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UNIVERSITE DE LIEGE FACULTE DE MEDECINE VETERINAIRE DEPARTEMENT DES SCIENCES DES DENREES ALIMENTAIRES SERVICE D’INSPECTION DES DENREES ALIMENTAIRES INVESTIGATION SUR LA QUALITE DU LAIT CRU PRODUIT DANS LE BASSIN LAITIER DE NIAMEY (NIGER) RESEARCH ON THE QUALITY OF RAW MILK PRODUCED IN THE DAIRY POOL OF NIAMEY (NIGER) Amadou MOROU MADOUGOU THESE PRESENTEE EN VUE DE L’OBTENTION DU GRADE DE Docteur en Sciences Vétérinaires ANNEE ACADEMIQUE 2019-2020 UNIVERSITE DE LIEGE FACULTE DE MEDECINE VETERINAIRE DEPARTEMENT DES SCIENCES DES DENREES ALIMENTAIRES SERVICE D’INSPECTION DES DENREES ALIMENTAIRES INVESTIGATION SUR LA QUALITE DU LAIT CRU PRODUIT DANS LE BASSIN LAITIER DE NIAMEY (NIGER) RESEARCH ON THE QUALITY OF RAW MILK PRODUCED IN THE DAIRY POOL OF NIAMEY (NIGER) Amadou MOROU MADOUGOU THESE PRESENTEE EN VUE DE L’OBTENTION DU GRADE DE Docteur en Sciences Vétérinaires ANNEE ACADEMIQUE 2019-2020 Jury composé de : Président : Thomas MARICHAL (Uliege, Belgique) Promoteur : Nicolas KORSAK (Uliege, Belgique) Co- Promoteur: Hamani MARICHATOU ( Université de Niamey, Niger) Membres du comité : Georges DAUBE (Uliege, Belgique) Véronique DELCENSERIE ( Uliege, Belgique) Membres extérieurs à l’ULiège : Nathalie GNANOU BESSE (Anses, France) Laurent GUILLIER (Anses, France) Membres internes à l’ULiège : Jean Luc HORNICK (Uliege, Belgique) Marianne SINDIC (Uliege, Belgique) Frédéric Rollin (Uliege, Belgique) Damien THIRY (Uliege, Belgique) i Remerciements Je mesure toute la difficulté d’établir une liste exhaustive de tous ceux qui ont bien voulu contribuer à l’aboutissement de cette thèse. Puissent celles ou ceux dont les noms n’ont pas été mentionnés sous ces lignes se rassurer de l’expression de toute ma profonde gratitude. Mes vifs remerciements sont d’abord adressés à mon promoteur, Nicolas KORSAK, et mon co-promoteur, Hamani MARICHATOU, pour m’avoir accompagné pendant ces années d’intenses et passionnantes recherches. Professeur Nicolas KORSAK, qui a dirigé ce travail avec un esprit innovateur. Votre rigueur, votre capacité d’analyse des problèmes et votre ouverture d’esprit m’ont permis de progresser dans mon travail de thèse. Merci pour m’avoir formé. Enfin, vos qualités scientifiques et humaines m’ont beaucoup marqué durant mes séjours belges. Professeur Hamani MARICHATOU, votre contribution à la réalisation de cette thèse m’a permis de tirer profil de votre expérience sur la problématique de l’élevage au Niger à travers nos multiples discussions de la conception du projet jusqu’à la finalisation de la thèse. Merci aussi de m’avoir accordé toute la confiance dès les premières heures de ce travail de thèse. J’adresse également toute ma reconnaissance au Professeurs Georges DAUBE et Véronique DELCENSERIE, membres du comité de pilotage de la thèse, pour la disponibilité, pour avoir accepté de participer au comité d’accompagnement de cette thèse. Merci pour votre contribution à l’amélioration de cette thèse. Mes remerciements vont à l’endroit du Professeur Thomas MARICHAL, pour avoir accepté de présider le Jury. Merci pour votre contribution à l’amélioration de cette thèse. Aux membres du jury, Professeurs Nathalie GNANOU BESSE, Laurent GUILLIER, Jean Luc HORNICK, Fédéric ROLLIN, Marianne SINDIC et Damien THIRY, je vous remercie d’avoir accepté de juger notre travail malgré vos multiples occupations. Vos observations et suggestions pertinentescontribueront significativement à l’amélioration de notre travail. Recevez l’expression de mes sincères remerciements. Je remercie le Docteur Nassim MOULA pour sa contribution inestimable dans la réalisation de mes travaux de recherche. Vos observations et conseils ont été très précieux durant toute la durée ii cette thèse. Merci pour toutes les facilités que vous m’avez offertes pour l’accomplissement de ce travail à toutes ses étapes. Je remercie le Docteur Bernard TAMINIAU. Vos contributions pertinentes ont beaucoup amélioré mes analyses métagénétiques. Auprès de vous, j’ai appris beaucoup de vos conseils et vos remarques dans la réalisation de ce travail de thèse. Je remercie le Docteur Issa HAMADOU pour toutes les facilités que vous m’avez offertes pour l’accomplissement de ce travail de thèse. Vos observations pertinentes ont beaucoup contribué àl’amélioration de mes travaux. Mes remerciements à toute l’équipe du Département des Denrées alimentaires (Professeurs Marie Louis SCIPPO et Antoine CLINQUART, Dr Caroline DOUNY Sébastien CREVECOEUR, Emilie CAUCHIE, Elisa MARTINEZ, Sarah LEBRUN, Pauline BONDUE, Barbara et Christine BAL). Au-delà