechanism-based treatments.

genetics↗

bioRxiv2025

'SpikeNburst' and 'Nicespike': Advanced Tools for Enhancing and Accelerating In Vitro High-Density Electrophysiology Analysis

High-density multi-electrode arrays (HD-MEAs) enable the recording of in vitro neuronal activity with exceptional spatial and temporal resolution. However, analysing these extensive datasets presents challenges, such as artefact removal, spike sorting, and accurate assessments of neuronal synchronization. Here, we introduce a structured protocol for conducting comprehensive HD-MEA analyses using two Python-based tools: spikeNburst and nicespike. This protocol provides a scalable and systematic approach to processing HD-MEA recordings, ensuring efficient data handling and robust analytical outcomes. The spikeNburst tool incorporates advanced methodologies for spike train filtering, burst and network burst detection, and synchronization analysis. Complementing this, we have implemented a full analysis pipeline in the nicespike tool, featuring GPU-accelerated spike sorting via template matching with Kilosort, enabling accurate identification of neuronal units across multiple electrodes. This protocol ensures more precise analyses by reducing redundancy and overestimation inherent in single-channel approaches. Moreover, both tools offer graphical user and command-line interfaces, ensuring accessibility for diverse user needs. We validated our protocol on in vitro neuronal culture recordings, demonstrating its suitability to identify somatic and dendritic features of neuronal units, characterize bursting behaviour, and quantify synchronization at both unit and network levels. By addressing critical limitations of existing methods, spikeNburst and nicespike provide a robust, scalable, and user-friendly framework for HD-MEA data analysis, enhancing the study of neural network dynamics and single-cell activity in detail.

neuroscience↗

bioRxiv2025

Uniform bacterial genetic diversity along the guts of mice inoculated with human stool

Environmental gradients throughout the digestive tract shape spatial variation in the composition and abundance of bacterial species along the gut. However, much less is known about how genetic diversity within bacterial species is distributed along the gut. Understanding this distribution is important because bacterial genetic variants confer traits that influence both microbiome function and host physiology, including local inflammation and nutrient metabolism. Thus, to understand how the microbiome functions at a mechanistic level, it is essential to understand how genetic diversity is organized along the gut. In this study, we profiled genetic diversity of approximately 30 common gut commensal bacteria in five regions along the gut lumen in germ-free mice colonized with the same healthy human stool sample. Although species composition varied considerably along the gut, genetic diversity within species was substantially more uniform. Driving this uniformity were similar strain frequencies along the gut, implying that multiple, genetically divergent strains of the same species can coexist within a host without spatially segregating. Additionally, the approximately 60 unique evolutionary adaptations arising within mice tended to sweep throughout the gut, showing little gut region specificity. We then analyzed metagenomic samples collected along the guts of conventional mice and healthy humans and found similar dynamics with their natural microbiomes, suggesting that uniform bacterial genetic diversity may be common to multiple host species. Together, our findings demonstrate that uniform spatial distribution of genetic diversity along the gastrointestinal tract is a robust feature of mammalian gut ecosystems.

microbiology↗

bioRxiv2024

A conserved genetic basis for commensal-host specificity through live imaging of colonization dynamics

Animals throughout the metazoa selectively acquire specific symbiotic gut bacteria from their environment that aid host fitness. Current models of colonization suggest these bacteria use weakly specific receptors to stick to host tissues and that colonization results when they stick in a region of the host gut that overlaps with their nutritional niche. An alternative model is that unique receptor-ligand binding interactions provide specificity for target niches. Here we use live imaging of individual symbiotic bacterial cells colonizing the gut of living Drosophila melanogaster to show that Lactiplantibacillus plantarum specifically recognizes a distinct physical niche in the host gut. We find that recognition is controlled by a colonization island that is widely conserved in commensals and pathogens from the Lactobacillales to the Clostridia. Our findings indicate a genetic mechanism of host specificity that is broadly conserved. One-Sentence SummaryHost-symbiont specificity is encoded by a conserved colonization island that provides molecular precision to host niche access.

microbiology↗

bioRxiv2023

Pervasive selective sweeps across human gut microbiomes

The human gut microbiome is composed of a highly diverse consortia of species which are continually evolving within and across hosts. The ability to identify adaptations common to many human gut microbiomes would not only reveal shared selection pressures across hosts, but also key drivers of functional differentiation of the microbiome that may affect community structure and host traits. However, to date there has not been a systematic scan for adaptations that have spread across human gut microbiomes. Here, we develop a novel selection scan statistic named the integrated Linkage Disequilibrium Score (iLDS) that can detect the spread of adaptive haplotypes across host microbiomes via migration and horizontal gene transfer. Specifically, iLDS leverages signals of hitchhiking of deleterious variants with the beneficial variant. Application of the statistic to[~] 30 of the most prevalent commensal gut species from 24 populations around the world revealed more than 300 selective sweeps across species. We find an enrichment for selective sweeps at loci involved in carbohydrate metabolism--potentially indicative of adaptation to features of host diet--and we find that the targets of selection significantly differ between Westernized and non-Westernized populations. Underscoring the potential role of diet in driving selection, we find a selective sweep absent from non-Westernized populations but ubiquitous in Westernized populations at a locus known to be involved in the metabolism of maltodextrin, a synthetic starch that has recently become a widespread component of Western diets. In summary, we demonstrate that selective sweeps across host microbiomes are a common feature of the evolution of the human gut microbiome, and that targets of selection may be strongly impacted by host diet.

evolutionary biology↗

bioRxiv2023

ARF6-dependent endocytic trafficking of the Interferon-γ receptor drives adaptive immune resistance in cancer.

