-
[hal-05619684] Longitudinal Follow‐Up of Gut and Salivary Microbiota in Children With Food Protein‐Induced Enterocolitis Syndrome
Background: Gut microbiota and their metabolites play a key role in digestive dysimmunity and tolerance breakdown, leading to pathologies such as food protein‐induced enterocolitis syndrome (FPIES). This study aimed to compare both the gut and salivary microbiota over time between the allergic and tolerant patients and the matched controls. Methods: Faecal and salivary samples were collected longitudinally from FPIES allergic patients on an elimination diet, and after their natural tolerance acquisition, and from matched controls (1:1 ratio). 16S rRNA gene sequencing and biostatistical analyses (ALDEx2, ANCOM‐BC, DESeq2, LEfSe, and MaAsLIN2) were used to compare microbiota composition between groups. The measurement of faecal short‐chain fatty acids (SCFAs) using gas chromatography evaluated the gut microbiota functions. Results: Thirty‐eight allergic patients were included (median age: 1.3 years), and 22 became tolerant over time. Allergic patients exhibited lower gut and salivary alpha‐diversities, and several different genera (12 in stools, including less Ruminococcus , and 2 in saliva), and higher relative abundance of acetate than the controls. With tolerance acquisition, faecal alpha‐diversities partially increased, whereas SCFAs normalised. Ultimately, there were more differences in faecal and salivary microbiota in allergic patients versus after tolerance acquisition (i.e., more Blautia , Ruminococcus , Faecalibacterium , Prevotella ‐9, and less Escherichia – Shigella in tolerant patients) than between the controls over time. Conclusion: The faecal and salivary dysbiosis observed in allergic patients with FPIES partially resolved after tolerance acquisition. Understanding the underlying mechanisms of dysbiosis is crucial to prevent and help manage FPIES. A prolonged follow‐up could determine whether dysbiosis resolution may be complete, and whether this early infancy dysbiosis has long‐term consequences on health.
ano.nymous@ccsd.cnrs.fr.invalid (Anaïs Lemoine) 12 May 2026
https://hal.sorbonne-universite.fr/hal-05619684v1
-
[hal-05507735] Plateforme @BRIDGe
La plateforme @BRIDGe propose une offre intégrée de services: de la conservation de l'échantillon biologique à son analyse au niveau tissulaire, cellulaire et moléculaire. Dédiée à la génomique des animaux domestiques, ses compétences et ses équipements lui permettent de participer à des projets concernant la biologie humaine ou des modèles biomédicaux. Elle est certifiée ISO 9001:2015 depuis 2018 pour toutes ses activités.
ano.nymous@ccsd.cnrs.fr.invalid (Delphine Muller) 12 Feb 2026
https://hal.inrae.fr/hal-05507735v1
-
[hal-05503909] A study of the integration by non-homologous end joining (NHEJ) of a trackable DNA cassette with randomly-generated borders into Yarrowia lipolytica genome sheds light on exogenous DNA extremities degradation and confirms the potential of NHEJ-mediated integration for the design of genome-scale insertional mutant libraries in non-conventional yeasts
<div><p>In order to analyse the fate of an exogenous DNA introduced into Yarrowia lipolytica cells, the authors designed a series of trackable DNA cassettes with randomly-generated borders able to integrate by NHEJ into the yeast genome. NGS sequencing of large libraries of insertional mutants provided for the first time data on the extent of degradation suffered by an exogenous DNA in Y. lipolytica cells, depending on its size and type of extremities. For all types of fragments, degradation prior to integration very rarely exceeded a dozen nucleotides. Significant differences were observed in the percentage of non-degraded fragments depending on the type of extremities: degradation was the lowest for blunt ends, it was slightly higher for 5' overhangs and markedly higher for 3' overhangs. This study also brought confirmation of the randomness and high coverage of NHEJ-mediated integration, providing a new tool for NHEJ-seq (Tn-seq-like) high-throughput analysis of gene fitness in Y. lipolytica.</p></div>
ano.nymous@ccsd.cnrs.fr.invalid (Marie-Noëlle Rossignol) 10 Feb 2026
https://hal.science/hal-05503909v1
-
[hal-05427908] Datasets of 16S rRNA gene amplicon sequences, metabolites, and soluble immune components in bronchoalveolar lavage samples from severe asthmatic and age-matched control children
Severe asthma (SA) is a heterogeneous condition characterized by multiple phenotypes, each characterized by different endotypes. Understanding the mechanisms occurring in the lungs of children with SA can help in understanding pathogenesis and in providing the most effective therapeutic strategies. This article describes microbiota, metabolites, and soluble immune components assessed in bronchoalveolar lavage (BAL) fluids from children with severe asthma (n = 20) and age-matched disease controls (n = 10). The article includes: (i) the protocol used to process BAL samples for 16S rRNA gene amplicon sequencing, metabolomic profiling and immune components assays; (ii) the bioinformatics steps applied to 16S rRNA and metabolomics dataset; (iii) an overview of the raw 16S rRNA gene amplicon sequencing data, presented as ASV and affiliation tables, raw data from untargeted metabolomics and the abundances of each of the eighty eight metabolites annotated with the highest confidence level, and concentrations of seventy three cytokines and of total IgG, IgA and IgE. Each dataset is available in the INRAE data repository (https://entrepot.recherche.data.gouv.fr/dataverse/inrae) with respective DOI: MICROBIOTA: 10.57745/LL3TFW, METABOLITES: 10.57745/1L8VRI, IMMUNE COMPONENTS: 10.57745/JOOGRQ These datasets provide valuable resources for further investigating the molecular mechanisms underlying severe asthma in children and its trajectories. They also offer the potential to identify a local signature of severe asthma through complementary multi-omics analyses and to discover local biomarkers associated with asthma endotypes. Datasets can also be reused to compare with other cohorts (children or adults) or to serve as reference datasets for other pulmonary diseases.
ano.nymous@ccsd.cnrs.fr.invalid (Mélanie Briard) 21 Dec 2025
https://hal.inrae.fr/hal-05427908v1
-
[hal-05458324] Single-cell omics uncover gene dynamics shaping embryonic and extra embryonic lineages in pig blastocysts
Late blastocyst development before implantation is a unique feature of ungulates, during which the epiblast proliferates and maintains pluripotency while extra-embryonic tissues expand dramatically, elongating to several tens of centimeters. The mechanisms coordinating these processes are not well understood. We performed single-cell omics profiling of porcine blastocysts from the hatched stage (E7) through early (E9) and late ovoid stages (E11). From 15,370 cells, we identified distinct embryonic and extra-embryonic populations with characteristic chromatin accessibility profiles. We reconstructed gene regulatory networks using enhancer-based eRegulons and validated them through motif occupancy analysis. Extra-embryonic tissues showed strong shifts in gene regulatory module activity at the onset of elongation, reflecting major transitions in morphogenesis and differentiation and the activation of pathways linked to cell morphology, proliferation, metabolism, trafficking, and biomolecule transport. In contrast, epiblast cells retained a stable transcriptional and regulatory identity from day 7 to day 11, immediately preceding the onset of gastrulation.
ano.nymous@ccsd.cnrs.fr.invalid (Adrien Dufour) 14 Jan 2026
https://hal.inrae.fr/hal-05458324v1
-
[hal-05688101] Exploring the relationships between the gut microbiome composition and movement patterns of laying hens in a multitier cage-free housing system
In this study we investigated the relation between caecal microbiota composition and movement patterns in laying hens. We used hens from Pure line matings of Hendrix Genetics to continuously monitor the movement of individuals in a connected three-tier aviary throughout the laying period, from 18 to 60 weeks of age. The aviary contained three vertical tiers: a top-level, mid-level, and lower-level. In addition, the aviary had a floor littered and an attached wintergarden which was accessible from approximately 21 WOA onwards. Differences in the hens' use of space were observed including: differences in the number of visits and time spent in the wintergarden and litter areas. Microbiota characterization, using 16S rRNA gene sequencing from 237 samples, revealed an association (P &lt; 0.05) between microbiome composition and the number of visits to the litter. We observed differences (adjusted P-value &lt; 0.05) between hens that frequently visited the litter (&gt;30 times/day) and those that visited the litter less often (&lt;10 times/day) in five bacterial families and seven genera. Notably, hens classified as visiting the litter less often, showed an increased abundance of Coriobacteriales, Peptococcales, Oribacterium and Lachnoclostridium taxa. Overall, this study offers new insights on the potential role of the microbiota in hen movement patterns.
