Additional file 1 of Weaning-associated feed deprivation stress causes microbiota disruptions in a novel mucin-containing in vitro model of the piglet colon (MPigut-IVM)
Creators: name: Gresse, Raphaële
name: Chaucheyras-Durand, Frédérique
name: Denis, Sylvain
name: Beaumont, Martin
name: Van de Wiele, Tom
name: Forano, Evelyne
name: Blanquet-Diot, Stéphanie
Publisher: name: figshare
Year: 2021
Subjects: subject: Microbiology
subject: FOS: Biological sciences

description: Additional file 1: Supplementary Table 1. Composition of the nutritive medium simulating the ileal chyme of 28 d old piglets. Supplementary Table 2. Primers and probes used for quantitative experiments on the MPigut-IVM in vitro gut microbiota. Supplementary Table 3. Number of sequences generated by the Illumina MiSeq run. Supplementary Table 4. Statistical analysis of the principal phyla and families detected by Illumina sequencing in the bioreactor (A) and on the mucin beads (B) during the fermentation #6, 7, 8 and 9 which were subjected to a feed deprivation stress of 48 h (n = 4 for each time point).. Means associated with a different letter are significantly different. P adj: adjusted P-values (FDR method). Supplementary Table 5. Identification of metabolites in NMR spectra. The numbers are reported in representative spectra in supplemental figure 1. s: singulet. d: doublet. t: triplet. q: quintuplet; m: multiplet. *: indicate the peak used for quantification. Supplementary Table 6. Statistical analysis of metabolites detected by NMR metabolomics in the bioreactor and bead medium. Means associated with a different letter are significantly different. P adj: adjusted P-values (FDR method). Supplementary Figure 1. Identification of metabolites in a representative NMR spectrum. Peaks are identified with a number corresponding to the metabolites described in supplementary Table 5. The inset shows the aromatic region (vertically expanded). Supplementary Figure 2. Composition and metabolic activity of the microbiota from the fecal inoculi in all fermentation runs: relative abundance of SCFA measured by gas chromatography (A), quantification of bacterial groups using QPCR (n = 6) (B) and relative abundance of the principal bacterial phyla (C), bacterial families (D), archaeal families (E) and alpha diversity based on Shannon index and the number of observed OTUs (F) measured by 16S Illumina sequencing. “F” = “Fermentation”. Supplementary Figure 3. In vitro microbiota composition inside the bioreactor medium (A) and on the mucin beads (B) of the MPigut-IVM during control assays (fermentations #1, 2 and 3), as measured by QPCR. Supplementary Figure 4. Relative abundance of the main bacterial phyla in the bioreactor medium (A) and on the mucin beads (B) of the MPigut-IVM during control assays (fermentations #1, 2 and 3), as measured by 16S Illumina sequencing. Supplementary Figure 5. Mean relative abundance of the archaeal families in the bioreactor medium (A) and on the mucin beads (B) of the MPigut-IVM during control assays (fermentations #1, 2 and 3), as measured by 16S Illumina sequencing. Supplementary Figure 6. Percentages of variation calculated to estimate the best day for the end of the stabilisation phase using the relative abundances of gas, SCFA and the top 10 families of the MPigut-IVM. Supplementary Figure 7. Principal component analysis (PCoA) plot with Bray-Curtis dissimilarity on the bacterial communities between in vivo samples from liminal and mucosal proximal colon and in vitro fermentation samples from the bioreactor medium and the mucin beads at day 7 corresponding to the end of stabilization phase. Supplementary Figure 8. In vitro microbiota composition in the bioreactor medium (a, b and c) and on the mucin beads (d, e and f) of the MPigut-IVM during the simulation of 12 h (a and d), 24 h (b and e) et 48 h (c and f) food deprivation stresses, as measured by QPCR (n = 1 for each time point). Supplementary Figure 9. Relative abundance of the main bacteria phyla in the bioreactor medium (A) and on the mucin beads (B) in the MPigut-IVM during the fermentations #6, 7, 8 and 9 which were subjected to a food deprivation stress of 48 h. Supplementary Figure 10. Relative abundance of the main bacteria phyla (A) and families (B) in the bead medium of the MPigut-IVM during the fermentations #6, 7, 8 and 9 which were subjected to a food deprivation stress of 48 h. Supplementary Figure 11. Alpha diversity measures on bacterial OTUs in the bioreactor medium (A) and on the mucin beads (B) of the MPigut-IVM during the fermentations #6, 7, 8 and 9 which were subjected to a food deprivation stress of 48 h (n = 4). Supplementary Figure 12. Evolution of the redox potential inside the MPigut-IVM during the fermentations #6, 7, 8 and 9 which were subjected to a 48 h food deprivation stress. Supplementary Figure 13. Effect of a food deprivation stress of 48 h on the gas composition inside the MPigut-IVM. This figure displays mean relative abundance values of gases and their error bars collected during the fermentations #6, 7, 8 and 9 (n = 4 for each time point).