de nos discussions purement professionnelles, vous avez partagé mon quotidien et souvent contribuéà le rendre plus agréable. Cette thèse a été réalisée grâce au soutien financier du Programme de Productivité Agricole en Afrique de l’Ouest (PPAAO-Niger) et j’exprime ma gratitude et mes remerciements à l’ensemble du personnel PPAAO et CRS/EL. J’exprime ma gratitude et mes remerciements à l’ensemble des doctorants, stagiaires pour vos contributions et vos encouragements. Mes remerciements vont ensuite au Ministère de l’Elevage en particulier à Mr DIAMOITOU Boukary, Secrétaire Général et Président du comité de pilotage des projets dudit Ministère ainsi que l’ensemble du personnel du laboratoire Central de l’Elevage (LABOCEL). Mes remerciements aux Dr Hamma Hamma, Dr BAARE Cathérine, Dr Souley Moutari, Mr DJIBO Hamidou, Ali Hamdallaye, Moumouni Kollo et l’ensemble des éleveurs et personnel des centres de collecte du bassin laitier de Niamey pour votre aides et vos encoragements dans la réalisation de cette thèse. Merci à ma femme et mes enfants, ma famille et mes ami(e)s: je tiens à exprimer ma profonde gratitude à mes parents ; mes frères et sœurs, mes oncles et tantes, mes cousins et cousines, mes neveux et nièces, merci pour vos soutiens divers et variés. Liste des figures Introduction Figure 1 : Carte administrative du Niger avec les pays limitrophes…………………………………...10 Figure 2 : Les principales races bovines du Niger……………………………………………………..14 Figure 3 : Appareil Delvotest et résultats……………………………………………………………...23 Section expérimentale Etude N°2 Figure 1 : Representation géographique de la zone d’étude…………………………………………...54 Etude N°3 Figure 1 : Répresentation géographique de la zone d’étude…………………………………………...77 Figure 2: Bacterial alpha –diversity……………………………………….………………………….81 Figure 3: Bacterial abundance of the 6 phylla common to the 36 raw milk…………………….…….82 Figure 4: Bacterial genera found in the raw milk……………………………………………………...82 Etude N°4 Figure 1: Area of Study……………………………………………………………………………....101 Figure 2: Breeds encountered in the area of study……………………………………………….…...102 Figure 3: Bacterial parameters………………………………………………………………………..105 Figure 4: Bacterial genera in raw milk from Hamdallaye and Kollo………………………………...107 Figure 5: Principal coordinate analysis plots based upon the Bray-Curtis dissimilarity……………..108 Discussion Figure 1: Effet des saisons sur la flore microbiènne en function des moyennes……………………128 iv Liste des tableaux Introduction Tableau N°1 : Quelques micro-organismes potentiellement rencontrés dans le lait cru de bovins et sources de contamination (Avis de l’AFSCA-15-2011)……………………………………………….15 Section expérimentale Etude N°1 Tableau 1 : Antimicrobial residue screening results…………………………………………...………39 Etude N°2 Tableau 1: Milieux sélectifs pour l’isolement des bactéries…………………………………………...57 Tableau 2 : Illustration de la répartition des résultats …………………………………………………60 Tableau 3 : Résultats des enquêtes sur le mode de consommation……………………………………61 Etude N°3 Tableau 1 : Mean values of bacteria isolated and encountered from the sites…………………………80 Tableau 2: Contamination of raw milk observed in the literature……………………………………..85 Discussion Tableau 1: Niveaux de contamination du lait dans différents pays africains………………...………122 Abréviations Abréviations ADN : Acide Désoxyribonucléique ARN : Acide Ribonucléique ASR : Aérobie Sulfito reducteur FCFA : Francs de la communauté financière d’Afrique INS : Institut National de la Statistique LABOCEL : laboratoire central de l’élevage (Niamey, Niger) ME : Ministère de l’Elevage (Niger) MEIA : Ministère d’Elevage et des Industries Animales (Niger) MRA : Ministère des Ressources Animales (Niger) OMS : Organisation Mondiale de la Santé ONG : Organisation Non Gouvernementale PCR : Polymerase Chain Reaction PIB : Produit Intérieur Brut RGAC : Recensement Général de l’Agriculture et du Cheptel (Niger) SDR : Stratégie de Développement Rural TAC : Total Aerobic Count UBT : Unité Bétail Tropical UE : Union Européenne UEMOA : Union Economique et Monétaire Ouest Africain Table des matières Résumé – Abstract .................................................................................................................................2 Préambule général .................................................................................................................................6 Introduction ...........................................................................................................................................9 1. Titre section 1.1. Elements d’information générale sur le Niger ...............................................10 2. Titre section 1. 2. Production laitière au Niger .........................................................................11 3. Titre section 1. 3. Microbiote du lait ........................................................................................15 4. Titre section 1. 4. Méthode de recherche des microorganismes et dosage des ATBS .............22 Objectifs ...............................................................................................................................................27
