Biology subjects

Dore, J.

Publications and source records attributed to Dore, J..

9 recordsLinked to original sources

bioRxiv2026

Fecal extracellular vesicles from adults with autism spectrum disorder affect mouse behavior and gut motility by targeting the neuronal nitrergic pathway

Beside behavioral symptoms, many patients with autism spectrum disorder (ASD) present gastrointestinal disorders and gut microbiota dysbiosis. In order to better understand the mechanisms underlying microbiota-gut-brain interactions in ASD, we isolated fecal extracellular vesicles (EVs), as a source of microbiota-derived EVs, from control individuals (f-EV-CTL) and patients with ASD (f-EV-ASD) to study in mice their impact on brain and gut. The f-EV-ASD induced hypersocial and anxiolytic-like behavior, and reduced gastrointestinal transit time compared to mice treated with f-EV-CTL. In the colon, f-EV-ASD altered motility through the enteric neuronal nitric oxide (NO)-sensitive component. f-EV-ASD potentiated NO signaling and disrupted intracellular calcium dynamics in enteric neurons. This effect was mediated by butyrate and valerate through FFAR3 receptor. Our findings establish fecal EVs as critical mediators of microbiota-host communication, linking microbial metabolites to altered behavior and gut function and identifying a potential mechanism underlying ASD pathophysiology.

physiology↗

bioRxiv2026

Hydrogen metabolism shapes gut microbiome into health-associated configurations

The human gut microbiome exhibits reproducible configurations, yet the ecological forces connecting them to health remain unclear. Here, using enterosignature-based stratification of 5,170 individuals from the Le French Gut cohort, we identified hydrogen disposal as a key determinant of population-scale microbiome configurations, independently replicated in a meta-cohort (n = 5,107). Microbial configurations followed a continuum of hydrogen recycling capacity and redox-associated functions, aligned with dietary patterns and health indicators. Methanogenesis-dominant partitions were associated with more favorable health profiles, whereas acetogenesis-enriched partitions exhibited features of low-grade inflammation, and increased digestive symptoms, perceived stress and antidepressant use. Experimental characterization of mucin profiles highlighted differences across partitions and alterations in Bacteroides-enriched configurations. Together, our findings support an ecological host-microbiome framework linking hydrogen metabolism, redox ecology, and host health, offering microbiome-informed targets for precision intervention. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=128 SRC="FIGDIR/small/722951v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@e7b8d1org.highwire.dtl.DTLVardef@116ab09org.highwire.dtl.DTLVardef@136f1f8org.highwire.dtl.DTLVardef@480097_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2026

Helotiales fungi as potential nutritional partners for non-mycorrhizal plants: a machine learning and experimental approach

BackgroundMost land plants depend on the ancestral arbuscular mycorrhizal (AM) symbiosis for phosphorus (P) acquisition. However, several plant lineages have independently lost this symbiosis, raising fundamental questions about how these non-mycorrhizal plants meet their nutritional requirements without this crucial partnership. ResultsComparative genomic analyses confirmed that Cyperaceae, Caryophyllaceae, and Brassicaceae lack genes essential for AM symbiosis, indicating that these lineages independently abandoned this association 90-122 million years ago. Field surveys of 42 wild populations across seven sites revealed that while non-mycorrhizal plants generally maintain shoot P levels comparable to those in AM neighbors, lower shoot P levels can be observed in low P soils. To identify fungal taxa potentially associated with P nutrition in non-mycorrhizal plants, we applied a machine-learning approach to predict plant P-accumulation from root microbiome composition. The model explained substantial variance in plant P-accumulation (57-69%), and identified 85 fungal taxa as key predictors of shoot P-accumulation, predominantly belonging to the Helotiales (28%) and Pleosporales (23%) orders. Experimental validation of two phylogenetically distant Helotiales lineages (Tetracladium maxilliforme OTU29 and Helotiales sp. OTU7), using isotopic tracing, demonstrated their capacity to enhance plant growth and transfer P (and N) to their native non-mycorrhizal hosts under P-limiting conditions. ConclusionsOur findings suggest that non-mycorrhizal plants engage in nutritional partnerships with diverse Helotiales lineages that could collectively contribute to their mineral nutrition. However, given the widespread distribution of these Helotiales fungi, including in roots of AM plants, they may play a broader role in plant nutrition, i.e. also in mycorrhizal hosts. This study provides proof of concept for a novel framework integrating machine-learning predictions with experimental validation to identify functionally important microbial partnerships in natural plant communities.

