Biology subjects

Ubeda, C.

Publications and source records attributed to Ubeda, C..

5 recordsLinked to original sources

bioRxiv2026

Defining nutrient dependencies of intestinal Klebsiella pneumoniae guides rational probiotic engineering

Klebsiella pneumoniae is a major cause of antibiotic-resistant infections, yet the ecological determinants enabling its intestinal expansion remain poorly defined. Here, we combined in vivo transcriptomics and metabolomics to identify carbon sources exploited by K. pneumoniae during colonization of the antibiotic-disrupted gut across strains and dietary contexts. Despite its metabolic breadth, K. pneumoniae consistently exploited a restricted set of substrates, including arabinose, raffinose, oligogalacturonate, arabitol, xylose, and gluconate, that contributed to intestinal fitness, with related metabolic signatures also observed in antibiotic-treated human samples. Guided by these findings, we engineered Escherichia coli Nissle to enhance consumption of these nutrients and assembled a defined consortium, NICHE, designed to reinforce colonization resistance through nutrient competition. NICHE restricted intestinal expansion of multidrug-resistant and hypervirulent K. pneumoniae in preventive and therapeutic settings, with efficacy influenced by dietary nutrient availability. Together, this work defines exploitable K. pneumoniae nutrient dependencies and a framework for rational probiotic engineering.

microbiology↗

bioRxiv2026

Gut microbiome changes over the course of multiple sclerosis differentially influence autoimmune neuroinflammation

Multiple sclerosis (MS) is the leading inflammatory and demyelinating disease of the central nervous system (CNS). MS begins with systemic inflammation and over time is compartmentalized within the CNS. Studies in humans, supported by animal experiments, suggest that the gut microbiome plays an important role in MS development. However, despite the dynamic nature of the disease, little is known on how the microbiome evolves over the course of MS and how these microbiome changes influence immune responses and disease progression. Here, using high-throughput sequencing, we identified distinct gut microbial communities with differential functional potential in MS patients stratified by time since disease onset. Importantly, using a humanized mouse model, we demonstrate that differences in microbial composition significantly impact disease outcomes. Microbiota from more recently diagnosed MS patients induced severe neuroimmune disease in mice, whereas microbiota from long-term MS patients and healthy individuals elicited only mild disease. Accordingly, we found that microbiota from earlier diagnosed MS patients exhibit a higher inflammatory potential. This was characterized by a reduced capacity to induce regulatory T cells in mice and an increased induction of pro-inflammatory cytokines in human peripheral blood mononuclear cells. Together, our results suggest that the ability of the gut microbiome to promote systemic inflammation and trigger MS pathology shifts over the course of the disease and is primarily critical during its early stages. These findings indicate that a limited therapeutic window should be considered when designing microbiome-based interventions for MS.

immunology↗

bioRxiv2023

Novel gut probiotic engages microbiota for recovery and pathobiont clearance while preventing inflammation

The microbiota inhabiting the mammalian gut serves as a protective barrier against pathogen invasion through a mechanism known as colonization resistance. Antibiotic treatments can inadvertently disturb the gut microbiota, compromising colonization resistance and increasing hosts susceptible to infections. Non-pneumoniae Klebsiella spp. members of the gut microbiota play a crucial role in colonization resistance and clearance from the gut of pathogenic Enterobacteriaceae following antibiotic-induced perturbations. Specifically, Klebsiella strain ARO112 a gut microbiota isolate, can effectively resist and clear Escherichia coli colonization after antibiotic-induced dysbiosis. We assessed the potential of Klebsiella sp ARO112 to promote clearance of Enterobacteriaceae pathobiont Adherent-Invasive E. coli (AIEC) in an Inflammatory Bowel Disease (IBD) mouse model susceptible to inflammatory episodes. In antibiotic-treated IBD-predisposed mice infected with the AIEC, Klebsiella sp. ARO112 promoted a faster recovery of gut microbiota members potentially involved in butyrate production and accelerated pathobiont clearance. Functionally, ARO112-driven microbiota recovery promoted higher butyrate levels and prevented intestinal inflammation compared to untreated animals. Conversely, treatment with the well-known probiotic E. coli Nissle 1917 enhanced AIEC colonization and inflammation. Furthermore, we assessed the safety of ARO112 as a potential next-generation probiotic; phenotypic comparison of ARO112 against closely related Enterobacteriaceae revealed its lower pathogenic potential, including being more recalcitrant to antibiotic resistance acquisition. Overall, our results showing that Klebsiella sp. ARO112 can resolve infections while contributing to the promotion of intestinal health, underscore its potential as a biotherapy agent that can disrupt inflammation-treatment-infection cycles. This potential extends beyond IBD patients, encompassing individuals with other inflammatory-based conditions related to microbiota imbalances.

