Early-life establishment of the swine gut microbiome and impact on host phenotypes.
Early bacterial colonization and succession within the gastrointestinal tract has been suggested to be crucial in the establishment of specific microbiota composition and the shaping of host phenotype. Here, the composition and dynamics of faecal microbiomes were studied for 31 healthy piglets across five age strata (days 14, 36, 48, 60 and 70 after birth) together with their mothers. Faecal microbiome composition was assessed by 16S rRNA gene 454-pyrosequencing. Bacteroidetes and Firmicutes were the predominant phyla present at each age. For all piglets, luminal secretory IgA concentration was measured at day 70, and body weight was recorded until day 70. The microbiota of suckling piglets was mainly represented by Bacteroides, Oscillibacter, Escherichia/Shigella, Lactobacillus and unclassified Ruminococcaceae genera. This pattern contrasted with that of Acetivibrio, Dialister, Oribacterium, Succinivibrio and Prevotella genera, which appeared increased after weaning. Lactobacillus fermentum might be vertically transferred via breast milk or faeces. The microbiota composition coevolved with their hosts towards two different clusters after weaning, primarily distinguished by unclassified Ruminococcaceae and Prevotella abundances. Prevotella was positively correlated with luminal secretory IgA concentrations, and body weight. Our study opens up new possibilities for health and feed efficiency manipulation via genetic selection and nutrition in the agricultural domain.
INRA, UMR1319 MICALIS, Jouy-en-Josas, France.|AgroParisTech, UMR1319 MICALIS, Jouy-en-Josas, France.|INRA, UMR 1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France.|AgroParisTech, UMR 1313 Génétique Animale et Biologie Intégrative, France.
Núria
N
Mach
UMR1282 ISP, INRA, Nouzilly, France.|UMR1282 ISP, Université de Tours, Tours, France.
Mustapha
M
Berri
INRA, UMR 1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France.|AgroParisTech, UMR 1313 Génétique Animale et Biologie Intégrative, France.
Jordi
J
Estellé
INRA, UMR1319 MICALIS, Jouy-en-Josas, France.|AgroParisTech, UMR1319 MICALIS, Jouy-en-Josas, France.
Florence
F
Levenez
INRA, UMR 1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France.|AgroParisTech, UMR 1313 Génétique Animale et Biologie Intégrative, France.
Gaëtan
G
Lemonnier
INRA, UMR 1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France.|AgroParisTech, UMR 1313 Génétique Animale et Biologie Intégrative, France.
Catherine
C
Denis
INRA, UMR 1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France.|AgroParisTech, UMR 1313 Génétique Animale et Biologie Intégrative, France.|CEA, DSV-IRCM-LREG, Jouy-en-Josas, France.
Jean-Jacques
JJ
Leplat
UMR1282 ISP, INRA, Nouzilly, France.|UMR1282 ISP, Université de Tours, Tours, France.
Claire
C
Chevaleyre
UE967 GEPA, INRA, Le Magneraud, France.
Yvon
Y
Billon
INRA, UMR1319 MICALIS, Jouy-en-Josas, France.|AgroParisTech, UMR1319 MICALIS, Jouy-en-Josas, France.
Joël
J
Doré
INRA, UMR 1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France.|AgroParisTech, UMR 1313 Génétique Animale et Biologie Intégrative, France.
Claire
C
Rogel-Gaillard
INRA, UMR1319 MICALIS, Jouy-en-Josas, France.|AgroParisTech, UMR1319 MICALIS, Jouy-en-Josas, France.
Patricia
P
Lepage
D000375:Aging; D000818:Animals; D001419:Bacteria / Q000145:classification* / Q000235:genetics*; D001835:Body Weight; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D000069196:Gastrointestinal Microbiome; D041981:Gastrointestinal Tract / Q000382:microbiology* / Q000502:physiology; D007071:Immunoglobulin A, Secretory / Q000032:analysis; D007413:Intestinal Mucosa / Q000276:immunology; D008969:Molecular Sequence Data; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D013552:Swine
D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D007071:Immunoglobulin A, Secretory; D012336:RNA, Ribosomal, 16S