Biology subjects

Gonzalez, E.

Publications and source records attributed to Gonzalez, E..

At least 19 recordsLinked to original sources

bioRxiv2026

Computational modeling of breast cancer metastases predicts response to dual checkpoint inhibition and reveals spatially-informed treatments

In advanced breast cancers, the highly suppressive tumor microenvironment contributes to poor responses to immune checkpoint inhibition. The degree of suppression varies by site of disease, which can affect metastatic progression. To investigate this phenomenon, we have developed an agent-based model of cell-cell interactions within the tumor microenvironment, specifically tuned to in vivo data from murine breast-to-lung metastases. The model includes nine functional cell types (cancer cells, M0-, M1-, and M2-like macrophages, CD4+ T cells, T regulatory cells [Tregs], CD8+ T cells, NK cells, and MDSC-like cells). We incorporated a novel continuum model to describe exhaustion of CD8+ T and NK cells, where their exhaustion is impacted by cell-cell interactions in the TME via direct and indirect interactions. We also modeled the effect of the immune checkpoint inhibitors (ICI) anti-PD-1 and anti-CTLA-4, termed "dual ICIs". We used this model to simulate the spatiotemporal trajectories of 19 metastases without treatment and with dual ICIs. The model predicted that dual ICIs lead to statistically significant reductions in cancer cell proliferation in seven of the metastases (37%), and spatial analyses of these metastases indicate they have structural similarities at multiple scales of tumor organization. Additionally, spatial analysis suggests that high colocalization of CD8+ T cells with Tregs could prevent dual ICIs from being effective, and simulation of Treg blockade combined with dual ICIs led to 15 total metastases having a statistically significant treatment effect (80% total). Thus, our model provides a highly resolved spatiotemporal platform for studying the cell-cell interactions that can drive resistance to ICIs in diverse TME settings and identifies potential therapeutic avenues to enhance the efficacy of emerging ICI therapies.

systems biology↗

bioRxiv2026

Discovery of a hydrolysis operon in Lachnospiraceae provides a genetic basis to understanding castalagin metabolism by the human microbiome in a clinical study.

Gut microbes metabolize the ellagitannin castalagin to ellagic acid and urolithins, a process associated with health effects for the host. Despite the use of the castalagin-rich camu camu extracts in clinical trials, the genes and taxa responsible for castalagin hydrolysis remain elusive. We used multi-omics to discover a castalagin associated hydrolase (cah) operon sparsely distributed in Lachnospiraceae. Analysis of fecal samples from a camu camu supplementation clinical trial demonstrates functional redundancy with prevalence of cah and other ellagic acid metabolism genes in different taxa explaining the prevalence of metabolites. Employing genome mining strategies, we discovered and validated ellagitannin metabolism genes in uncharacterized and uncultured species. We further identified flavogallonic acid as a prevalent metabolite of castalagin in human fecal samples. Collectively, this work provides a genetic basis for castalagin metabolism to urolithins and flavogallonic acid end-metabolites and sets the stage to study the role of metabolism in clinical trials.

microbiology↗

bioRxiv2026

Knock-in = knock-out: differential fitness effects of cardinal mutations in Anopheles stephensi

The kynurenine pathway metabolizes tryptophan into 3-hydroxykynurenine (3-HK), a precursor for ommochrome eye pigments synthesized via the cardinal (cd) gene in mosquitoes. While cd disruption was presumed neutral, we observed fitness costs in Anopheles stephensi knock-in but not knock-out cd mutants. Here we investigated this anomaly further by assessing survival, fecundity, and midgut integrity across multiple cd mutant lines. Heterozygous knock-in lines, expressing a fluorescent marker and guide RNA for CRISPR/Cas9, exhibited reduced survival post-blood feeding, larva-to-adult survival deficits, and midgut barrier dysfunction, whereas knock-outs showed no such costs. Oral supplementation with xanthurenic acid partially rescued knock-in mortality, implicating oxidative stress linked to 3-HK metabolism. Expression analyses suggest transgene insertion effects, rather than cd disruption, underlie these fitness costs. These findings highlight the importance of evaluating insertional effects in gene drive target selection and support cd as a viable target for genetic control strategies in An. stephensi.

genetics↗

bioRxiv2026

A novel preclinical mouse model recapitulates progressive phenotypes of Bryant-Li-Bhoj Syndrome