ano.nymous@ccsd.cnrs.fr.invalid (Anaïs Cazals) 10 Jul 2026
https://hal.inrae.fr/hal-05688101v1
-
[hal-04426679] Analysis of Polycerate Mutants Reveals the Evolutionary Co-option of HOXD1 to Determine the Number and Topology of Horns in Bovidae
In the course of evolution, pecorans (i.e. higher ruminants) developed a remarkable diversity of osseous cranial appendages, collectively referred to as ‘headgear’, which likely share the same origin and genetic basis. However, the nature and function of the genetic determinants underlying their number and position remain elusive. Jacob and other rare populations of sheep and goats, are characterized by polyceraty, the presence of more than two horns. Here, we characterize distinct POLYCERATE alleles in each species, both associated with defective HOXD1 function. We show that haploinsufficiency at this locus results in the splitting of horn bud primordia, likely following the abnormal extension of an initial morphogenetic field. These results highlight the key role played by this gene in headgear patterning and illustrate the evolutionary co-option of a gene involved in the early development of bilateria to properly fix the position and number of these distinctive organs of Bovidae.
ano.nymous@ccsd.cnrs.fr.invalid (Aurélie Allais-Bonnet) 12 Nov 2025
https://hal.science/hal-04426679v1
-
[hal-05387588] Preconditioning donors with corticosteroids improves early lung graft immunity
Preclinical studies have recently revealed the critical role of innate immunity in determining lung transplantation outcomes. Although the International Society for Heart and Lung Transplantation recommends highdose corticosteroid administration to donors, this practice is inconsistently applied worldwide. Investigating its impact on the donor lung's innate immune responsean unexplored area -could provide valuable evidence to support adoption of donor preconditioning with corticosteroids, beyond their traditional administration to recipients. Method: We used a cross-circulatory pig platform that consists of a donor lung placed extracorporeally and connected to the circulation of a recipient pig whose leukocytes are fluorescently labeled. Results: Donor preconditioning -compared to recipient's treatment alonereduced the presence of CD3 pos T-cells in the graft from both the donor and recipient, and enhanced the anti-inflammatory profile of alveolar macrophages, at least during the first 10 hours of donor-recipient interaction. The alveolar macrophages isolated from corticosteroid-preconditioned pig lungs exhibited decreased gene expression of T-cell-attracting chemokines during the 10-hour reperfusion period, correlating with the reduced T-cell infiltration. Similarly, human lung macrophages showed lower expression of these T-cell-attracting chemokines and higher anti-inflammatory profiles with corticosteroid treatment.
ano.nymous@ccsd.cnrs.fr.invalid (Isabelle Schwartz-Cornil) 28 Nov 2025
https://hal.inrae.fr/hal-05387588v1
-
[hal-05220930] Dual-transcriptomics on microdissected cells reveals functional specialisation of symbiont-bearing-cells and contrasted responses to nutritional stress in the cereal weevil
Insects thriving on a nutritionally imbalanced diet often establish long-term relationships with intracellular symbiotic bacteria (endosymbionts), which complement their nutritional needs and improve their physiological performances. Endosymbionts are in host specialised cells, called the bacteriocytes, which in many insects group together to form a symbiotic organ, the bacteriome. The cereal weevil Sitophilus oryzae houses multiple bacteriomes at the adult mesenteric caeca. Results Using microscopic cell imaging, we revealed that bacteriomes consist of several cell types, including progenitor cells, peripheral bacteriocytes, central bacteriocytes and epithelial cells. By combining laser capture microdissection and dual RNA-sequencing, we showed that both host cell types and their associated endosymbionts express distinct transcriptional profiles. The comparison between peripheral bacteriocytes and midgut cells from insects artificially deprived from endosymbionts (aposymbiotic) unravelled cellular pathways modulated by the presence of endosymbionts. The cell-specific response to endosymbionts in peripheral bacteriocytes includes a boost of fatty-acid and amino acid metabolisms. We found that central bacteriocytes overexpress transport and G-protein signalling-related genes when compared to peripheral bacteriocytes, indicating a signalling and/or transport function of these cells. Diet composition strongly impacts host and endosymbiont gene expression and reveals a molecular trade-off among metabolic pathways. Conclusions This study provides evidence on how endosymbionts interfere and enhance metabolic performances of insect bacteriocytes and highlights key genes involved in the bacteriocyte differentiation and metabolic pathways.
ano.nymous@ccsd.cnrs.fr.invalid (Nikoletta Galambos) 03 Sep 2025
https://hal.science/hal-05220930v1
-
[hal-05194736] Single-cell omics reveal distinct gene regulatory dynamics underpinning embryonic and extraembryonic lineage functions during pig blastocyst development
The late-stage development of the blastocyst before implantation is a unique feature of ungulates. During this period, the epiblast proliferates and remains pluripotent for several days before gastrulation begins. Simultaneously, extra-embryonic tissues undergo significant growth, elongating to several tens of centimeters. However, the mechanisms that regulate and synchronize these processes remain poorly understood. In this study, we analyzed transcriptomic and epigenomic data at the single-cell level from early and late porcine blastocyst cells, spanning from the hatched blastocyst stage (E7) to early (E9) and late ovoid blastocyst (E11). We characterized 15,370 blastocyst cells, clustering them into distinct embryonic and extra-embryonic populations with specific chromatin accessibility landscapes. For each population, we inferred gene regulatory networks based on enhancer-driven gene regulation modules (eRegulons) and validated them through motif occupancy visualization. Our findings reveal strong dynamics in gene regulatory module activity within extra-embryonic tissues at the onset of blastocyst elongation, while gene regulatory activity in the epiblast remains relatively stable.
ano.nymous@ccsd.cnrs.fr.invalid (Adrien Dufour) 31 Jul 2025
https://hal.inrae.fr/hal-05194736v1
-
[hal-05186005] HARMONI: Evaluating advanced microbiota characterization methods for host and environmental samples using DNA metabarcoding and metagenomic sequencing
Background: The study of microbiota and their actions on the environment and their living hosts is a major field of biology, today and for decades to come. Understanding and controlling the microbiota associated with plants, animals and food is a lever for achieving the objectives of the transition to sustainable agricultural production systems. Research faces many technical challenges that must be overcome before reaching meaningful and reproducible biological conclusions. In this context, biological resource centres (BRCs) must be prepared to the processing and characterization of microbiota-oriented samples, in the continuity of their missions of collection, preservation and distribution of perfectly characterized biological resources. Results: In the HARMONI project, five BRCs worked collaboratively to implement and assess methods for microbiota analyses. Samples were collected from a diversity of sources: chicken caeca, human feces, kefir and soil. The data were generated using 16S metabarcoding, short read metagenomic sequencing, and long read metagenomic sequencing. We tested different tools for microbial exploration, using reference free softwares for alpha and beta diversity assessment (SIMKA [1], ESKRIM [2]), and referenceguided microbial annotation using MetaPhlAn4 [3], sylph [4] and Meteor2 [5]. Conclusions: Overall, metabarcoding and metagenomic based microbial composition are in agreement with the major impacts observed between the different sample treatment technics. However, the microbial richness and species composition exploration significantly depend on the sequencing method and software used and their associated database. Finally, while long read metagenomic sequencing provide consistent results with metagenomic short read for microbial annotation, it highly depend on the quality of the sample treated. The HARMONI project was funded by the GIS-IBISA convention N° 2021-203.
