title: Shifting the paradigm from pathogens to pathobiome: new concepts in the light of meta-omics.
abstract: The concept of pathogenesis has evolved considerably over recent years, and the scenario "a microbe + virulence factors = disease" is probably far from reality in a number of cases. Actual pathogens have extremely broad biological diversity and are found in all major groups of microorganisms (viruses, bacteria, fungi, protozoa…). Their pathogenicity results from strong and often highly specific interactions they have with either their microbial environment, hosts and/or arthropod vectors. In this review, we explore the contribution of metagenomic approaches toward understanding pathogens within the context of microbial communities. With this broader view, we discussed the concept of "pathobiome" and the research questions that this raises.
authors.affiliation: INRA, UMR BIPAR (Enva/Anses) USC INRA Maisons-Alfort, France.
authors.forename: Muriel
authors.initials: M
authors.lastname: Vayssier-Taussat
authors.affiliation: CIRAD, UMR CMAEE Petit-Bourg, Guadeloupe, France ; INRA, UMR 1309 CMAEE Montpellier, France ; INRA, Université de Toulouse, INP, ENVT, UMR 1225, IHAP Toulouse, France.
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Albina
authors.affiliation: INRA, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro) Montferrier-sur-Lez, France.
authors.forename: Christine
authors.initials: C
authors.lastname: Citti
authors.affiliation: INRA, Institut de Recherche en Horticulture et Semences, UMR 1345 Angers, France.
authors.forename: Jean-Franҫois
authors.initials: JF
authors.lastname: Cosson
authors.affiliation: INRA, UMR 1290, BIOGER-CPP, INRA AgroParis Tech Thiverval-Grignon, France.
authors.forename: Marie-Agnès
authors.initials: MA
authors.lastname: Jacques
authors.affiliation: INRA, UMR 1253 STLO Rennes, France.
authors.forename: Marc-Henri
authors.initials: MH
authors.lastname: Lebrun
authors.affiliation: Agrocampus Ouest, UMR 1253 STLO Rennes, France ; INRA, UMR 1333 DGIMI Montpellier, France.
authors.forename: Yves
authors.initials: Y
authors.lastname: Le Loir
authors.affiliation: INRA, UMR 1319, Micalis Jouy-en-Josas, France.
authors.forename: Mylène
authors.initials: M
authors.lastname: Ogliastro
authors.affiliation: CIRAD/UMR BGPI TA A54/K Montpellier Cedex 5, France.
authors.forename: Marie-Agnès
authors.initials: MA
authors.lastname: Petit
authors.affiliation: UMR 1332 Biologie du Fruit et Pathologie, INRA Villenave d'Ornon Cedex, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Roumagnac
authors.affiliation: UMR 1332 Biologie du Fruit et Pathologie, Université de Bordeaux Villenave d'Ornon Cedex, France.
authors.forename: Thierry
authors.initials: T
authors.lastname: Candresse
mesh_terms: D000818:Animals; D054884:Host-Pathogen Interactions; D006801:Humans; D064307:Microbiota; D037521:Virulence Factors / Q000378:metabolism*
chemical_list: D037521:Virulence Factors
keywords: interactions; microbial ecosystem; next generation sequencing