Bryant-Li-Bhoj Syndrome (BLBS; OMIM: 619720, 619721) is a Mendelian neurogenetic condition, first described in 2020, with a mixed neurodevelopmental/neurodegenerative phenotype and variable systemic features. To date, 100 affected individuals with 74 unique causative variants have been published. Clinical data and prior functional work in multiple model systems have emphasized the utility of interrogating the pathogenesis of multiple causal variants to identify a convergent, therapeutically targetable mechanism. Additionally, the ability to evaluate the efficacy of future therapeutics relies on the availability of a robustly validated preclinical model. Here, we characterize the developmental and neurobehavioral phenotypes of a novel BLBS mouse model harboring one of the most recurrent causative variants (h3-3a p.T45I). H3.3T45I mice recapitulate the BLBS natural history: perinatal growth restriction, delayed developmental milestones, and progressive motor and gait impairments. Adult mice additionally display craniofacial differences, impaired nest building, hyperactivity in a social context, and male-specific elevated aggression. The non-invasive, clinically translatable endpoints established here provide a validated preclinical platform for evaluating therapeutics for a community whose current standard of care is symptom management. Summary StatementA new mouse model mirrors the developmental delays, motor decline, and behavioral changes seen in individuals with this rare, progressive genetic brain disorder, providing a foundation for testing future therapies.

genetics↗

bioRxiv2026

A novel machine-learning classification model detects oxidative fiber type transitions in a rabbit model of cerebral palsy

The distribution of slow-and fast-twitch fiber types in a skeletal muscle heavily influences its physiology. Muscle biopsy studies indicate atypical fiber type composition and fiber size variation in children with cerebral palsy (CP), but subjects have variable treatment history and a variety of muscles affected, so uncertainties remain. In this study, we developed a novel machine-learning classification model to perform high-throughput fiber typing of complete transverse muscle sections. Our XGBoost algorithm-based prediction model yielded a balanced accuracy score of 0.89 and a macro F1-score of 0.89, reflecting its ability to robustly predict muscle fiber type from myosin heavy chain (MyHC) isoform immunofluorescence intensities and morphological descriptors. This is the first reported fiber type classifier to consider hybrid fibers, which is a major advance, considering at least 20% of myofibers are hybrid yet they are routinely overlooked due to difficulty in their detection. We used this classification model to define fiber types of more than 7 million myofibers from flexor-extensor muscle pairs in rabbits that experienced hypoxia-ischemia (HI) injury in utero (modeling CP), and typically developing sham rabbits. We observed an oxidative fiber type shift in flexor muscles (biceps brachii and tibialis anterior) of HI rabbits at postnatal day (P)14-20 and P30-32 (weaning age). This altered fiber type composition imparts reduced contractile force and is amenable to sustained muscle activity; it may reflect chronic low-frequency motor unit activation. This work supports prior clinical reports that developmental trajectories of muscle fibers are disrupted in CP.

neuroscience↗

bioRxiv2026

A class act: HDAC1-Malat1 regulates MDSC apoptosis and cell cycling to decrease suppression of T cells

Myeloid derived suppressor cells (MDSCs) are key players in the immune-suppressed tumor microenvironment (TME) and significantly contribute to immune checkpoint inhibition (ICI) resistance, making them favorable targets for cancer immunotherapy. Epigenetic reprogramming of MDSCs using histone deacetylase (HDAC) inhibitors shows promise to sensitize the TME to ICIs. However, the molecular mechanism of HDAC inhibition in MDSCs has yet to be elucidated. Murine and human MDSC models treated with Entinostat revealed that the long non-coding RNA Malat1 downregulates pSTAT3 and decreases MDSC-mediated suppression of T cell proliferation. Through HDAC inhibitor screens, we identified HDAC1 as preferentially regulating Malat1 expression, STAT3 activation, and MDSC suppression. We also show that HDAC1 inhibition increases MDSC apoptosis by shifting pro-vs. anti-apoptotic signals and increases G0/G1 cell cycle arrest via decreasing G1-S transition cyclin-CDK complexes. Collectively, our findings provide a multi-pronged mechanism of HDAC inhibition in MDSCs that inform the development of future rational combination therapies. One Sentence SummaryHDAC1 inhibition in MDSCs increases Malat1, decreases pSTAT3, induces apoptosis/cell cycle arrest, and decreases suppression of T cells

immunology↗

bioRxiv2026

FASTERCC: Accelerating Flux Consistency Testing and Context-Specific Reconstruction for Large-Scale Metabolic Network Models