ano.nymous@ccsd.cnrs.fr.invalid (Lindsay Goulet) 25 Jul 2025
https://hal.science/hal-05186005v1
-
[hal-04612462] SARS-CoV2 infection in whole lung primarily targets macrophages that display subset-specific responses
Abstract Deciphering the initial steps of SARS-CoV-2 infection, that influence COVID-19 outcomes, is challenging because animal models do not always reproduce human biological processes and in vitro systems do not recapitulate the histoarchitecture and cellular composition of respiratory tissues. To address this, we developed an innovative ex vivo model of whole human lung infection with SARS-CoV-2, leveraging a lung transplantation technique. Through single-cell RNA-seq, we identified that alveolar and monocyte-derived macrophages (AMs and MoMacs) were initial targets of the virus. Exposure of isolated lung AMs, MoMacs, classical monocytes and non-classical monocytes (ncMos) to SARS-CoV-2 variants revealed that while all subsets responded, MoMacs produced higher levels of inflammatory cytokines than AMs, and ncMos contributed the least. A Wuhan lineage appeared to be more potent than a D614G virus, in a dose-dependent manner. Amidst the ambiguity in the literature regarding the initial SARS-CoV-2 cell target, our study reveals that AMs and MoMacs are dominant primary entry points for the virus, and suggests that their responses may conduct subsequent injury, depending on their abundance, the viral strain and dose. Interfering on virus interaction with lung macrophages should be considered in prophylactic strategies.
ano.nymous@ccsd.cnrs.fr.invalid (Thien-Phong Vu Manh) 22 May 2025
https://hal.inrae.fr/hal-04612462v1
-
[hal-04980787] Local, environmental and trace metal effects on gut microbiota diversity in urban feral pigeons
Nowadays, understanding the biotic responses to the enhanced urbanization need to encompass not the only the physiological and phenotypic features but also the related microbiota of wildlife animals. One of main threats in urban ecosystems is the chemical pollution. Thus, we have explored whether the cloacal microbiota of feral pigeons (Columba livia) is impacted by both their geographical foraging area, and metal exposure in an urban context. First, pigeons were captured in 4 specific areas of Paris (France) and placed in captivity. By applying a 16SrRNA metabarcoding approach, we observed that the gut microbiota diversity was structured according to the capture sites, with strong variation of Actinobacteria, Bacilli and Clostridia, that could be linked to the granivorous or low-protein diets. Subsequently, we experimentally exposed these pigeons to zinc and/or lead (two-factor cross design) during 90 days in a non-urban environment, but no impact on the composition nor diversity of pigeon gut microbiota, has been observed after 45 and 90 days of metal exposures. However, the composition and diversity significantly differed from the microbiota at the capture period, with the emergence of taxa belonging to Corynebacterium and Bifidobacterium in captive conditions. These data highlight a strong impact of the lifestyles (captivity in non-urban environment) on the gut microbiota composition. In parallel, we hypothesized that the diet and the local environment might have smoothed the impact of the metal exposure for pigeons that could quickly change the structure of their gut microbiota. Our findings shed light on the effects of urban pollution and environment on bird communities, that can be extended to their gut microbiota causing potential additive or synergic negative effects to host organisms and populations.
ano.nymous@ccsd.cnrs.fr.invalid (Clarence Schmitt) 04 Dec 2025
https://hal.sorbonne-universite.fr/hal-04980787v1
-
[hal-05005963] Illuminating microalgal biofilms using advanced photonic imaging techniques
This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
ano.nymous@ccsd.cnrs.fr.invalid (Julia Mougin) 26 Mar 2025
https://hal.inrae.fr/hal-05005963v1
-
[hal-05010158] La sélection de l'hôte est efficace pour orienter le microbiote intestinal chez le porc
Le microbiote, qui représente l’ensemble des communautés des microorganismes présents chez un individu, participe à l’élaboration des caractéristiques de son hôte. Son implication dans de nombreux processus métaboliques de son hôte ont été largement démontrés. Afin de préciser le déterminisme génétique du microbiote intestinal chez le porc, nous avons mené une expérience de sélection sur la base des abondances relatives de quatre genres bactériens, estimées à partir de données de séquençage de l’ADN 16S des génomes bactériens présents dans les fèces de porc de 60 jours d’âge. Nous avons sélectionné deux lignées de porcs avec comme objectif une augmentation de l’abondance relative des genres Prevotella et Mitsuokella (lignée HPM), ou des genres Ruminococcus et Treponema (lignée HRT), qui sont les genres différentiant des deux entérotypes (PM et RT, respectivement) observés chez le porc dans nos conditions expérimentales. Nous avons confirmé que ces abondances relatives sont des caractères avec des héritabilités modérées de l’ordre de 0,3 qui peuvent être sélectionnés. Nous avons également estimé l’évolution contrastée de l’ensemble des genres bactériens dans les deux lignées et observé l’augmentation de la fréquence des entérotypes RT et PM de manière divergente pour chaque lignée au fil des générations de sélection. La relation entre l’abondance relative de Prevotella (soit l’entérotype PM) et la croissance post-sevrage a été confirmée ; en revanche l’incidence sur d’autres caractères de croissance ou de composition corporelle est très limitée.
ano.nymous@ccsd.cnrs.fr.invalid (Catherine Larzul) 28 Mar 2025
https://hal.inrae.fr/hal-05010158v1
-
[hal-05299987] Development of a rabbit model of uterine rupture after caesarean section, Histological, biomechanical and polarimetric analysis of the uterine tissue
Uterine rupture is a major complication of caesarean section (CS) associated with a high foetal and maternal morbidity. The objective is to develop an in-vivo model of uterus healing and rupture after CS in order to analyse histological phenomena controlling scarring tissue development and potential cause of defects. Eighteen pregnant primiparous female rabbits were bred naturally. At caesarean, after 28 days of gestation, foetuses were either extracted through a longitudinal incision in one of the uterine horns (“CS horn”) or via a short incision at the tip of the contralateral horn (“control horn”). The uterine horns were sutured by single layer, all by the same surgeon. They were mated again 14 days later and euthanized at G28. Genital tracts were collected for histological, biomechanical and polarimetric analyses. Macroscopically, 2/18 presented a dehiscence and 1/18 a spontaneous rupture. The mean thickness of the scarred area was significantly lower 0.9 mm [0.7-1.4] that the non-scarring area on CS horns 2.2 [1.6-2.3] or control horns 2 [1.5-2.3] (p&lt;0.0001). The scar zone was statistically more fibrous (p&lt;0.0001), containing fewer vessels (p=0.03) and oestrogen (p&lt;0.001) and progesterone receptors (p&lt;0.0001). After balloon inflation, ruptured occurred in the scar zone in 8 out of 17 cases (47%). Polarimetry revealed that the scar zone was statistically inhomogeneous (73%). Multifactorial analysis allowed to identify groups with poor uterine healing and less resistant to rupture (balloon inflation) mostly in case of thin myometrium in the scar and a group with strong resistant to rupture and correct healing characteristics. Lay summary Caesarean section rates are rising across the world. When a caesarean section is carried out, it can lead to scarring on the uterus that can affect its resistance to pressure. During the next pregnancy, the uterus can tear, increasing risks to the mother and baby. We carried out caesarean sections in a rabbit, allowing us to analyse the scar on the uterus, the healing and tissue resistance. The scarred part of the uterus was statistically thinner, more fibrous and contained fewer vessels and hormone receptors than the area without scarring. Under similar conditions, poor healing was observed in some animals, reducing resistance in following pregnancies. These results suggest that individual and genetic factor have an effect on healing after a caesarean section. This study may enable us to improve our knowledge and management care for patients who have a caesarean section in order to reduce complications.
ano.nymous@ccsd.cnrs.fr.invalid (Elodie Debras) 07 Oct 2025
https://hal.science/hal-05299987v1
-
[hal-04780403] Challenging the paradigm of an amniote-restricted mesonephric contribution to the gonad. -of the pronephric field contribution to the gonads in teleosts
Despite the fact that diverse systems, various upstream determinants and plastic gene regulatory networks trigger gonadal formation amongst vertebrates, the adult gonads are however very similar in morphology, cellular organization and physiology. Whether common ontophylogenic process occasionally canalize this organismal convergence is unknown. While the archetypal amniote primordial gonads are derived on the surface of the mesonephros from the intermediate mesoderm, and rapidly develop into two rudimentary compartments, -the cortex and the medulla-, the source of medullar cell precursors remains a controversial aspect of gonadal development. Especially, the possible recruitment of underlying cells from the mesonephros to the epithelial population and their respective final contribution to the whole gonad amongst vertebrates is still a matter of debate. While teleost gonads have many features in common with those of other vertebrates, the general understanding is that teleost gonads originate only from one primordium, the cortex or peritoneal wall. Hence, unlike in other amniote vertebrates, the early gonad does not –or would not- have any equivalent to the medulla that is derived from the interrenal or mesonephric blastema. However, our data using fluorescent transgenic reporter medaka lines, in vivo cell lineage tracing, single cell analyses and gain/loss of function challenge this paradigm and clearly point to a possible pronephric contribution to the gonad in medaka. Consequently, the importance of a pro/mesonephric field contribution to the gonads has now to be reconsidered in an evolutionary perspective amongst the whole vertebrate clade.
