Contributors: Mathématiques et Informatique Appliquées du Génome à l'Environnement Jouy-En-Josas (MaIAGE); Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE); Interactions hôtes-agents pathogènes Toulouse (IHAP); Ecole Nationale Vétérinaire de Toulouse (ENVT); Institut National Polytechnique (Toulouse) (Toulouse INP); Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP); Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE); Biologie de la Reproduction, Environnement, Epigénétique & Développement (BREED); École nationale vétérinaire d'Alfort (ENVA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE); Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH); VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE); Science et Technologie du Lait et de l'Oeuf (STLO); Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers; Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro); Unité Expérimentale du Pin (UEP); Infectiologie et Santé Publique (UMR ISP); Université de Tours (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE); Département Physiologie Animale et Systèmes d'Elevage (PHASE); Génétique Animale et Biologie Intégrative (GABI); AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE); This work is part of the MICROCOSM project funded by the INRAE Metaprogramme MEM. This project also received a financial contribution by the national veterinary school of Toulouse, ENVT, and by the INRAE PHASE department.
نبذة مختصرة : This study has been carried out at the INRAE “Domaine Expérimental du Pin” (https://doi.org/10.15454/1.5483257052131956E12), which has been approved by the national legislation on animal care (French Ministry of Agriculture certification no. D 61-157-001). All experiments involving animals were approved by the local Ethics Committee in Animal Experiment and the French Ministry of Higher Education, Research and Innovation (APAFIS#3066-201511301610897 v2).The authors would like to thank the entire staff of the Le Pin beef and dairy cattle experimental unit for its technical assistance during the sampling campaign. We thank all the members from the sequencing platform of Genome Quebec for their help and all their efforts in the realization of this project, with special thanks to Mr Frederick Robidoux, Mrs Julie Boudeau, Mrs Hao Fan Yam and Mr Pierre Lepage. We are grateful to the INRAE MIGALE bioinformatics facility (https://doi.org/10.15454/1.5572390655343293E12) for providing computing and storage resources. ; International audience ; Background:Host-associated microbes are major determinants of the host phenotypes. In the present study, we used dairy cows with different scores of susceptibility to mastitis with the aim to explore the relationships between microbiota composition and different factors in various body sites throughout lactation as well as the intra- and inter-animal microbial sharing.Results:Microbiotas from the mouth, nose, vagina and milk of 45 lactating dairy cows were characterized by metataxonomics at four time points during the first lactation, from 1-week pre-partum to 7 months post-partum. Each site harbored a specific community that changed with time, likely reflecting physiological changes in the transition period and changes in diet and housing. Importantly, we found a significant number of microbes shared among different anatomical sites within each animal. This was between nearby anatomic sites, with up to 32% of the total number of Amplicon Sequence Variants (ASVs) of the oral ...
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