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2. High Throughput Sequencing and Network Analysis Disentangle the Microbial Communities of Ticks and Hosts Within and Between Ecosystems

Author

Estrada-Peña, A., Cabezas-Cruz, A., Pollet, T., Vayssier-Taussat, M., Cosson, J.F., Faculty of Veterinary Medicine, The University of Sydney, Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Meta-program Meta-omics des Ecosystems Microbiens (MEM) of the French National Institut for Agricultural Research (INRA). COST Action TD1303 (EurNegVec)., Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, and Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de la Recherche Agronomique (INRA)-École nationale vétérinaire d'Alfort (ENVA)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)

Subjects
DNA, Bacterial, [SDV]Life Sciences [q-bio], Ixodes ricinus, lcsh:QR1-502, microbiome, next generation sequencing (NGS), DNA, Ribosomal, lcsh:Microbiology, ticks, Cellular and Infection Microbiology, RNA, Ribosomal, 16S, Animals, Cluster Analysis, network analysis, Ecosystem, Phylogeny, Original Research, Bacteria, Ixodes, Arvicolinae, Microbiota, Computational Biology, High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA, voles, Metagenomics, Spleen
Abstract

International audience; We aimed to develop a framework, based on graph theory, to capture the ecological meaning behind pure pair comparisons of microbiome-derived data. As a proof of concept, we applied the framework to analyze the co-occurrence of bacteria in either Ixodes ricinus ticks or the spleen of one of their main hosts, the vole Myodes glareolus. As a secondary lymphoid organ, the spleen acts as a filter of blood and represents well the exposure to microorganisms circulating in the blood; including those acquired and transmitted by ticks during feeding. The microbiome of 301 and 269 individual tick and vole samples, respectively, were analyzed using next generation sequencing (NGS) of 16S rRNA. To assess the effect of habitat on ecological communities of bacteria associated to ticks and voles, two different biotopes were included in the study, forest, and ecotone. An innovative approach of NGS data analysis combining network analysis and phylogenies of co-occuring of bacteria was used to study associations between bacteria in individual samples. Of the 126 bacterial genera found in ticks and voles, 62% were shared by both species. Communities of co-occurring bacteria were always more phylogenetically diverse in ticks than in voles. Interestingly, ~80% of bacterial phylogenetic diversity was found in ~20% of ticks. This pattern was not observed in vole-associated bacteria. Results revealed that the microbiome of I. ricinus is only slightly related to that of M. glareolus and that the biotope plays the most important role in shaping the bacterial communities of either ticks or voles. The analysis of the phylogenetic signal of the network indexes across the 16S rRNA-derived tree of bacteria suggests that the microbiome of both ticks and voles has high phylogenetic diversity and that closest bacterial genera do not co-occur. This study shows that network analysis is a promising tool to unravel complex microbial communities associated to arthropod vectors and vertebrate hosts.

Published
2018

3. 16S rRNA amplicon sequencing forepidemiological surveys of bacteria in wildlife

Author

Galan, M., Razzauti, M., Bard, E., Bernard, M., Brouat, Carine, Charbonnel, N., Dehne-Garcia, A., Loiseau, A., Tamisier, L., Vayssier-Taussat, M., Vignes, H., and Cosson, J.F.

Abstract

The human impact on natural habitats is increasing the complexity of human-wildlife interactions and leading to the emergence of infectious diseases worldwide. Highly successful synanthropic wildlife species, such as rodents, will undoubtedly play an increasingly important role in transmitting zoonotic diseases. We investigated the potential for recent developments in 16S rRNA amplicon sequencing to facilitate the multiplexing of the large numbers of samples needed to improve our understanding of the risk of zoonotic disease transmission posed by urban rodents in West Africa. In addition to listing pathogenic bacteria in wild populations, as in other high-throughput sequencing (HTS) studies, our approach can estimate essential parameters for studies of zoonotic risk, such as prevalence and patterns of coinfection within individual hosts. However, the estimation of these parameters requires cleaning of the raw data to mitigate the biases generated by HTS methods. We present here an extensive review of these biases and of their consequences, and we propose a comprehensive trimming strategy for managing these biases. We demonstrated the application of this strategy using 711 commensal rodents, including 208 Mus musculus domesticus, 189 Rattus rattus, 93 Mastomys natalensis, and 221 Mastomys erythroleucus, collected from 24 villages in Senegal. Seven major genera of pathogenic bacteria were detected in their spleens: Borrelia, Bartonella, Mycoplasma, Ehrlichia, Rickettsia, Streptobacillus, and Orientia. Mycoplasma, Ehrlichia, Rickettsia, Streptobacillus, and Orientia have never before been detected in West African rodents. Bacterial prevalence ranged from 0% to 90% of individuals per site, depending on the bacterial taxon, rodent species, and site considered, and 26% of rodents displayed coinfection. The 16S rRNA amplicon sequencing strategy presented here has the advantage over other molecular surveillance tools of dealing with a large spectrum of bacterial pathogens without requiring assumptions about their presence in the samples. This approach is therefore particularly suitable to continuous pathogen surveillance in the context of disease-monitoring programs.