ano.nymous@ccsd.cnrs.fr.invalid (Alexandra Depince) 13 Nov 2024
https://hal.inrae.fr/hal-04780403v1
-
[hal-04709443] Immune traits are affected by genetic selection for faecal enterotypes in pigs
The faecal microbiota of 60-day-old Large White pigs reared in same conditions can be structured into two enterotypes, for which the keystone genera are Prevotella (P) and Mitsuokella (M) or Ruminococcus (R) and Treponema (T). We generated two pig lines HPM and HRT selected for the relative abundance of either P and M or R and T, respectively. Each line showed an increase in the prevalence of the selected enterotype over three successive generations. We used 40 animals per line from the 3rd generation to investigate if at 60 days of age, they display differences in the microbiota of the small and large intestines, and in immune traits. Using 16S gene sequencing, the two lines were shown to harbour strong microbiota differences at the descending colon (648/1334 ASV and 79/144 genera differentially abundant), with less differences at the ileal Peyer's patches (38/435 ASV and 18/126 genera). Piglets from the HPM line exhibited a higher number of eosinophils and natural IgM, while piglets from the HRT line showed higher counts of CD4+ CD8+ T cells and stronger phagocytosis activity. Overall, our results show that direct genetic selection for the composition of the faecal microbiota is not only associated with changes in the microbiota of other sections of the gut, but also with host traits related to immunity. Those divergent pig lines are therefore a powerful tool for better understanding the combined effects of host genetics and gut microbiota on phenotypes relevant to sustainable livestock systems, including health and immune traits.
ano.nymous@ccsd.cnrs.fr.invalid (Fany Blanc) 25 Sep 2024
https://hal.inrae.fr/hal-04709443v1
-
[hal-05203884] Uterine healing after cesarean, Development of a rabbit model
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Elodie Debras) 08 Aug 2025
https://hal.inrae.fr/hal-05203884v1
-
[hal-04444928] A cross-circulatory platform for monitoring innate responses in lung grafts
Lung transplantation is the only curative option of end-stage chronic respiratory diseases. However the survival rate is only about 50% at 5 years. Whereas experimental evidences support that innate allo-responses impact on the clinical outcome, the knowledge of the involved mechanisms is limited. Here, we evaluate a cross-circulatory platform for monitoring the early recruitment and activation of immune cells in an extracorporeal donor lung by coupling blood perfusion to cell mapping with a fluorescent marker in the pig, a commonly-used species for lung transplantation. The perfusing pig cells were easily detectable in lung cell suspensions, in broncho-alveolar lavages and in different areas of lung sections, indicating infiltration of the organ. Myeloid cells (granulocytes and monocytic cells) were the dominantly recruited subsets. Between 6 and 10 h of perfusion, recruited monocytic cells presented a strong upregulation of MHC class II and CD80/86 expression, whereas alveolar macrophages and donor monocytic cells showed no significant modulation of expression. Altogether the cross-circulation model permits to monitor the initial encounter between perfusing cells and lung graft, in an easy, rapid, and controllable manner, for generating robust information on innate response and testing targeted therapies for improvement of lung transplantation outcome.
ano.nymous@ccsd.cnrs.fr.invalid (Glorion Matthieu) 04 Jun 2024
https://hal.inrae.fr/hal-04444928v1
-
[hal-04446339] Impact of negative energy balance on transcriptomic profiles of three endometrial cell types isolated by laser capture microdissection in postpartum dairy cows
Abstract Background: In postpartum dairy cows, the energy needs to satisfy high milk production induces a more or less pronounced Negative Energy Balance (NEB) status. NEB associated with fat mobilization impairs reproductive function. This study investigated the specific impact of NEB on gene expression in the three main types of endometrial cells at time planned for insemination and implantation. Endometrial cell types (stromal, glandular and luminal epithelial cells) were isolated by laser micro-dissection allowing the study of constitutive gene expression and their specific response to NEB. Methods: Nine Swedish Red cows receiving a control diet or a mild restricted diet to induce differences of energy balance were categorized into mild (MNEB, n = 5) and severe negative energy balance (SNEB, n = 4). The three endometrial cell types: luminal (LE), glandular (GE) epithelium and stroma (ST) were collected by laser microdissection from endometrial biopsies performed at 80 days postpartum. Results: Transcriptome profiles obtained by RNA sequencing revealed differences in constitutive gene expression between the three cells types and also differences in specific responses related to the severity of NEB. Number of differentially expressed genes between SNEB and MNEB cows was higher in ST than in LE and GE, respectively. SNEB was associated with differential expression of genes related to metabolic processes and embryo-maternal interactions in ST. Under-expression of genes related to cell structure was found in GE whereas genes related to pro-inflammatory pathways were over-expressed. Genes associated to adaptive immunity were under-expressed in LE. Conclusion: The three different main cells types of the endometrium, have very different patterns of gene expression. The severity of NEB after calving is associated with changes in gene expression at time of breeding. Specific alterations in GEs are associated with activation of pro-inflammatory mechanisms. Concomitantly, changes in the expression of genes related to cell to cell interactions and maternal recognition of pregnancy takes place in ST. The combination of these effects possibly altering the uterine environment and embryo maternal interactions may negatively influence the establishment of pregnancy.
ano.nymous@ccsd.cnrs.fr.invalid (Wiruntita Chankeaw) 03 Jun 2024
https://hal.inrae.fr/hal-04446339v1
-
[hal-04489470] Understanding bovine embryo elongation: a transcriptomic study of trophoblastic vesicles
During the process of elongation, the embryo increases in size within the uterus, while the extra-embryonic tissues (EETs) develop and differentiate in preparation for implantation. As it grows, the ovoid embryo transforms into a tubular form first and then a filamentous form. This process is directed by numerous genes and pathways, the expression of which may be altered in the case of developmental irregularities such as when the conceptus is shorter than expected or when the embryo develops after splitting. In bovines, efforts to understand the molecular basis of elongation have employed trophoblastic vesicles (TVs)-short tubular EET pieces that lack an embryo-which also elongate in vivo. To date, however, we lack molecular analyses of TVs at the ovoid or filamentous stages that might shed light on the expression changes involved. Methods : Following in vivo development, we collected bovine conceptuses from the ovoid (D12) to filamentous stages (D18), sectioned them into small pieces with or without their embryonic disc (ED), and then, transferred them to a receptive bovine uterus to assess their elongation abilities. We also grew spherical blastocysts in vitro up to D8 and subjected them to the same treatment. Then, we assessed the differences in gene expression between different samples and fully elongating controls at different stages of elongation using a bovine array (10 K) and an extended qPCR array comprising 224 genes across 24 pathways. Results: In vivo, TVs elongated more or less depending on the stage at which they had been created and the time spent in utero. Their daily elongation rates differed from control EET, with the rates of TVs sometimes resembling those of earlier-stage EET. Overall, the molecular signatures of TVs followed a similar developmental trajectory as intact EET from D12-D18. However, within each stage, TVs and intact EET displayed distinct expression dynamics, some of which were shared with other short epithelial models. Conclusion : Differences between TVs and EET likely result from multiple factors, including a reduction in the length and signaling capabilities of TVs, delayed elongation from inadequate uterine signals, and modified crosstalk between the conceptus and the uterus. These findings confirm that close coordination between uterine, embryonic, and extra-embryonic tissues is required to orchestrate proper elongation and, based on the partial differentiation observed, raise questions about the presence/absence of certain developmental cues or even their asynchronies.
