title: Phylogenetic network analysis applied to pig gut microbiota identifies an ecosystem structure linked with growth traits.
abstract: The ecological interactions within the gut microbial communities are complex and far from being fully understood. Here we report the first study that aims at defining the interaction network of the gut microbiota in pigs and comparing it with the enterotype-like clustering analysis. Fecal microbiota of 518 healthy piglets was characterized by 16S ribosomal RNA gene sequencing. Two networks were constructed at the genus and operational taxonomic unit levels. Within-network interactions mirrored the human gut microbiota relationships, with a strong co-exclusion between Prevotella and Ruminococcus genera, and were consistent with the two enterotype-like clusters identified in the pig microbiota. Remarkably, the cluster classification of the individuals was significantly associated with the body weight at 60 days of age (P=0.005) and average daily gain (P=0.027). To the best of our knowledge, this is the first study to provide an integrated overview of the porcine gut microbiota that suggests a conservation of the ecological community interactions and functional architecture between humans and pig. Moreover, we show that the microbial ecosystems and porcine growth traits are linked, which allows us to foresee that the enterotype concept may have an important role in the animal production industry.
authors.affiliation: Génétique Animale et Biologie Intégrative, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.
authors.forename: Yuliaxis
authors.initials: Y
authors.lastname: Ramayo-Caldas
authors.affiliation: Génétique Animale et Biologie Intégrative, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.
authors.forename: Nuria
authors.initials: N
authors.lastname: Mach
authors.affiliation: Institut National de la Recherche Agronomique, UMR1319 Microbiologie de l'Alimentation au service de la Santé, Jouy-en-Josas, France.|AgroParisTech, UMR1319 Microbiologie de l'Alimentation au service de la Santé, Jouy-en-Josas, France.
authors.forename: Patricia
authors.initials: P
authors.lastname: Lepage
authors.affiliation: Institut National de la Recherche Agronomique, UMR1319 Microbiologie de l'Alimentation au service de la Santé, Jouy-en-Josas, France.|AgroParisTech, UMR1319 Microbiologie de l'Alimentation au service de la Santé, Jouy-en-Josas, France.
authors.forename: Florence
authors.initials: F
authors.lastname: Levenez
authors.affiliation: Génétique Animale et Biologie Intégrative, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.
authors.forename: Catherine
authors.initials: C
authors.lastname: Denis
authors.affiliation: Génétique Animale et Biologie Intégrative, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.
authors.forename: Gaetan
authors.initials: G
authors.lastname: Lemonnier
authors.affiliation: Génétique Animale et Biologie Intégrative, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.|Commissariat à l'énergie atomique et aux énergies alternatives, DSV-IRCM-LREG, Jouy-en-Josas, France.
authors.forename: Jean-Jacques
authors.initials: JJ
authors.lastname: Leplat
authors.affiliation: UE967 GEPA, Institut National de la Recherche Agronomique, Le Magneraud, France.
authors.forename: Yvon
authors.initials: Y
authors.lastname: Billon
authors.affiliation: UMR1282 ISP, Université de Tours, Tours, France.
authors.forename: Mustapha
authors.initials: M
authors.lastname: Berri
authors.affiliation: Institut National de la Recherche Agronomique, UMR1319 Microbiologie de l'Alimentation au service de la Santé, Jouy-en-Josas, France.|AgroParisTech, UMR1319 Microbiologie de l'Alimentation au service de la Santé, Jouy-en-Josas, France.
authors.forename: Jöel
authors.initials: J
authors.lastname: Doré
authors.affiliation: Génétique Animale et Biologie Intégrative, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.
authors.forename: Claire
authors.initials: C
authors.lastname: Rogel-Gaillard
authors.affiliation: Génétique Animale et Biologie Intégrative, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.
authors.forename: Jordi
authors.initials: J
authors.lastname: Estellé
mesh_terms: D000818:Animals; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism; D058448:Biota; D016000:Cluster Analysis; D005243:Feces / Q000382:microbiology; D000069196:Gastrointestinal Microbiome; D006801:Humans; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D013552:Swine / Q000254:growth & development* / Q000378:metabolism / Q000382:microbiology*
chemical_list: D012336:RNA, Ribosomal, 16S