Published
2016

4. Pathobiome diversity and co-infection patterns in a community of rodents

Author

Abbate, Jessica, Galan, Maxime, Chaval, Yannick, Gotteland, Cécile, Gilot-Fromont, Emmanuelle, Poulle, Marie-Lazarine, Sironen, Tarja, Voutilainen, Lina, Henttonen, Heikki, Gasqui, Patrick, Cosson, J.F., Charbonnel, A., ProdInra, Migration, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Unité de recherche Comportement et Ecologie de la Faune Sauvage (CEFS), Institut National de la Recherche Agronomique (INRA), Université de Lyon (COMUE), Université de Reims Champagne-Ardenne (URCA), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, UPE, European Union Reference Laboratory for equine diseases (EURL), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Finnish Forest Research Institute, Unité de Recherche d'Épidémiologie Animale (UR EpiA), 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), Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de la Recherche Agronomique (INRA)-École nationale vétérinaire d'Alfort (ENVA)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), University of Helsinki, and École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie

Subjects
[SDV] Life Sciences [q-bio], [SDE] Environmental Sciences, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2015

5. Protocols for field and laboratory rodent studies

Author

Herbreteau, Vincent, Chaval, Y., Cosson, J.F., Morand, S., Herbreteau, Vincent (ed.), Jittapalapong, S. (ed.), Rerkamnuaychoke, W. (ed.), Chaval, Y. (ed.), Cosson, J.F. (ed.), and Morand, S. (ed.)

Subjects
SEXE, ESPECE, IDENTIFICATION, ANALYSE DE LABORATOIRE, RAT, CARACTERE MORPHOLOGIQUE, MESURE, ANIMAL, ADULTE, JUVENILE, METHODOLOGIE, RONGEUR
Published
2011

6. Protocols for field and laboratory rodent studies

Author

Auffray, J.C., Blasdell, K., Bordes, F., Chabé, M., Chaisiri, K., Charbonnel, N., Chaval, Y., Claude, J., Cosson, J.F., Dei-Cas, E., Desquesnes, M., Dobigny, Gauthier, Douangboupha, B., Galan, M., Haukisalmi, V., Henttonen, H., Herbreteau, Vincent, Hugot, J.P., Jiyipong, T., Latinne, A., Michaux, J., Milocco, C., Morand, S., Pagès, M., Phoophitpong, D., Pumhom, P., Ribas Salvador, A., Soonchan, S., Suputtamongkol, Y., Waengsothorn, S., Waywa, D., Xuéreb, A., Herbreteau, Vincent (ed.), Jittapalapong, S. (ed.), Rerkamnuaychoke, W. (ed.), Chaval, Y. (ed.), Cosson, J.F. (ed.), and Morand, S. (ed.)

Subjects
ANALYSE DE LABORATOIRE, LABORATOIRE, RAT, ANIMAL, HYGIENE, METHODOLOGIE, RONGEUR
Published
2011

8. Forêts de failles et forêts galeries au sud du Mali : deux voies pour la pérennité des refuges guinéens en zone soudanienne

Author

Birnbaum, P., Granjon, Laurent, Blanc, P., Chevallier, M.H., Cosson, J.F., Duplantier, Jean-Marc, Duvall, C., Fahr, J., Florence, J., Forget, P.M., Gautier, D., Gazull, L., Trébuchon, J.F., Lecompte, E., Niagaté, B., Nivet, C. (ed.), McKey, D. (ed.), and Legris, C. (ed.)