ano.nymous@ccsd.cnrs.fr.invalid (Séverine A Degrelle) 05 Mar 2024
https://hal.inrae.fr/hal-04489470v1
-
[hal-04616642] Dynamics of the viral community on the surface of a French smear-ripened cheese during maturation and persistence across production years
The surface of smear-ripened cheeses constitutes a dynamic microbial ecosystem resulting from the successive development of different microbial groups such as lactic acid bacteria, fungi, and ripening bacteria. Recent studies indicate that a viral community, mainly composed of bacteriophages, also represents a common and substantial part of the cheese microbiome. However, the composition of this community, its temporal variations, and associations between bacteriophages and their hosts remain poorly characterized. Here, we studied a French smear-ripened cheese by both viral metagenomics and 16S metabarcoding approaches to assess both the succession of phages and bacterial communities on the cheese surface during cheese ripening and their temporal variations in ready-to-eat cheeses over the years of production. We observed a clear transition of the phage community structure during ripening with a decreased relative abundance of viral species (vOTUs) associated with Lactococcus phages, which were replaced by vOTUs associated with phages infecting ripening bacteria such as Brevibacterium, Glutamicibacter, Pseudoalteromonas, and Vibrio . The dynamics of the phage community was strongly associated with bacterial successions observed on the cheese surface. Finally, while some variations in the distribution of phages were observed in ready-to-eat cheeses produced at different dates spanning more than 4 years of production, the most abundant phages were detected throughout. This result revealed the long-term persistence of the dominant phages in the cheese production environment. Together, these findings offer novel perspectives on the ecology of bacteriophages in smear-ripened cheese and emphasize the significance of incorporating bacteriophages in the microbial ecology studies of fermented foods. IMPORTANCE The succession of diverse microbial populations is critical for ensuring the production of high-quality cheese. We observed a temporal succession of phages on the surface of a smear-ripened cheese, with new phage communities showing up when ripening bacteria start covering this surface. Interestingly, the final phage community of this cheese is also consistent over large periods of time, as the same bacteriophages were found in cheese products from the same manufacturer made over 4 years. This research highlights the importance of considering these bacteriophages when studying the microbial life of fermented foods like cheese.
ano.nymous@ccsd.cnrs.fr.invalid (Thomas Paillet) 18 Jul 2025
https://hal.inrae.fr/hal-04616642v1
-
[hal-04225678] Targeted mutation and inactivation of the kinesin light chain 3 protein-encoding gene have no impact on mouse fertility
Abstract The kinesin light chain 3 protein (KLC3) is the only member of the kinesin light chain protein family that was identified in post-meiotic mouse male germ cells. It plays a role in the formation of the sperm midpiece through its association with both spermatid mitochondria and outer dense fibers (ODF). Previous studies showed a significant correlation between its expression level and sperm motility and quantitative semen parameters in humans, while the overexpression of a KLC3-mutant protein unable to bind ODF also affected the same traits in mice. To further assess the role of KLC3 in fertility, we used CRISPR/Cas9 genome editing in mice and investigated the phenotypes induced by the invalidation of the gene or of a functional domain of the protein. Both approaches gave similar results, i.e. no detectable change in male or female fertility. Testis histology, litter size and sperm count were not altered. Apart from the line-dependent alterations of Klc3 mRNA levels, testicular transcriptome analysis did not reveal any other changes in the genes tested. Western analysis supported the absence of KLC3 in the gonads of males homozygous for the inactivating mutation and a strong decrease in expression in males homozygous for the allele lacking one out of the five tetratricopeptide repeats. Overall, these observations raise questions about the supposedly critical role of this kinesin in reproduction, at least in mice where its gene mutation or inactivation did not translate into fertility impairment.
ano.nymous@ccsd.cnrs.fr.invalid (Nathalie Daniel-Carlier) 03 Oct 2023
https://hal.inrae.fr/hal-04225678v1
-
[hal-04714371] Massive detection of cryptic recessive genetic defects in dairy cattle mining millions of life histories
Background: Dairy cattle breeds are populations of limited effective size, subject to recurrent outbreaks of recessive defects that are commonly studied using positional cloning. However, this strategy, based on the observation of animals with characteristic features, may overlook a number of conditions, such as immune or metabolic genetic disorders, which may be confused with pathologies of environmental etiology. Results: We present a data mining framework specifically designed to detect recessive defects in livestock that have been previously missed due to a lack of specific signs, incomplete penetrance, or incomplete linkage disequilibrium. This approach leverages the massive data generated by genomic selection. Its basic principle is to compare the observed and expected numbers of homozygotes for sliding haplotypes in animals with different life histories. Within three cattle breeds, we report 33 new loci responsible for increased risk of juvenile mortality and present a series of validations based on large-scale genotyping, clinical examination, and functional studies for candidate variants affecting the NOA1, RFC5, and ITGB7 genes. In particular, we describe disorders associated with NOA1 and RFC5 mutations for the first time in vertebrates. Conclusions:The discovery of these many new defects will help to characterize the genetic basis of inbreeding depression, while their management will improve animal welfare and reduce losses to the industry.
ano.nymous@ccsd.cnrs.fr.invalid (Florian Besnard) 30 Sep 2024
https://hal.inrae.fr/hal-04714371v1
-
[hal-04386368] Faecalibacterium duncaniae A2-165 regulates the expression of butyrate synthesis, ferrous iron uptake, and stress-response genes based on acetate consumption
The promising next-generation probiotic Faecalibacterium prausnitzii is one of the most abundant acetate-consuming, butyrate-producing bacteria in the healthy human gut. Yet, little is known about how acetate availability affects this bacterium's gene expression strategies. Here, we investigated the effect of acetate on temporal changes in the transcriptome of F. duncaniae A2-165 cultures using RNA sequencing. We compared gene expression patterns between two growth phases (early stationary vs. late exponential) and two acetate levels (low: 3 mM vs. high: 23 mM). Only in low-acetate conditions, a general stress response was activated. In high-acetate conditions, there was greater expression of genes related to butyrate synthesis and to the importation of B vitamins and iron. Specifically, expression was strongly activated in the case of the feoAABC operon, which encodes a FeoB ferrous iron transporter, but not in the case of the feoAB gene, which encodes a second putative FeoAB transporter. Moreover, excess ferrous iron repressed feoB expression but not feoAB. Lastly, FeoB but not FeoAB peptides from strain A2-165 were found in abundance in a healthy human fecal metaproteome. In conclusion, we characterized two early-stationary transcriptomes based on acetate consumption and this work highlights the regulation of feoB expression in F. duncaniae A2-165.
ano.nymous@ccsd.cnrs.fr.invalid (Sophie Verstraeten) 10 Jan 2024
https://hal.inrae.fr/hal-04386368v1
-
[hal-04807017] Cellular specialization inside the symbiotic organ of an insect pest: deciphering the dialog between host and symbiotic bacteria and their adaptation to different dietetic conditions
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Nikoletta Galambos) 27 Nov 2024
https://hal.science/hal-04807017v1
-
[hal-04214068] Comparison of goat and cow milk-derived extracellular vesicle miRNomes
Abstract miRNAs present in milk are mainly found in extracellular vesicles (EVs), which are nanosized membrane vesicles released by most of the cell types to ensure intercellular communication. The majority of the studies performed so far on these vesicles have been conducted on human and cow’s milk and focused on their miRNA content. The objectives of this study were to profile the miRNA content of purified EVs from five healthy goats and to compare their miRNome to those obtained from five healthy cows, at an early stage of lactation. EV populations were morphologically characterized using Transmission Electron Microscopy and Nanoparticle Tracking Analysis. The presence of EV protein markers checked by Western blotting and the absence of contamination of preparations by milk proteins. The size distribution and concentration of bovine and goat milk-derived EVs were similar. RNA-sequencing were performed, and all sequences were mapped to the cow genome identifying a total of 295 miRNAs. This study reports for the first-time a goat miRNome from milk EVs and its validation using cow miRNomes.