microbiology↗

bioRxiv2023

Differences in vertical and horizontal transmission dynamics shape plasmid distribution in clinical enterobacteria

Conjugative plasmids play a key role in the dissemination of antimicrobial resistance (AMR) genes across bacterial pathogens. AMR plasmids are widespread in clinical settings, but their distribution is not random, and certain associations between plasmids and bacterial clones are particularly successful. For example, the globally spread carbapenem resistance plasmid pOXA-48 can use a wide range of enterobacterial species as hosts, but it is usually associated with a small number of specific Klebsiella pneumoniae clones. These successful associations represent an important threat for hospitalized patients. However, knowledge remains limited about the factors determining AMR plasmid distribution in clinically relevant bacteria. Here, we combined in vitro and in vivo experimental approaches to analyze pOXA-48-associated AMR levels and conjugation dynamics in a collection of wild type enterobacterial strains isolated from hospitalized patients. Our results reveal significant variability in these traits across different bacterial hosts, with Klebsiella spp. strains showing higher pOXA-48-mediated AMR and conjugation frequencies than Escherichia coli strains. Using experimentally determined parameters, we developed a simple mathematical model to interrogate the contribution of AMR levels and conjugation permissiveness to plasmid distribution in bacterial communities. The simulations revealed that a small subset of clones, combining high AMR levels and conjugation permissiveness, play a critical role in stabilizing the plasmid in different polyclonal microbial communities. These results help to explain the preferential association of plasmid pOXA-48 with K. pneumoniae clones in clinical settings. More generally, our study reveals that species- and strain-specific variability in plasmid-associated phenotypes shape AMR evolution in clinically relevant bacterial communities. Significance statementConjugative plasmids disseminate AMR genes across bacterial pathogens. Understanding the rules governing plasmid dynamics in bacterial communities is therefore crucial to controlling the global AMR crisis. In this study, we analyzed the dynamics of an AMR plasmid of great clinical relevance, pOXA-48, in a collection of wild type bacteria recovered from hospitalized patients. We reported a high degree of variability in two key plasmid-associated phenotypes, AMR level and conjugation ability, across the collection of clinical bacteria. Using simulations based on the experimental results, we studied how successful associations between AMR plasmids and clinical strains can arise in bacterial communities. Our results revealed that accounting for variability in plasmid-associated phenotypes help to understand the evolution of AMR in clinical settings.

microbiology↗

bioRxiv2019

Perturbation of the human gut microbiome by a non-antibiotic drug contributes to the resolution of autoimmune disease

The trillions of microorganisms (microbiota) found within the human gut play a critical role in shaping the immune system, yet these complex microbial communities are also highly sensitive to numerous environmental factors. While much of the focus to date has been on dietary intake, emerging data has begun to suggest that the use of pharmaceutical drugs, even those that are not considered to be antibiotics, can alter the human gut microbiota with unknown consequences for treatment outcomes. Here, we use a combination of in vitro, in vivo, and ex vivo methods to demonstrate that the first-line therapy for rheumatoid arthritis (RA), methotrexate (MTX), has off-target effects on the human gut microbiota, resulting in a significant growth advantage for drug-resistant Firmicutes over the Bacteroidetes, which tend to be more sensitive. Longitudinal analyses of the gut microbiotas of RA patients revealed that MTX-induced shifts in bacterial relative abundance are associated with improved drug response and transplant experiments in gnotobiotic mice show that these shifts lead to reduced inflammation. Together, these results suggest that the mechanism-of-action of non-antibiotic drugs may be due in part to off-target effects on the gut microbiota, while providing a critical first step towards explaining long-standing differences in drug response between patients.

microbiology↗