Subjects
CONSERVATION DE LA NATURE, FORET, STRUCTURE DU PEUPLEMENT, BIODIVERSITE, SAVANE FORET GALERIE, MOSAIQUE FORET SAVANE, INVENTAIRE FAUNISTIQUE, DIVERSITE SPECIFIQUE, EXPLOITATION DES RESSOURCES NATURELLES, RONGEUR, STRUCTURE GENETIQUE, INVENTAIRE DE VEGETATION, ANTHROPISATION, ARBRE, PHYLOGENIE, TELEDETECTION, CHAUVE SOURIS, ZONE REFUGE
Published
2010

9. Introduction à l'épidémiologie intégrative des maladies infectieuses et parasitaires

Author

Brouat, Carine, Duplantier, Jean-Marc, Charbonnel, N., Cosson, J.F., Guégan, Jean-François (ed.), and Choisy, Marc (ed.)

Subjects
SELECTION, EPIDEMIOLOGIE, PROGRAMME DE RECHERCHE, ENVIRONNEMENT, BORRELIOSE, RONGEUR, BRUCELLOSE, RELATION HOTE PARASITE, GENETIQUE DE POPULATION, COMMUNAUTE, PARASITISME, LEISHMANIOSE, PHYLOGENIE, PARASITE, LEPTOSPIROSE, MALADIE EMERGENTE, NEMATODE, ZOONOSE, PESTE, MARQUEUR MICROSATELLITE, TUBERCULOSE, RICKETTSIOSE, PATHOLOGIE ANIMALE, FACTEUR BIOTIQUE, SENSIBILITE RESISTANCE, DYNAMIQUE DE POPULATION, RESERVOIR
Published
2009

10. Multiple paternity occurs with low frequency in the territorial roe deer, Capreolus capreolus

Author

Vanpé, Cécile, Kjellander, P., Gaillard, Jean-Michel, Cosson, J.F., Galan, M., Hewison, A.J.M., Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Biodémographie évolutive, Département écologie évolutive [LBBE], Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Unité de recherche Comportement et Ecologie de la Faune Sauvage (CEFS), Institut National de la Recherche Agronomique (INRA), Swedish University of Agricultural Sciences (SLU), Université de Lyon, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and 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)

Subjects
FERTILIZATION INSURANCE, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], INDIVIDUAL HETEROZYGOSITY, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV]Life Sciences [q-bio], MICROSATELLITES, INBREEDING AVOIDANCE, OFFSPRING SURVIVAL, FEMALE MULTIPLE MATING, PATERNITY ANALYSES, RELATEDNESS, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, reproductive and urinary physiology
Abstract

International audience; An explanation for female multiple mating when males offer no material benefits but sperm remains elusive, largely because of a lack of empirical support for the genetic benefits hypothesis. We used 21 microsatellite markers to test for multiple paternities among 88 litters of roe deer, Capreolus capreolus, and to investigate the inbreeding avoidance hypothesis as a potential mechanism for the evolution of female multiple mating. From paternity analyses, we found that 13.5% of polytocous litters were sired by more than one male. We also found that a half-sib relationship was more likely than a full-sib relationship for 20.5% of all litters. This is the first report of multiple paternities in a territorial ungulate species. In support of the inbreeding avoidance hypothesis, we found that parents who were strongly related produced offspring with lower individual heterozygosity that survived less well during their first summer than fawns with unrelated parents. In addition, fawns from multiple paternity litters survived their first summer better than fawns from single paternity litters. However, it remains unclear whether all female multiple paternity events in this species are provoked by an initial consanguineous mating.

