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Article

Longitudinal Analysis of the Microbiota Composition and Enterotypes of Pigs from Post-Weaning to Finishing

1
UMR 1348 PEGASE, Agrocampus-Ouest, INRA, F-35590 Saint-Gilles, France
2
UMR 1388 GenPhySE, Université de Toulouse, INRA, INPT, ENVT, F-31320 Castanet Tolosan, France
*
Author to whom correspondence should be addressed.
Microorganisms 2019, 7(12), 622; https://doi.org/10.3390/microorganisms7120622
Received: 9 October 2019 / Revised: 6 November 2019 / Accepted: 22 November 2019 / Published: 28 November 2019
(This article belongs to the Section Gut Microbiota)
The present study aimed at investigating the evolution of pigs’ fecal microbiota composition from post-weaning to finishing in a longitudinal analysis. The experiment was conducted on 160 Pietrain × (Large White × Landrace) castrated male and female pigs in two replicates. Feces were collected at 52, 99, 119, 140, and 154 days of age for further 16S rRNA sequencing to analyze the microbiota composition. Pig microbiota evolved strongly from 52 to 99 days of age with an increased abundance of Streptococcaceae and a decreased abundance of Lactobacillaceae. During the finishing stage, microbiota kept evolving at a slower rate. To link the community structure to the performances, the fecal samples were clustered into enterotypes sharing a similar bacterial composition. At 52 days, two enterotypes dominated either by Lactobacillus or by PrevotellaSarcina were identified. They differed from the two enterotypes determined from 99 to 154 days which were dominated either by Lactobacillus or by TuricibacterClostridium sensu stricto. During this time period, 75% of the pigs switched enterotypes. The enterotypes were not related to differences in the overall growth or feeding performance. The enterotype definition was time-dependent and seemed to be related to the sex type at 99 days of age. View Full-Text
Keywords: longitudinal analysis; microbiota; finishing pig; enterotype longitudinal analysis; microbiota; finishing pig; enterotype
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    Doi: https://doi.org/10.15454/GCON7E
    Description: Supplementary Materials: The following are available online at www.mdpi.com/xxx/s1, Figure S1: Experimental design, Figure S2: Distribution of samples across sex, time points, replicates, and type of analysis, Figure S3: Non Metric Distance Scaling (NMDS) representation of the microbiota evolution across ages using Bray-Curtis distance in female pigs, Figure S4: Silhouette indexes, Calinski-Harabasz (CH) indexes and plots of the clusters of samples based on the genus relative abundance at 52, 99, 119, 140, and 154 days of age, Figure S5: Ratio of FE1 enterotypes at Day 154 in the CC, DC, CD and DD experimental groups corresponding to pigs fed with a control finisher diet, exposed to a DON-contaminated diet between 113 d and 119 d, between 134 d et 140 d, and both between 113 d and 119 d, and 134 d and 140 d of age, respectively, Figure S6: Significant MetaCyc pathway predicted by PICRUST, Table S1: Composition of experimental growing and finishing diets, Table S2: DON challenge effect on female pigs’ fecal microbiota diversity and phyla relative abundance, Table S3: P-values from Kruskal-Wallis tests for differences in genus relative abundance between the enterotypes at post-weaning (PWE1 vs PWE2) and at finishing (FE1 vs FE2), Table S4: Group file, Table S5: PICRUST prediction of Kegg orthologs, Table S6: PICRUST prediction of Metacyc pathway abundance, Table S7: Statistics on the predicted Metacyc abundance predicted by PICRUST.
MDPI and ACS Style

Le Sciellour, M.; Renaudeau, D.; Zemb, O. Longitudinal Analysis of the Microbiota Composition and Enterotypes of Pigs from Post-Weaning to Finishing. Microorganisms 2019, 7, 622. https://doi.org/10.3390/microorganisms7120622

AMA Style

Le Sciellour M, Renaudeau D, Zemb O. Longitudinal Analysis of the Microbiota Composition and Enterotypes of Pigs from Post-Weaning to Finishing. Microorganisms. 2019; 7(12):622. https://doi.org/10.3390/microorganisms7120622

Chicago/Turabian Style

Le Sciellour, Mathilde, David Renaudeau, and Olivier Zemb. 2019. "Longitudinal Analysis of the Microbiota Composition and Enterotypes of Pigs from Post-Weaning to Finishing" Microorganisms 7, no. 12: 622. https://doi.org/10.3390/microorganisms7120622

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