The increase in size of metabolic network models especially with the advent of single-cell data calls for scalable reconstruction and analysis tools. Such models, often used for drug discovery and the analysis of microbial communities rely on consistency testing and reconstruction algorithms such as FASTCORE and FASTCC. However, with models nowadays comprising hundreds of thousands of reactions, the running times of such algorithms increased from few minutes to hours or days even with high performance computing. Experiments that require multiple reconstructions, such as parameter tuning or cross-validation, are practically infeasible in very large networks. Here we introduce FASTERCC, a new version of FASTCC, that leverages structural information for removing type I and II dead-ends, the orientation of reversible reactions and correcting the reversibility of reactions that are structurally incapable of carrying flux in both directions prior to any feasibility tests. These improvements reduce drastically the running time of FASTERCC by a median 20-fold speedup in comparison to FASTCC for networks with a larger number of block reactions. The model cleaning performed by FASTERCC also reduces the computational time of downstream analyses, notably of FASTCORE up to 50%.

systems biology↗

bioRxiv2025

TBCK Deficiency Alters Ribosomal Function, RNA Splicing, and miRNA Networks: Insights from Multi-Omics Analyses

TBC1 domain-containing kinase (TBCK) is an important protein with implications in brain development. Biallelic variants in the TBCK gene are known to cause TBCK-related neurodevelopmental disorder (OMIM #616900) [1], a rare genetic multisystemic disease characterized by developmental delay, variable developmental regression, seizures, and premature death in late childhood for which no cure is currently available. Though previous work has provided a better understanding of the proteins role, the mechanism for how TBCK variants affect gene expression and protein regulation has remained understudied. To better understand the impact of these alterations, and using an unbiased approach, we employed the power of multi-omics to define the cellular consequences at the transcript and protein level. Our comprehensive analysis uncovered significant disruptions in ribosomal and translation-related pathways with widespread alternative splicing defects, and key miRNA changes that validate previously reported molecular findings. This work provides a clearer molecular framework for TBCK dysfunction in TBCK-/- cells and offers a valuable foundation to identify potential therapeutic targets.

genetics↗

bioRxiv2025

Integrating multiplexing into confineable gene drives effectively overrides resistance in Anopheles stephensi

Anopheles stephensi is a major malaria vector mainly present in southern Asia and the Arabian Peninsula. Since 2012 it has invaded several countries of eastern Africa, stimulating urgent efforts to develop more efficient strategies for vector control such as CRISPR/Cas9-based homing gene drives. Target site resistance is a significant challenge to the deployment of these systems. When a double-stranded break is repaired by NHEJ, it can lead to mutations which destroy the target site, making that allele unrecognizable to the sgRNA and resistant to further cleavage. The use of multiple sgRNAs has the potential to solve this issue. We performed experimental crosses to assess the homing and cutting efficiency of two different multiplexing strategies targeting the cardinal locus, in the presence and absence of a resistance allele. We found pre-existing mutations at one sgRNA target site did not significantly reduce the homing efficiency for either strategy. Modelling indicates that while both strategies can overcome resistance allele formation, the fitness of the drive-carrying alleles is a critical factor in determining the overall performance and persistence of a split drive.

genetics↗

bioRxiv2025

Beyond RECIST: mathematical modeling and Bayesian inference reveal the importance of immune parameters in metastatic breast cancer

Successful immunotherapies must overcome patient- and organ-specific tumor heterogeneities to mount an effective response. Yet tumor dynamics remain poorly characterized in organ-specific contexts and associated immune environments. To quantify heterogeneous tumor responses, we developed methods to fit mathematical models of the tumor-immune dynamics to patients undergoing combination therapy for metastatic breast cancer: checkpoint inhibition via nivolumab + ipilimumab combined with entinostat, as measured by RECIST criteria. In a subset of patients additional immune dynamics were quantified by spatial proteomics. Bayesian parameter inference revealed that only immune-modulatory parameters controlled response; parameters controlling cytotoxicity were uninformative. Through posterior parameter sampling and simulation, we created virtual tumor cohorts, enabling extrapolation beyond the data to predict probabilities of response in metastatic lesions where no data exist. We validated pre-dictions from our virtual tumor population using held-out data characterizing off-target lesions from the patient cohort. Profile-wise likelihood analysis revealed that scans in the week immediately following treatment hold particularly high value in identifying the tumor dynamics. Overall, we demonstrate how through modeling & inference cohort size limitations can be over-come through the creation of virtual tumor populations, giving insight into the site-specific mechanisms of disease progression and response.