ano.nymous@ccsd.cnrs.fr.invalid (Zuzana Krupova) 21 Sep 2023
https://hal.inrae.fr/hal-04214068v1
-
[hal-04807966] Cellular specialization inside the symbiotic organ of an insect pest: deciphering the dialog between host and symbiotic bacteria and their adaptation to different dietetic conditions
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Nikoletta Galambos) 27 Nov 2024
https://hal.science/hal-04807966v1
-
[hal-04289008] Understanding Bovine Embryo Elongation: A Multi-Omic Study with Trophoblastic Vesicle Models
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Séverine A. Degrelle) 16 Nov 2023
https://hal.inrae.fr/hal-04289008v1
-
[hal-05203851] Uterus healing after cesarean: development of a rabbit model
Uterine Scar area on C-section horn Normal area on C-section horn Control horn Wilcoxon Mann-Whitney Test *p&lt;0,05 **p&lt;0,01***p&lt;0,001 Mean thickness area Cesarean: Representation and incision of the Csection horn C-section horn with normal scar • Left: Macroscopic view • Right: Section 5µm, haematoxylineosin-safran staining. The objective is to develop an in-vivo model of uterus healing after cesarean in order to analyze histological phenomena controlling scarring tissue development and potential cause of defects.
ano.nymous@ccsd.cnrs.fr.invalid (Elodie Debras) 08 Aug 2025
https://hal.inrae.fr/hal-05203851v1
-
[hal-04210385] Recent genomic contributions to understanding Mycobacterium avium subsp. paratuberculosis evolution and transmission dynamics
Introduction and objectives. Paratuberculosis or Johne's disease is a chronic intestinal disease caused by Mycobacterium avium ssp. paratuberculosis (Map), primarily affecting ruminants and present worldwide. Despite the implementation of control programs in most developed countries, and the consequent financial efforts required, the prevalence rate of paratuberculosis remains very high, at around 50% in European herds and 8% in U.S herds. This worrying situation is due to a lack of knowledge about the biology of this pathogen and its transmission dynamics. Map's genomic studies, initiated in 2016, have recently multiplied thanks to the development of 3rd generation sequencing. Here we present a review of the contribution of Map genomic studies to our understanding of this pathogen and the epidemiology of Johne's disease. Materials and methods The articles collected for this synthesis encompass more than 820 genomes available in the NCBI SRA, GenBank, and ENA databases and 15 complete genomes. Map strains were distributed over 5 continents and have been isolated from a variety of hosts but mainly ruminants. We selected studies for which epidemiological data were available. Results, discussion and conclusion Analysis of the pangenome shows that Map is a clonal species with a core genome of 98%. The advent of next-generation sequencing has not only made it possible to establish relationships down to the strain level, but has also revealed genome-wide differences between strains, making it possible to establish Map's population structure by country and between countries. Phylogenetic analyses combined with data on animals, including their movements, provide a better understanding of Map's transmission dynamics. Map genomics has also revealed the notion of mixed infection in animals. Taken together, these data further our knowledge of this pathogen and offer new prospects for improving the prevention and control of Johne's disease.
ano.nymous@ccsd.cnrs.fr.invalid (Franck Biet) 18 Sep 2023
https://hal.inrae.fr/hal-04210385v1
-
[hal-04728107] ITGA6 homozygous splice-site mutation causes junctional epidermolysis bullosa in Charolais cattle
Junctional epidermolysis bullosa (JEB), characterized by mechanically induced blisters of the skin and mucous membranes, is one of the most painful and life threatening recessive genetic disorders described in humans and other animal species. Congenital skin fragility resembling JEB was recently reported in three Charolais calves born in two distinct herds from unaffected parents. Phenotypic and genetic analyses were carried out to describe this condition and its molecular etiology. Genealogical, clinical and histological examinations confirmed the diagnosis of recessive JEB, even if affected calves showed milder symptoms than those of another form of JEB, previously reported in the same breed, and due to a homozygous deletion of ITGB4. Homozygosity mapping followed by analysis of the whole genome sequences of 2 cases and 5031 control individuals enabled us to prioritize a splice donor site of ITGA6 (c.2160+1G>T; Chr2 g.24112740C>A) as the most compelling candidate variant. This substitution showed a perfect genotype-phenotype correlation in the two affected pedigrees and was found to segregate only in Charolais, and at a very low frequency (f=1.6*10-4) after genotyping 186,154 animals from 15 breeds. Finally, RT-PCR analyses revealed increased retention of ITGA6 introns 14 and 15 in a heterozygous mutant cow as compared with a matched control. The mutant mRNA is predicted to cause a frameshift (ITGA6 p.I657Mfs1) affecting the assembly of the Integrin α6β4 dimer and its correct anchoring to the cell membrane. This dimer is a key component of the hemidesmosome anchoring complex, which ensures the attachment of basal epithelial cells to the basal membrane. In conclusion, we report a rare example of partial phenocopies observed in the same breed and due to mutations affecting two members of the same protein dimer, as well as the first evidence of an ITGA6 mutation causing JEB in livestock species.
ano.nymous@ccsd.cnrs.fr.invalid (Cécile Grohs) 09 Oct 2024
https://hal.inrae.fr/hal-04728107v1
-
[hal-04189843] Cell type- and time-dependent biological responses in ex vivo perfused lung grafts
In response to the increasing demand for lung transplantation, ex vivo lung perfusion (EVLP) has extended the number of suitable donor lungs by rehabilitating marginal organs. However despite an expanding use in clinical practice, the responses of the different lung cell types to EVLP are not known. In order to advance our mechanistic understanding and establish a refine tool for improvement of EVLP, we conducted a pioneer study involving single cell RNA-seq on human lungs declined for transplantation. Functional enrichment analyses were performed upon integration of data sets generated at 4 h (clinical duration) and 10 h (prolonged duration) from two human lungs processed to EVLP. Pathways related to inflammation were predicted activated in epithelial and blood endothelial cells, in monocyte-derived macrophages and temporally at 4 h in alveolar macrophages. Pathways related to cytoskeleton signaling/organization were predicted reduced in most cell types mainly at 10 h. We identified a division of labor between cell types for the selected expression of cytokine and chemokine genes that varied according to time. Immune cells including CD4+ and CD8+ T cells, NK cells, mast cells and conventional dendritic cells displayed gene expression patterns indicating blunted activation, already at 4 h in several instances and further more at 10 h. Therefore despite inducing inflammatory responses, EVLP appears to dampen the activation of major lung immune cell types, what may be beneficial to the outcome of transplantation. Our results also support that therapeutics approaches aiming at reducing inflammation upon EVLP should target both the alveolar and vascular compartments.
ano.nymous@ccsd.cnrs.fr.invalid (Carla Gouin) 29 Aug 2023
https://hal.inrae.fr/hal-04189843v1
-
[hal-04218343] Phenotyping of organoids: contribution of an integrated platform for their characterization
Classical 2D in vitro cell cultures have shown their limits, and the development of "organotypic" cell cultures of epithelial tissues seems a good way to replace animal biopsies. Organoids are 3D organotypic cell cultures derived from animal tissue stem cells. Development of protocols for obtaining organoids from different organs is underway at INRAE in Jouy-en-Josas. Their characterization is an important step to verify cell differentiation. At the Animal Genetics and Integrative Biology unit (INRAE UMR1313 GABI), the Genetics, Microbiota, Health (GeMS) team has developed the production of pig intestinal organoids. The @BRIDGe (Animal Biological Resources for Integrated and Digital Genomics) platform of the GABI unit brings its expertise in histology and molecular biology for the characterization of the organoids obtained by those production protocols.