Adaptive immune resistance (AIR) is a protective process used by cancer to escape elimination by CD8+ T cells. Inhibition of immune checkpoints PD-1 and CTLA-4 specifically target Interferon-gamma (IFN{gamma})-driven AIR. AIR begins at the plasma membrane where tumor cell-intrinsic cytokine signaling is initiated. Thus, plasma membrane remodeling by endomembrane trafficking could regulate AIR. Herein we report that the trafficking protein ADP-Ribosylation Factor 6 (ARF6) is critical for IFN{gamma}-driven AIR. ARF6 prevents transport of the receptor to the lysosome, augmenting IFN{gamma}R expression, tumor intrinsic IFN{gamma} signaling and downstream expression of immunosuppressive genes. In murine melanoma, loss of ARF6 causes resistance to immune checkpoint blockade (ICB). Likewise, low expression of ARF6 in patient tumors correlates with inferior outcomes with ICB. Our data provide new mechanistic insights into tumor immune escape, defined by ARF6-dependent AIR, and support that ARF6-dependent endomembrane trafficking of the IFN{gamma} receptor influences outcomes of ICB.

cancer biology↗

bioRxiv2022

Community diversity is associated with intra-species genetic diversity and gene loss in the human gut microbiome

The human gut microbiome contains a diversity of microbial species that varies in composition over time and across individuals. These species (and strains within species) can migrate across hosts and evolve by mutation and recombination within hosts. How the ecological process of community assembly interacts with intra-species diversity and evolutionary change is a longstanding question. Two contrasting hypotheses have been proposed based on ecological observations and theory: Diversity Begets Diversity (DBD), in which taxa tend to become more diverse in already diverse communities, and Ecological Controls (EC), in which higher community diversity impedes diversification within taxa. Previously, using 16S rRNA gene amplicon data across a range of environments, we showed a generally positive relationship between taxa diversity and community diversity at higher taxonomic levels, consistent with the predictions of DBD (Madi et al., 2020). However, this positive diversity slope reaches a plateau at high levels of community diversity. Here we show that this general pattern holds at much finer genetic resolution, by analyzing intra-species strain and nucleotide variation in static and temporally sampled shotgun-sequenced fecal metagenomes from cohorts of healthy human hosts. We find that both intra-species polymorphism and strain number are positively correlated with community Shannon diversity. This trend is consistent with DBD, although we cannot exclude abiotic drivers of diversity. Shannon diversity is also predictive of increases in polymorphism over time scales up to [~]4-6 months, after which the diversity slope flattens and then becomes negative--consistent with DBD eventually giving way to EC. Also supporting a complex mixture of DBD and EC, the number of strains per focal species is positively associated with Shannon diversity but negatively associated with richness. Finally, we show that higher community diversity predicts gene loss in a focal species at a future time point. This observation is broadly consistent with the Black Queen Hypothesis, which posits that genes with functions provided by the community are less likely to be retained in a focal species genome. Together, our results show that a mixture of DBD, EC, and Black Queen may operate simultaneously in the human gut microbiome, adding to a growing body of evidence that these eco-evolutionary processes are key drivers of biodiversity and ecosystem function.

evolutionary biology↗

bioRxiv2021

Ecological Stability Emerges at the Level of Strains in the Human Gut Microbiome

The human gut microbiome harbors substantial ecological diversity at the species level, as well as at the strain level within species. In healthy hosts, species abundance fluctuations in the microbiome are thought to be stable, and these fluctuations can be described by macroecological laws. However, it is less clear how strain abundances change over time. An open question is whether individual strains behave like species themselves, exhibiting stability and following the macroecological relationships known to hold at the species level, or whether strains have different dynamics, perhaps due to the relatively close phylogenetic relatedness of co-colonizing lineages. Here, we analyze the daily dynamics of intra-specific genetic variation in the gut microbiomes of four healthy, densely longitudinally sampled hosts. First, we find that overall genetic diversity in a large majority of species is stationary over time, despite short-term fluctuations. Next, we show that fluctuations in abundances in approximately 80% of strains analyzed can be predicted with a stochastic logistic model (SLM)--an ecological model of a population experiencing environmental fluctuations around a fixed carrying capacity which has previously been shown to capture statistical properties of species abundance fluctuations. The success of this model indicates that strain abundances typically fluctuate around a fixed carrying capacity, suggesting that most strains are dynamically stable. Finally, we find that the strain abundances follow several empirical macroecological laws known to hold at the species level. Together, our results suggest that macroecological properties of the human gut microbiome, including its stability, emerge at the level of strains.

ecology↗