Published
2009

11. Molecular evidence of Pleistocene bidirectional faunal exchange between Europe and the Near East: the case of the bicolored shrew (Crocidura leucodon, Soricidae)

Author

Dubey, S., Cosson, J.F., Vohralík, V., Krystufek, B., Diker, E., Vogel, P., Department of Ecology and Evolution, Université de Lausanne (UNIL), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Department of zoology, Charles University [Prague] (CU), University of Primorska, and Trakya University

Subjects
Base Sequence, Geography, Shrews, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Molecular Sequence Data, Population Dynamics, Sequence Analysis, DNA, Cytochromes b, APOLIPOPROTEIN B GENE, Biological Evolution, DNA, Mitochondrial, PHYLOGEOGRAPHY, Europe, Middle East, Social Isolation, CYTOCHROME B GENE, Animals, Animal Migration, CROCIDURA LEUCODON, Apolipoproteins B/chemistry, Apolipoproteins B/genetics, Cytochromes b/chemistry, Cytochromes b/genetics, DNA, Mitochondrial/chemistry, Phylogeny, Shrews/anatomy & histology, Shrews/classification, Apolipoproteins B
Abstract

Correspondance: sylvain.dubey@unil.ch; International audience; We sequenced 1077 bp of the mitochondrial cytochrome b gene and 511 bp of the nuclear Apolipoprotein B gene in bicoloured shrew (Crocidura leucodon, Soricidae) populations ranging from France to Georgia. The aims of the study were to identify the main genetic clades within this species and the influence of Pleistocene climatic variations on the respective clades. The mitochondrial analyses revealed a European clade distributed from France eastwards to north-western Turkey and a Near East clade distributed from Georgia to Romania; the two clades separated during the Middle Pleistocene. We clearly identified a population expansion after a bottleneck for the European clade based on mitochondrial and nuclear sequencing data; this expansion was not observed for the eastern clade. We hypothesize that the western population was confined to a small Italo-Balkanic refugium, whereas the eastern population subsisted in several refugia along the southern coast of the Black Sea

Published
2007

12. Dispersal in Mastomys natalensis mice: use of fine-scale genetic analyses for pest management

Author

van Hooft, W.F., Cosson, J.F., Vibe-Petersen, S., Leirs, H., van Hooft, W.F., Cosson, J.F., Vibe-Petersen, S., and Leirs, H.

Abstract

Mastomys natalensis is the major pest rodent in sub-Saharan Africa. In this study, population genetic techniques were used to gain new insights into its dispersal behaviour, a critical parameter in pest management. Using 11 microsatellites, 272 individuals from a 300 ha area in Tanzania were genotyped. Genetic diversity was high, with no isolation by distance and little differentiation between field plots far apart, indicating a large effective population size and high dispersal rates in agreement with ecological observations. On the other hand, genetic differentiation between nearby field plots, isolation by distance within a single field plot and kin clustering were also observed. This apparent contradiction may be explained by yearly founder effects of a small number of breeding individuals per square area, which is consistent with the presence of linkage disequilibrium. An alternative, not mutually exclusive explanation is that there are both dispersing and sedentary animals in the population. The low-density field plots were characterized by low relatedness and small genetic distances to other field plots, indicating a high turnover rate and negative density-dependent dispersal. In one field plot female-biased dispersal was observed, which may be related to inbreeding avoidance or female competition for resources. Most juveniles appeared to be local recruits, but they did not seem to stay in their native area for more than two months. Finally, possible implications for pest management are discussed

Published
2008

16. Protocols for field and laboratory rodent studies

Author

Chaval, Y., Waengsothorn, S., Claude, J., Soonchan, S., Herbreteau, Vincent, Herbreteau, Vincent (ed.), Jittapalapong, S. (ed.), Rerkamnuaychoke, W. (ed.), Chaval, Y. (ed.), Cosson, J.F. (ed.), and Morand, S. (ed.)

Subjects
STOCKAGE, SPECIMEN TYPE, COLLECTION ZOOLOGIQUE, RAT, ANIMAL, BASE DE DONNEES, METHODOLOGIE, RONGEUR
Published
2011

17. Protocols for field and laboratory rodent studies

Author

Dobigny, Gauthier, Xuéreb, A., Herbreteau, Vincent (ed.), Jittapalapong, S. (ed.), Rerkamnuaychoke, W. (ed.), Chaval, Y. (ed.), Cosson, J.F. (ed.), and Morand, S. (ed.)

Subjects
ANALYSE DE LABORATOIRE, RAT, CULTURE DE TISSUS, ANIMAL, CARYOTYPE, PRELEVEMENT, METHODOLOGIE, CYTOGENETIQUE, RONGEUR
Published
2011

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