ano.nymous@ccsd.cnrs.fr.invalid (Julie Rivière) 26 Sep 2023
https://hal.inrae.fr/hal-04218343v1
-
[hal-04217727] Spatiotemporal analysis of melanoma heterogeneity in a spontaneous swine model at single-cell resolution
Introduction Melanoma is the deadliest skin cancer, with an increasing incidence especially in young adults. Melanoma may appear in nearly all pigmented animals. In the MeLiM minipig model, cutaneous melanomas develop during the perinatal period. They display many traits of malignancy as in humans. Intriguingly, MeLiM melanomas spontane-ously regress with a concomitant immune response. In other words, this cancer is totally "cured" within 6 months, with no side effect other than lesion and coat depigmentation. Compared to current immunotherapies, this model provides cues for cancer treatment with a high success rate and few adverse effects. Single-cell RNA-seq and spatial transcriptomics analysis could give indications on intratumor heterogeneity at the individual level, investigat-ing clonal evolution and the involvement of the microenvironment. Material and Methods Frozen samples spanning different time points during tumor evolution, from early lesions to progressive lesions sampled in couples of littermates were selected. Screening of conditions on nuclei isolation and purification for sin-gle-cell and depigmentation strategies for spatial analysis was achieved with RNA integrity and image analysis. Single-nucleus RNA-seq libraries and Visium transcriptomics were performed with the 10X Genomics technology. Results and Discussion We will present considerations for the best protocols adapted to our samples and a landscape of MeLiM lesions obtained after analysis of 61000 single cells. The analysis of cell types as cell cycle scores was consistent with immunofluorescence studies. Spatially resolved transcriptomics enabled to localize part of the cells identified in the single-cell libraries. Conclusions This study will help understand the regression mechanisms in MeLiM minipigs.
ano.nymous@ccsd.cnrs.fr.invalid (Giorgia Egidy) 26 Sep 2023
https://hal.inrae.fr/hal-04217727v1
-
[hal-04798331] Cellular specialization inside the symbiotic organ of an insect pest: deciphering the dialog between host and symbiotic bacteria and their adaptation to different dietetic conditions
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Nikoletta Galambos) 22 Nov 2024
https://hal.science/hal-04798331v1
-
[hal-04159117] Biomineralization of magnetic nanoparticles in stem cells
Iron is one of the most common metals in the human body, with an intrinsic metabolism including proteins involved in its transport, storage, and redox mechanisms. A less explored singularity is the presence of magnetic iron in the organism, especially in the brain. The capacity of human stem cells to biosynthesize magnetic nanoparticles was recently demonstrated, using iron released by the degradation of synthetic magnetic nanoparticles. To evidence a magnetic biomineralization in mammalian cells, it is required to address the biosynthesis of magnetic nanoparticles in cells supplied exclusively with non-magnetic iron salt precursors. Herein, mouse and human mesenchymal stem cells were incubated with ferric quinate for up to 36 days. By optimizing the concentration and culture time, and by measuring both total intracellular iron content and cellular magnetic signals, the biosynthesis of magnetic nanoparticles was found to occur from 14 days of continuous iron incubation and was correlated with important doses of intracellular iron. The local electronic structure and chemical environment of intracellular iron were further characterized by XAS spectroscopy at the Fe K-edge, showing a total conversion of Fe2+ to Fe3+ when using ferrous salts (ascorbate and sulfate), and a transformation towards ferrihydrite as well as a small proportion of a magnetic phase.
ano.nymous@ccsd.cnrs.fr.invalid (Alexandre Fromain) 22 Nov 2023
https://hal.inrae.fr/hal-04159117v2
-
[hal-04125597] Integrin alpha 6 homozygous splice-site mutation causes a new form of junctional epidermolysis bullosa in Charolais cattle
Background Inherited epidermolysis bullosa (EB) is a group of painful and life-threatening genetic disorders that are characterized by mechanically induced blistering of the skin and mucous membranes. Congenital skin fragility resembling EB was recently reported in three Charolais calves born in two distinct herds from unaffected parents. Phenotypic and genetic analyses were carried out to describe this condition and its molecular etiology. Results Genealogical, pathological and histological investigations confirmed the diagnosis of recessive EB. However, the affected calves showed milder clinical signs compared to another form of EB, which was previously reported in the same breed and is caused by a homozygous deletion of the ITGB4 gene. Homozygosity mapping followed by analysis of the whole-genome sequences of two cases and 5031 control individuals enabled us to prioritize a splice donor site of ITGA6 (c.2160 + 1G > T; Chr2 g.24112740C > A) as the most compelling candidate variant. This substitution showed a perfect genotype–phenotype correlation in the two affected pedigrees and was found to segregate only in Charolais, and at a very low frequency (f = 1.6 × 10 −4 ) after genotyping 186,154 animals from 15 breeds. Finally, RT-PCR analyses revealed increased retention of introns 14 and 15 of the ITGA6 gene in a heterozygous mutant cow compared with a matched control. The mutant mRNA is predicted to cause a frameshift (ITGA6 p.I657Mfs1) that affects the assembly of the integrin α6β4 dimer and its correct anchoring to the cell membrane. This dimer is a key component of the hemidesmosome anchoring complex, which ensures the attachment of basal epithelial cells to the basal membrane. Based on these elements, we arrived at a diagnosis of junctional EB. Conclusions We report a rare example of partial phenocopies observed in the same breed and due to mutations that affect two members of the same protein dimer, and provide the first evidence of an ITGA6 mutation that causes EB in livestock species.
ano.nymous@ccsd.cnrs.fr.invalid (Mekki Boussaha) 12 Jun 2023
https://hal.inrae.fr/hal-04125597v1
-
[hal-04116782] A cross-circulatory platform for monitoring innate allo-responses in lung grafts
Lung transplantation is the only curative option for end-stage chronic respiratory diseases. However the survival rate is only about 50% at 5 years. Although experimental evidences have shown that innate allo-responses impact on the clinical outcome, the knowledge of the involved mechanisms involved is limited. We established a cross-circulatory platform to monitor the early recruitment and activation of immune cells in an extracorporeal donor lung by coupling blood perfusion to cell mapping with a fluorescent marker in the pig, a commonly-used species for lung transplantation. The perfusing pig cells were easily detectable in lung cell suspensions, in broncho-alveolar lavages and in different areas of lung sections, indicating infiltration of the organ. Myeloid cells (granulocytes and monocytic cells) were the dominant recruited subsets. Between 6 and 10 h of perfusion, recruited monocytic cells presented a strong upregulation of MHC class II and CD80/86 expression, whereas alveolar macrophages and donor monocytic cells showed no significant modulation of expression. This cross-circulation model allowed us to monitor the initial encounter between perfusing cells and the lung graft, in an easy, rapid, and controllable manner, to generate robust information on innate response and test targeted therapies for improvement of lung transplantation outcome.
ano.nymous@ccsd.cnrs.fr.invalid (Matthieu Glorion) 05 Jun 2023
https://hal.inrae.fr/hal-04116782v1
-
[hal-04295803] MULTI-OMIC AND LONGITUDINAL APPROACH FOR BIOMARKERS DISCOVERY IN FOOD PROTEIN INDUCED ENTEROCOLITIS SYNDROME (FPIES)
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Anaïs Lemoine) 20 Nov 2023
https://hal.inrae.fr/hal-04295803v1
-
[hal-04225490] Saccharomyces boulardii CNCM I-745 supplementation during and after antibiotic treatment positively influences the bacterial gut microbiota
Antibiotic effects on gut bacteria have been widely studied, but very little is known about the consequences of such treatments on the mycobiota, the fungal part of the microbiota and how the length of administration influences both microbiota. Here, we examined the effect of antibiotics (ATB) on the composition of bacterial and fungal microbiota and how the administration of Saccharomyces boulardii CNCM I-745 influences both microbiota. In order to get closer to the human microbiota, the mice used in this study were subjected to fecal microbiota transfer (FMT) using human feces and subsequently called human microbiotaassociated (HMA) mice. These mice were then treated with amoxicillinclavulanate antibiotics and supplemented with S. boulardii during and after ATB treatment to understand the effect of the yeast probiotic on both bacterial and fungal microbiota. Bacterial and fungal microbiota analyses were done using 16S and ITS2 rRNA amplicon-based sequencing. Results We showed that the administration of S. boulardii during ATB treatment had very limited effect on the fungal populations on the long term, once the yeast probiotic has been cleared from the gut. Concerning bacterial microbiota, S. boulardii administration allowed a better recovery of bacterial populations after the end of the ATB treatment period. Additionally, 16S and ITS2 rRNA sequence analysis revealed that 7 additional days of S. boulardii administration (17 days in total) enhanced the return of the initial bacterial equilibrium. In this study, we provide a comprehensive analysis of how probiotic yeast administration can influence the fungal and bacterial microbiota in a model of broad-spectrum antibiotherapy.