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  • A Report of 28 Unrecorded Bacterial Species, Phylum Bacteroidetes, in Korea

    A Report of 28 Unrecorded Bacterial Species, Phylum Bacteroidetes, in Korea

    Journal104 of Species Research 7(2):104-113, 2018JOURNAL OF SPECIES RESEARCH Vol. 7, No. 2 A report of 28 unrecorded bacterial species, phylum Bacteroidetes, in Korea Soohyun Maeng1, Chaeyun Baek1, Jin-Woo Bae2, Chang-Jun Cha3, Kwang-Yeop Jahng4, Ki-seong Joh5, Wonyong Kim6, Chi Nam Seong7, Soon Dong Lee8, Jang-Cheon Cho9 and Hana Yi1,10,* 1Department of Public Health Sciences, Graduate School, Korea University, Seoul 02841, Republic of Korea 2Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea 3Department of Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea 4Department of Life Sciences, Chonbuk National University, Jeonju 54896, Republic of Korea 5Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Yongin 17035, Republic of Korea 6Department of Microbiology, Chung-Ang University College of Medicine, Seoul 06973, Republic of Korea 7Department of Biology, Sunchon National University, Suncheon 57922, Republic of Korea 8Faculty of Science Education, Jeju National University, Jeju 63243, Republic of Korea 9Department of Biological Sciences, Inha University, Incheon 22201, Republic of Korea 10School of Biosystem and Biomedical Science, Korea University, Seoul 02841, Republic of Korea *Correspondent: [email protected] In order to investigate indigenous prokaryotic species diversity in Korea, various environmental samples from diverse ecosystems were examined. Isolated bacterial strains were identified based on 16S rRNA gene sequences, and those exhibiting at least 98.7% sequence similarity with known bacterial species, but not reported in Korea, were selected as unrecorded species. 28 unrecorded bacterial species belonging to the phylum Bacteroidetes were discovered from various habitats including wastewater, freshwater, freshwater sediment, wet land, reclaimed land, plant root, bird feces, seawater, sea sand, tidal flat sediment, a scallop, marine algae, and seaweed.
  • C G M 2 0 1 8 [0 4 on D Er Z O E K S R a Pp O

    C G M 2 0 1 8 [0 4 on D Er Z O E K S R a Pp O

    Update of the bacterial the of bacterial Update intaxonomy the classification lists of COGEM CGM 2018 - 04 ONDERZOEKSRAPPORT report Update of the bacterial taxonomy in the classification lists of COGEM July 2018 COGEM Report CGM 2018-04 Patrick L.J. RÜDELSHEIM & Pascale VAN ROOIJ PERSEUS BVBA Ordering information COGEM report No CGM 2018-04 E-mail: [email protected] Phone: +31-30-274 2777 Postal address: Netherlands Commission on Genetic Modification (COGEM), P.O. Box 578, 3720 AN Bilthoven, The Netherlands Internet Download as pdf-file: http://www.cogem.net → publications → research reports When ordering this report (free of charge), please mention title and number. Advisory Committee The authors gratefully acknowledge the members of the Advisory Committee for the valuable discussions and patience. Chair: Prof. dr. J.P.M. van Putten (Chair of the Medical Veterinary subcommittee of COGEM, Utrecht University) Members: Prof. dr. J.E. Degener (Member of the Medical Veterinary subcommittee of COGEM, University Medical Centre Groningen) Prof. dr. ir. J.D. van Elsas (Member of the Agriculture subcommittee of COGEM, University of Groningen) Dr. Lisette van der Knaap (COGEM-secretariat) Astrid Schulting (COGEM-secretariat) Disclaimer This report was commissioned by COGEM. The contents of this publication are the sole responsibility of the authors and may in no way be taken to represent the views of COGEM. Dit rapport is samengesteld in opdracht van de COGEM. De meningen die in het rapport worden weergegeven, zijn die van de auteurs en weerspiegelen niet noodzakelijkerwijs de mening van de COGEM. 2 | 24 Foreword COGEM advises the Dutch government on classifications of bacteria, and publishes listings of pathogenic and non-pathogenic bacteria that are updated regularly.