microbiology↗

bioRxiv2026

Multifaceted roles of extracellular vesicles in Agrobacterium fabrum C58 lifestyles

Bacterial extracellular vesicles (EVs) constitute a key driver of interspecies and inter-kingdom communication, and shape bacterial ecology, yet their role as a dynamic delivery system remains underexplored. Here, we show that the plant pathogen Agrobacterium fabrum C58 modulates its EVs in response to virulence-inducing conditions. Our multi-omics analysis revealed that these virulence-state EVs are significantly enriched in effectors from the Type IV secretion system and toxins from the Type VI secretion system, which were previously known to be delivered by conventional contact-dependent mechanisms. We demonstrate that these EVs can directly transfer virulence effectors into plant host cells, enhancing tumor formation. Furthermore, we show that these EVs can interact with and influence the development of several environmental bacteria. Finally, A. fabrum C58 EVs elicit distinct plant host metabolome responses compared to whole cells. Our findings establish EVs as a crucial and dynamic component of bacterial virulence and inter-kingdom communication, providing a new perspective on how bacteria adapt to and manipulate their environment.

microbiology↗

bioRxiv2024

Needle in a haystack: culturing plant-beneficial Helotiales lineages from plant roots

Root-associated Helotiales fungi are increasingly recognized as beneficial fungal partners promoting plant growth under nutrient-limited conditions, particularly in non-mycorrhizal hosts, lacking the ancestral arbuscular mycorrhizal symbiosis. However, the ecology of these fungi is still cryptic as relatively few lineages have been successfully cultivated from roots for further study. Here, we attempted the mass isolation of root endophytic fungi to evaluate the recovery of known plant-beneficial Helotiales lineages using a tailored culture-based approach. We sampled six wild non-mycorrhizal species from the Brassicaceae, Caryophyllaceae, and Cyperaceae, growing in nutrient-limited alpine soils. We isolated 602 root endophytes and compared this culturable diversity with the one observed via fungal ITS2 metabarcoding. Metabarcoding revealed that Helotiales taxa dominated the fungal communities, with 43% of these detected taxa also represented in our collection. Accordingly, most root endophytes in our collection (53%) were Helotiales. These isolates, some with P solubilisation potential, belonged primarily to three Helotialean clades and were phylogenetically related to plant growth-promoting or mycorrhizal-like strains. This analysis highlights that roots of alpine non-mycorrhizal plants are reservoirs of plant-beneficial root-endophytic Helotiales, and the isolates obtained are a promising resource to explore the plant-beneficial mechanisms and ecological traits of these fungi.

microbiology↗

bioRxiv2023

Increased spontaneous Ca2+ activity in Cardiac Purkinje cells after myocardial infarction; A consequence of a dramatic shift of SERCA isoforms as potential adaptation to acute ischemia?

BackgroundStudies of Purkinje cells (Pcells) from canine hearts have suggested an increase of Ca2+-release by the sarcoplasmic reticulum (SR) but also reported a potential augmentation of SR-Ca2+-uptake after MI. Abnormal increase of SR-Ca2+-uptake in heart cells is novel and contrasts with the reduction of this function in cells of failing heart. Our study examined the origin of this increased SR-Ca2+-uptake by considering a change in SR-Ca2+ pump (SERCA2) expression in Purkinje fibers (PFs) post MI. MethodsPcells were isolated from canine hearts 48Hrs post MI. Intracellular Ca2+-activity was captured by confocal microscopy. Purkinje-typical Ca2+ events were analyzed to probe the regional Ca2+-dynamics within Pcells. A Purkinje-specific numerical model assisted in the interpretation of Ca2+-anomalies detected in Pcells Ca2+-transients. SR-Ca2+-uptake system was studied by immunofluorescence in Pcells from canine, ovine and human hearts post MI. SERCA protein and gene expressions in PFs and myocardium were measured by Western Blots and RT-qPCR in a classical porcine model of MI. Results48Hrs after MI, Pcells showed 60% increase in spark-rate and 37% acceleration of Ca2+ wave decay. In the model of normal wave, 35% increase of Ca2+-uptake rate reproduced the actual post-MI wave alterations. In apparent contrast with increased Ca2+-uptake rate, SERCA2 protein expression was reduced in canine, sheep, and human Pcells after MI. In pig MI model, the protein level of cardiac-specific SERCA2-splicing variant SERCA2a was reduced by 52% in the whole infarcted ventricle whereas the "non-cardiac" SERCA2b level was increased by 120%. In the infarcted regions, PFs showed 30% downregulation of SERCA2a gene expression and 630% upregulation of SERCA2b. ConclusionOur results confirm that elevated spontaneous Ca2+-activity in post-MI PFs is due to increased SR-Ca2+-uptake within Pcells. Data suggest that a replacement of "cardiac" SERCA2a by the "non-cardiac" SERCA2b sub-isoform in cardiac cells in response to ischemia is implicated in this alteration.