ano.nymous@ccsd.cnrs.fr.invalid (Madeleine Spatz) 02 Oct 2023
https://hal.inrae.fr/hal-04225490v1
-
[hal-03860146] Milk proteins as a feed restriction signature indicating the metabolic adaptation of dairy cows
Milk production in dairy cows is affected by numerous factors, including diet. Feed restriction is known to have little impact on milk total protein content but its effect on the fine protein composition is still poorly documented. The objective of this study was to describe the effects of two feed restriction trials of different intensities on the milk protein composition of Holstein cows. One restriction trial was of high intensity (H: 8 mid-lactation Holstein cows) and the second of moderate intensity (M: 19 peak lactation Holstein cows). Feed restriction decreased the milk protein yield for caseins under the M trial and of all six major milk proteins under the H trial. These decreased yields lead to lower concentrations of αs1-, αs2- and β-caseins during the H trial. The milk proteome, analyzed on 32 milk samples, was affected as a function of restriction intensity. Among the 345 proteins identified eight varied under the M trial and 160 under the H trial. Ontology analyses revealed their implication in carbohydrate, lipid and protein metabolisms as well as in the immune system. These proteins reflected adaptations of the animal and mammary gland physiology to feed restriction and constituted a signature of this change.
ano.nymous@ccsd.cnrs.fr.invalid (Antoine Leduc) 18 Nov 2022
https://hal.inrae.fr/hal-03860146v1
-
[hal-03800214] Managing genetic diversity in breeding programs of small populations: the case of French local chicken breeds
Background On-going climate change will drastically modify agriculture in the future, with a need for more sustainable systems, in particular regarding animal production. In this context, genetic diversity is a key factor for adaptation to new conditions: local breeds likely harbor unique adaptive features and represent a key component of diversity to reach resilience. However, local breeds often suffer from small population sizes, which puts these valuable resources at risk of extinction. In chickens, population management programs were initiated a few decades ago in France, relying on a particular niche market that aims at promoting and protecting local breeds. We conducted a unique comprehensive study of 22 French local breeds, along with four commercial lines, to evaluate their genetic conservation status and the efficiency of the population management programs. Results Using a 57K single nucleotide polymorphism (SNP) chip, we demonstrated that both the between- and within-breed genetic diversity levels are high in the French local chicken populations. Diversity is mainly structured according to the breeds’ selection and history. Nevertheless, we observed a prominent sub-structuring of breeds according to farmers’ practices in terms of exchange, leading to more or less isolated flocks. By analysing demographic parameters and molecular information, we showed that consistent management programs are efficient in conserving genetic diversity, since breeds that integrated such programs earlier had older inbreeding. Conclusions Management programs of French local chicken breeds have maintained their genetic diversity at a good level. We recommend that future programs sample as many individuals as possible, with emphasis on both males and females from the start, and focus on a quick and strong increase of population size while conserving as many families as possible. We also stress the usefulness of molecular tools to monitor small populations for which pedigrees are not always available. Finally, the breed appears to be an appropriate operational unit for the conservation of genetic diversity, even for local breeds, for which varieties, if present, could also be taken into account.
ano.nymous@ccsd.cnrs.fr.invalid (Gwendal Restoux) 11 Jul 2023
https://hal.inrae.fr/hal-03800214v1
-
[hal-04788646] Cellular specialization inside the symbiotic organ of an insect pest: deciphering the dialog between host and symbiotic bacteria and their adaptation to different dietetic conditions
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Nikoletta Galambos) 18 Nov 2024
https://hal.science/hal-04788646v1
-
[hal-04146084] Effet de la génétique et du microbiote sur la réponse vaccinale et le bien-être des poules pondeuses dans deux environnements d'élevage.
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Alexandre Lecoeur) 29 Jun 2023
https://hal.inrae.fr/hal-04146084v1
-
[hal-04233098] Phenotypic variability of porcine gut organoids provide opportunities for genotype to phenotype studies
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Smahane Chalabi) 09 Oct 2023
https://hal.inrae.fr/hal-04233098v1
-
[hal-04217828] Caractérisation clinique, histologique et transcriptomique d’une réponse immunitaire antitumorale efficiente chez le porc
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Giorgia Egidy) 26 Sep 2023
https://hal.inrae.fr/hal-04217828v1
-
[hal-03771102] Comparative analysis of the caecal tonsil transcriptome in two chicken lines experimentally infected with Salmonella Enteritidis
Managing Salmonella enterica Enteritidis (SE) carriage in chicken is necessary to ensure human food safety and enhance the economic, social and environmental sustainability of chicken breeding. Salmonella can contaminate poultry products, causing human foodborne disease and economic losses for farmers. Both genetic selection for a decreased carriage and gut microbiota modulation strategies could reduce Salmonella propagation in farms. Two-hundred and twenty animals from the White Leghorn inbred lines N and 6 1 were raised together on floor, infected by SE at 7 days of age, transferred into isolators to prevent orofecal recontamination and euthanized at 12 days post-infection. Caecal content DNA was used to measure individual Salmonella counts (ISC) by droplet digital PCR. A RNA sequencing approach was used to measure gene expression levels in caecal tonsils after infection of 48 chicks with low or high ISC. The analysis between lines identified 7516 differentially expressed genes (DEGs) corresponding to 62 enriched Gene Ontology (GO) Biological Processes (BP) terms. A comparison between low and high carriers allowed us to identify 97 DEGs and 23 enriched GO BP terms within line 6 1 , and 1034 DEGs and 288 enriched GO BP terms within line N. Among these genes, we identified several candidate genes based on their putative functions, including FUT2 or MUC4, which could be involved in the control of SE infection, maybe through interactions with commensal bacteria. Altogether, we were able to identify several genes and pathways associated with differences in SE carriage level. These results are discussed in relation to individual caecal microbiota compositions, obtained for the same animals in a previous study, which may interact with host gene expression levels for the control of the caecal SE load.
ano.nymous@ccsd.cnrs.fr.invalid (Anaïs Cazals) 07 Sep 2022
https://hal.inrae.fr/hal-03771102v1
-
[hal-04260945] Novel blood biomarkers to predict better responses to vaccination in chicken
Because of the multiple factors controlling host responses to vaccines or to infections, more effective disease control strategies should be developed in an integrated animal health management approach, including prevention, cure, environment control and breeding for improved immunocompetence. The impact of host genetic variation in shaping innate and adaptive immune response is an emerging lever to consider in new vaccination strategies. Indeed, in the same flock, not all birds even vaccinated simultaneously and with the same dose, will respond equally to a vaccine. This study aimed at, 1- utilizing the host genetic variability of the response to Eimeria maxima vaccination of chickens to search for blood biomarkers predictive of vaccine response intensities; then 2- to test the candidate biomarkers in validation populations for another vaccine response, to Newcastle Disease Virus Vaccine (NDV). For the search of biomarkers to E. maxima vaccine, 90 male commercial broilers (Cobb 500) were used. Nine days after vaccination with 100 E. maxima Weybridge strain oocysts at 16d, a subset of 79 birds were challenged with 50,000 parasites of the homologous species/strain. Body weight gain, lesion scores, parasite load and IL-10 serum levels were used to assess birds' responses. Birds were ranked according to their vaccine responses and RNAseq data were produced from blood sampled prior vaccination for 63 birds representing the diversity of responses. For each response phenotype, high and low responders were selected (upper and lower quartiles) and sparse Partial Least Squares-Discriminant Analyses (sPLS-DA) were carried out to identify the best predictive blood biomarkers classifying birds into each group. Finally, 108 candidate genes, predictive with accuracy higher than 97% for all vaccine responses, were selected. A custom OpenArray for highthroughput RTqPCR assays was then design to test the candidate biomarkers in validation populations. First test was performed on a population of White Leghorn selected birds displaying a large variability of response to NDV vaccine. This is a proof of concept that blood before vaccination can be used as a relevant source of biomarkers predictive of vaccine responses. Future researches, combining genetic variability of response to vaccine and disease and novel vaccines, pave the way for better and more efficient vaccination through "precision vaccination" and "personalized health management".
ano.nymous@ccsd.cnrs.fr.invalid (Marie-Hélène Pinard-van Der Laan) 26 Oct 2023
https://hal.science/hal-04260945v1