systems biology↗

bioRxiv2025

A multiplex extracellular interactome screening method employing high-avidity nanoparticles

Metazoan cells signal to each other via direct contact between cell surface proteins (CSPs) and by interactions of CSP receptors with secreted ligands. CSP extracellular domain (ECD) interactions control organ development and physiology and are perturbed in disease states. However, because they cannot be accurately assessed using standard high-throughput screening techniques, they are underrepresented in protein interaction databases. Many ECD interactions are of low affinity, and their detection in vitro requires taking advantage of avidity effects, typically by multimerization of fusion proteins. Assays that test only one or a few interactions in each binding reaction are inadequate for global interactome screening. Here we describe a new multiplex method that uses purified dimeric ECD fusion proteins coupled to 60-mer nanoparticles as soluble prey, and the same dimers coupled to spectrally distinguishable fluorescent microspheres (beads) as bait. We add one prey to a mixture of up to 500 baits in a single well, then use a Luminex FLEXMAP 3D (FM3D) instrument to read out bait identity and prey binding. The FM3D measures the fluorescent dye ratio for each bead and simultaneously determines the amount of epitope-tagged prey bound to that bead. We use the method, denoted as the Multiplex Interactome Assay (MPIA), to analyze a proof-of-concept (PoC) set of 41 CSPs and secreted protens that is derived from larger collections examined in two interactome screens that used ELISA-based binding assays. By analyzing interactions among PoC proteins, we compared the MPIA with earlier screening methods. The MPIA has a dynamic range that is at least 30-fold greater than ELISA-based assays and appears to be more sensitive. By coupling the MPIA to an automated protein production and purification platform, we hope to be able to conduct a screen for interactions among thousands of human CSPs and secreted ligands.

molecular biology↗

bioRxiv2025

An Automated End-to-End Workflow for Production of Secreted Proteins in Transfected Mammalian Cells

The advancement of automation technologies has helped to enable a surge in large-scale screening efforts across fields such as molecular biology, protein biochemistry, cell biology, and structural biology. In the context of this "omics"-driven research, there is a need to generate automation platforms that are more flexible and less expensive, so that they can be utilized for basic research conducted by small groups. A key challenge in automation lies in developing methods that can replicate fine motor techniques that are normally performed manually by researchers at the bench. We are engaged in a large-scale project to map interactions among human cell-surface and secreted proteins and assess their effects on cells. This project involves production of a library of more than 2000 recombinant His-tagged fusion proteins secreted from transfected Expi293 cells. To execute such a project with a small group at an academic institution required construction of an affordable automated system that could also be used by other investigators. This led us to develop a high-throughput, 96-well format automation platform for end-to-end protein production. The workflow includes transformation of E. coli, plasmid DNA preparation, transient transfection, protein purification, desalting and buffer exchange, protein quantification, and normalization of protein concentrations, resulting in assay-ready proteins. The system is built around an in-house engineered modular robotic platform that integrates liquid handling with a suite of interchangeable plug-and-play mobile enclosed device modules. Housed within a BSL-2 sterile environment, the platform enables flexible, fully automated workflows and can be readily customized for diverse user-defined protocols.

biochemistry↗

bioRxiv2025

Detection of West Nile Virus via Retrospective Mosquito Arbovirus Surveillance in the United Kingdom

In March 2025, as part of on-going enhanced surveillance for mosquito-borne Orthoflaviviruses, West Nile virus (WNV) RNA was detected in two pools of female Aedes vexans collected in July 2023 in Nottinghamshire, England. Viral RNA detection was achieved via reverse transcription-qPCR. Sequencing and subsequent phylogenetic analysis of a 402 bp fragment indicated that the detections clustered with WNV lineage 1a. The exact origin of this virus remains unclear, but this finding indicates a historic WNV presence in the United Kingdom (UK). Surveillance has not provided evidence of further viral transmission to date.

molecular biology↗

bioRxiv2025

Cancer systems immunology reveals myeloid - T cell interactions and B cell activation mediate response to checkpoint inhibition in metastatic breast cancer