cell biology↗

bioRxiv2020

Changes in cellular signaling patterns before and after stroke in the middle cerebral arteries of stroke prone spontaneously hypertensive rats

BackgroundHemorrhagic stroke is associated with loss of middle cerebral artery (MCA) autoregulation in the stroke-prone spontaneously hypertensive rat (SHRsp). The signaling mechanism associated with the functional loss has yet to be defined. We hypothesize that physiological alterations coincide with changes to cerebrovascular inflammatory and contractile signaling and altered calcium signaling. METHODS: SHRsp rats were fed a high salt (4% NaCl) diet and sacrificed at 9 weeks of age for pre-stroke and after evidence of stroke for post-stroke samples. The MCAs were isolated for measuring protein levels using immunofluorescence (IF) & western blot (WB) for inflammatory signaling and contractile proteins. Tissues surrounding the MCA were analyzed for neuro-inflammation, neuronal damage, total and activated inflammatory proteins (ERK1/2 and p38MAPK), cerebrovascular contraction (PKC and MLC), and transient receptor potential V4 (TRPV4) expression. RESULTS: Our data show increase in activated inflammatory proteins after stroke with an associated decrease in expression of activated contractile proteins and TRPV4 channel expression compared to pre-stroke MCA. The post-stroke samples also show significant increase in neuro-inflammation and neuronal damage compared to pre-stroke samples. CONCLUSIONAn increase in activated/total (p38 MAPK &ERK1/2) is accompanied by a decrease in activated/total PKC & TRPV4 channel expression in post-stroke SHRsps. The decrease in vessel structural integrity and altered vascular tone of the MCAs may affect its ability to contract in response to pressure. Significant neuro-inflammation and neuronal damage in the brain tissues surrounding the MCA in post-stroke samples suggest MCA dysfunction is accompanied with neuronal and neural damage during stroke.

molecular biology↗

bioRxiv2020

Gut microbiome, diet and symptom interactions in irritable bowel syndrome

While several studies have documented associations between dietary habits and microbiota composition and function in healthy subjects, no study explored these associations in patients with irritable bowel syndrome (IBS), and especially in relation to symptoms. Here, we used a novel approach that combined data from 4-day food diary, integrated into a food tree, together with gut microbiota (shotgun metagenomic) for IBS patients (N=149) and healthy subjects (N=52). Paired microbiota and food-based trees allowed to detect new association between subspecies and diet. Combining co-inertia analysis and linear regression models, exhaled gas levels and symptom severity could be predicted from metagenomic and dietary data. IBS patients with severe symptoms had a diet enriched in food items of poorer quality, a high abundance of gut microbial enzymes involved in hydrogen metabolism in correlation with animal carbohydrate (mucin/meat-derived) metabolism. Our study provides unprecedented resolution of diet-microbiota-symptom interactions and ultimately paves the way for personalized nutritional recommendations.

microbiology↗

bioRxiv2017

Prediction of the intestinal resistome by a novel 3D-based method

The intestinal microbiota is considered to be a major reservoir of antibiotic resistance determinants (ARDs) that could potentially be transferred to bacterial pathogens. Yet, this question remains hypothetical because of the difficulty to identify ARDs from intestinal bacteria. Here, we developed and validated a new annotation method (called pairwise comparative modelling, PCM) based on homology modelling in order to characterize the Human resistome. We were able to predict 6,095 ARDs in a 3.9 million protein catalogue from the Human intestinal microbiota. We found that predicted ARDs (pdARDs) were distantly related to known ARDs (mean amino-acid identity 29.8%). Among 3,651 pdARDs that were identified in metagenomic species, 3,489 (95.6%) were assumed to be located on the bacterial chromosome. Furthermore, genes associated with mobility were found in the neighbourhood of only 7.9% (482/6,095) of pdARDs. According to the composition of their resistome, we were able to cluster subjects from the MetaHIT cohort (n=663) into 6 \"resistotypes\". Eventually, we found that the relative abundance of pdARDs was positively associated with gene richness, but not when subjects were exposed to antibiotics. Altogether, our results support that most ARDs in the intestinal microbiota should be considered as intrinsic genes of commensal microbiota with a low risk of transfer to bacterial pathogens.

microbiology↗