Additional file 1 of Agaricus subrufescens fermented rye affects the development of intestinal microbiota, local intestinal and innate immunity in suckling-to-nursery pigs
Creators: name: Wen, Caifang
name: Geervliet, Mirelle
name: de Vries, Hugo
name: Fabà, Lluís
name: den Hil, Petra J. Roubos-van
name: Skovgaard, Kerstin
name: Savelkoul, Huub F. J.
name: Schols, Henk A.
name: Wells, Jerry M.
name: Tijhaar, Edwin
name: Smidt, Hauke
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Physiology
subject: FOS: Biological sciences
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1: Table S1. Weaner and nursery diet. Table S2. Primers used for microfluidic qPCR. Fig. S1. The effect of ROM oral supplementation for pig on body weight in over time (A), average daily feed intake (B) and feed conversion ratio (C) in nursery phase. Control (Ctrl) and treatment (ROM) groups are represented by colour blue and yellow, respectively. Data is shown as the means ± the standard error of the mean (SEM). No significant differences on either body weight, average daily feed intake or feed conversion ratio were observed between both groups. Fig. S2. Comparison of faecal microbial alpha diversity between ROM and Ctrl groups over time, with metrics of observed richness (A), phylogenetic diversity (B), Shannon diversity (C) and inverse Simpson (InvSimpson) (D). Data was separated according to weaning for Linear Mixed-Effects Model analysis and no statistically significant differences were observed between the two treatment groups either during pre- or post-weaning phase, with any index of alpha diversity. Treatment (ROM) and control (Ctrl) groups are represented by colour yellow and blue, respectively. The vertical line indicates weaning on day 28. Fig. S3. Principal coordinate analysis (PCoA) of faecal microbial composition over time, based on unweighted UniFrac (A) and weighted UniFrac (B) distance metrics. Data was separated according to weaning on day 28 to assess the effect of time and treatment on microbial variation using PERMANOVA. Colours represent different time points, and shapes represent different treatment groups (circles, ROM; triangles, Ctrl). The percentages at the axes indicate the variation explained. Fig. S4. Genera showing tendencies to be differential abundant between ROM and Ctrl pigs during pre-or post weaning. Genera were identified through GAMLSS-BEZI model with random effect. The p value was corrected by FDR for multiple testing. The yellow and blue colours represent treated (ROM) and control (Ctrl) groups, respectively. Fig. S5. Comparisons of gut luminal microbial alpha diversity between ROM) and Ctrl groups over time. The jejunal, ileal and caecal luminal microbial alpha diversity are shown in (A–D), (E–H) and (I–L), respectively, with metrics of observed richness, phylogenetic diversity, Shannon diversity and inverse Simpson (InvSimpson), from left to right. Differences were assessed with a Linear Mixed-Effects Model for jejunal, ileal and caecal luminal microbial alpha diversity for all time points, respectively. Treatment (ROM) and control (Ctrl) groups are represented by colour yellow and blue, respectively. Fig. S6. Principal coordinate analysis (PCoA) plots for the overall microbial composition of intestinal luminal digesta at different locations, based on unweighted- and weighted UniFrac metrics. Significance of the effect of time and treatment on jejunal- (A, B), ileal- (C, D) and caecal (E, F) luminal microbiota at ASV level was assessed by PERMANOVA. Colours represent different time points, and shapes represent different treatment groups (circles, ROM; triangles, Ctrl). The percentages at the axes indicate the variation explained. Fig. S7. Bar plots representing relative abundance in individual pig jejunal (A–C) and caecal (D–F) luminal contents of specific taxa identified as differential features by LEfSe for pigs between control (class: Ctrl) and treatment (class: ROM) on day 70. The solid black horizontal line indicates the mean relative abundance within each class. Fig. S8. Redundancy analysis (RDA) tri-plots for the association between the variation of gene expression and environmental variables of time, treatment, pH and BW. A and B illustrates the association between ileal and caecal mucosa expressed genes with environmental variables of time, treatment, pH value and body weight (BW), respectively. C shows the association between the caecal mucosal gene expression and treatment, pH values and BW. Blue and yellow colours represent control (Ctrl) and treated (ROM) groups and shapes show the different time points. Dark grey arrows indicate environmental variables and light grey arrows show best fitting genes in the model. The percentages at the axes indicate the variation explained by the first two canonical axes. Fig. S9. Correlation analysis between the relative abundance of predominant ileal luminal genera and mucosal gene expression on day 27. The orange and blue coloured circles correspond to a positive and negative statistical correlation with an adjusted p value &lt; 0.05, respectively. Insignificant correlations were shown as blank. Fig. S10. Correlation analysis between the relative abundance of predominant ileal luminal genera and mucosal gene expression on day 44. The orange and blue coloured circles correspond to a positive and negative statistical correlation with an adjusted p value &lt; 0.05, respectively. Fig. S11. Correlation analysis between the relative abundance of predominant caecal luminal genera and mucosal gene expression on day 27. The orange and blue coloured circles correspond to a positive and negative statistical correlation with an adjusted p value &lt; 0.05, respectively. Insignificant correlations were shown as blank. Fig. S12. Correlation analysis between the relative abundance of predominant caecal luminal genera and mucosal gene expressions on day 44. The orange and blue coloured circles correspond to a positive and negative statistical correlation with an adjusted p value &lt; 0.05, respectively. Insignificant correlations were shown as blank.