Sensitization of the immune-suppressed tumor microenvironment (TME) of breast cancer by histone deacetylase inhibition shows promise, but the mechanisms of sensitization are unknown. We investigated the TME of breast-to-lung metastases by combining experimental and clinical data with theory. Knowledge-guided subclustering of single-cell RNA-sequencing data and cell circuits analysis identified 39 cell states and salient interactions, of which myeloid, T cell and B cell subpopulations were most affected by treatment. Using functional immunologic assays, we verified that inhibition of the ICAM pathway partially recapitulated treatment effects. Mathematical modeling of tumor-immune dynamics confirmed that tumor reduction required simultaneous modulation of multiple TME interactions. We found evidence that treatment affected anti-tumor antibody production. Analysis of patient biopsies via spatial proteomics corroborated preclinical findings: in responders we observed increased B cell activation, mature tertiary lymphoid structures, and increased CD8+ T cell--macrophage distances with treatment. Overall, this study provides a framework for the discovery of cell-cell interactions that govern responses in complex TMEs. Statement of significanceThis study provides a framework for the discovery of cell-cell interactions that control responses in complex TMEs. We not only identify impactful tumor immunologic interactions that facilitate sensitization of the metastatic TME but also demonstrate how interdisciplinary data integration fuels cancer systems immunology to accelerate discovery of mechanisms of successful immunotherapeutic response in breast cancers and other previously unresponsive solid tumor types.

cancer biology↗

bioRxiv2025

Vesicular Rps6 released by astrocytes regulate local translation and enhance synaptic markers in neurons

In neurons, like in any other cell, their function often relies on the fine tuning of their protein levels, which is achieved by the balance between protein synthesis and turnover. Defects in protein homeostasis frequently leads to neuronal dysfunction and neurological disorders. Given their extreme morphological complexity and high compartmentalization, neurons highly depend on the asymmetrical distribution of their proteome. The common belief is that proteins that sustain axonal, dendritic and synaptic functions are synthesized in the soma and then transported to distal neuronal compartments. However, there is a complementary mechanism by which the mRNAs, and not the proteins, are transported to distal subneuronal domains, and once they reach their destination they are locally translated. Although once considered heretical, local translation (or local protein synthesis) is now widely accepted by the scientific community. Nonetheless there is one question that remains largely unexplored in the field and that is whether local translation in dendrites, axons and synapses is fully regulated by the neuron itself or if non-neuronal cells (e.g. glia) can modulate this mechanism in a non-cell-autonomous manner. Here we show that astroglia regulates local protein synthesis and enhances synaptic markers by releasing extracellular vesicles (EVs) containing ribosomal protein Rps6. To our knowledge this is the first report that directly demonstrates glial control of local translation in neurons through EV-mediated glia-to-neuron communication.

neuroscience↗

bioRxiv2025

Stiffening cells with light

Fluorescence microscopy is widely used to observe structures and dynamic processes in living cells and organisms and is often used as if it were purely innocuous to the cells or structures of interest. However, it can lead to phototoxicity, which can affect the cellular behavior and lead to erroneous interpretations of the observations. The major cause of cell damage through phototoxicity is the production of reactive oxygen species (ROS), which can form crosslinks between intracellular molecules, including proteins and nucleic acids. By using profile microindentation and atomic force microscopy, we demonstrate that the excitation of various fluorescent probes leads to a large increase in the stiffness of several cell types within seconds of illumination. The stiffening exhibits a dose-dependent response, where longer exposure times to exciting light are correlated with larger stiffening. This photostiffening effect explains why T cells loaded with the Fluo-4 Calcium probe stop emitting a protrusion within seconds after the excitation light is turned on. We observed photostiffening in different cell types and fluorophores. We showed that repeated cell indentation alone led to cell stiffening as well as excitation with blue or UV light in the absence of a fluoroph ore. However, in the latter case, the stiffening was much smaller than that when the fluorophore was excited. We used both sharp and blunt indenters to show that stiffening occurred not only at the cell cortex level but also deeper in the cell interior and that photostiffening is independent of actin cytoskeleton organization. We correlated the increase in cell stiffness with the production of intracellular reactive oxygen species and reproduced cell stiffening by incubating cells with a ROS inducer, H2O2. The excitation of the photosensitizer Pheophorbide a, which induces a specific type of reactive oxygen species, namely singlet oxygen, also led to cell stiffening. This study reminds the experimentalists that it is crucial to perform controls when using fluorescence. It further allows us to propose exploiting photostiffening as a new method for rapidly quantifying phototoxicity. SignificanceThis study reveals a direct relationship between fluorescence excitation and cell mechanical properties. The generality of th is phenomenon across diverse fluorophores and cell types highlights the importance of controlling phototoxicity in fluorescence experiments, in particular in complex, quantitative cell biology and biophysical experiments, but also reveals an unexpected rol e of intracellular reactive oxygen species production and identifies cell stiffness as a proxy for assessing the efficacy of photodynamic therapy.

biophysics↗

bioRxiv2024

Intratumoral CXCL12 Gradients Contextualize Tumor Cell Invasion, Migration and Immune Suppression in Breast Cancer

Although the CXCL12/CXCR4 pathway has been prior investigated for its prometastatic and immuno- suppressive roles in the tumor microenvironment, evidence on the spatiotemporal regulation of these hallmarks has been lacking. Here, we demonstrate that CXCL12 forms a gradient specifically around cancer cell intravasation doorways, also known as Tumor Microenvironment of Metastasis (TMEM) doorways, thus facilitating the chemotactic translocation of prometastatic tumor cells expressing CXCR4 toward the perivascular TMEM doorways for subsequent entry into peripheral circulation. Fur- thermore, we demonstrate that the CXCL12-rich micro-environment around TMEM doorways may cre- ate immunosuppressive niches, whereby CD8+ T cells, despite being attracted to these regions, often exhibit reduced effector functions, limiting their efficacy. While the CXCL12/CXCR4 pathway can mini- mally influence the overall composition of immune cell populations, it biases the distribution of CD8+ T cells away from TMEM doorways, justifying its prior-established role as immunosuppressive factor for CD8+ T cells. Our research suggests that the complex interactions between CXCL12 and the various tumor and immune cell types contributes not only to the completion of the initial steps of the metastatic cascade, but also offers an immunological "sanctuary" to prometastatic tumor cells homed around TMEM doorways. Overall, our study enhances our current understanding on the mechanisms, via which CXCL12 orchestrates tumor cell behavior and immune dynamics, potentially guiding future thera- peutic strategies to combat breast cancer metastasis and improve anti-tumor immunity.

cancer biology↗

bioRxiv2024

Identification of novel fructo-oligosaccharide bacterial consumers by pulse metatranscriptomics in a human stool sample

Dietary fibres influence the composition of the human gut microbiota and directly contribute to its downstream effects on host health. As more research supports the use of glycans as prebiotics for therapeutic applications, the need to identify the gut bacteria that metabolize glycans of interest increases. Fructooligosaccharide (FOS) is a common diet-derived glycan that is fermented by the gut microbiota and has been used as a prebiotic. Despite being well studied, we do not yet have a complete picture of all FOS-consuming gut bacterial taxa. To identify new bacterial consumers, we used a short exposure of microbial communities in a stool sample to FOS or galactomannan as the sole carbon source to induce glycan metabolism genes. We then performed metatranscriptomics, paired with whole metagenomic sequencing (WMS), and 16S amplicon sequencing. The short incubation induced genes involved in carbohydrate metabolism, like carbohydrate-active enzymes (CAZymes), including glycoside hydrolase family 32 genes, which hydrolyze fructan polysaccharides like FOS and inulin. Interestingly, FOS metabolism transcripts were notably overexpressed in Blautia species not previously reported to be fructan consumers. We therefore validated the ability of different Blautia species to ferment fructans by monitoring their growth and fermentation in defined media. This pulse metatranscriptomics approach is a useful method to find novel consumers of prebiotics and increase our understanding of prebiotic metabolism by CAZymes in the gut microbiota. SignificanceComplex carbohydrates are key contributors to the composition of the human gut microbiota and play an essential role in the microbiotas effects on host health. Understanding which bacteria consume complex carbohydrates, or glycans, provides a mechanistic link between dietary prebiotics and their beneficial health effects, an essential step for their therapeutic application. Here, we used a pulse metatranscriptomics pipeline to identify bacterial consumers based on glycan metabolism induction in a human stool sample. We identified novel consumers of FOS among Blautia species, expanding our understanding of this well-known glycan. Our approach can be applied to identify consumers of understudied glycans and expand our prebiotic repertoire. It can also be used to study prebiotic glycans directly in stool samples in distinct patient populations to help delineate the prebiotic mechanism.

microbiology↗