Additional file 5 of Development of a rational framework for the therapeutic efficacy of fecal microbiota transplantation for calf diarrhea treatment
Creators: name: Islam, Jahidul
name: Tanimizu, Masae
name: Shimizu, Yu
name: Goto, Yoshiaki
name: Ohtani, Natsuki
name: Sugiyama, Kentaro
name: Tatezaki, Eriko
name: Sato, Masumi
name: Makino, Eiji
name: Shimada, Toru
name: Ueda, Chise
name: Matsuo, Ayumi
name: Suyama, Yoshihisa
name: Sakai, Yoshifumi
name: Furukawa, Mutsumi
name: Usami, Katsuki
name: Yoneyama, Hiroshi
name: Aso, Hisashi
name: Tanaka, Hidekazu
name: Nochi, Tomonori
Publisher: name: figshare
Year: 2022
Subjects: subject: Space Science
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Science Policy

description: Additional file 4: Fig. S1. Overview of farm specific cow and disease condition. The effect of FMT on enteritis and weak calf syndrome disease prevention in successful and unsuccessful treatments. (A) Farm specific cows’ number. (B) Success rate evaluated by presence and absence of enteritis and weak calf syndrome before and after FMT for recipient (n = 14) in successful treatments and recipient (n = 6) in unsuccessful treatments. ‘+, presence; ‘-, absence. Fig. S2. Clinical parameter. Clinical efficacy of FMT on successful and unsuccessful treatments based on day-0 (before FMT) and day-7 (after FMT). Data are expressed as mean±SD, shown for R-0-success (n = 14), R-0-failure (n = 6), R-7-success (n = 14), and R-7-failure (n = 4). γ-GT, Gamma-Glutamyl Transferase; MCV, mean corpuscular volume; MCH, mean corpuscular hemoglobin; MCHC, mean corpuscular hemoglobin concentration. *P &lt;0.05 (Student’s t-test). Fig. S3. Microbial composition based on phylum level. Relative abundances are shown as mean ± SEM for donor (n = 13), recipient 0 (n = 13), recipient 1 (n = 13), and recipient 7 (n = 13) in successful treatments, and donor (n = 4), recipient 0 (n = 4), recipient 1 (n = 4), and for recipient 7 (n = 4) in unsuccessful treatments. P-values (*P &lt;0.05, **P &lt;0.01) indicate statistical significance either successful or unsuccessful treatments by one-way ANOVA followed by tukey multiple comparison test. P-values (††P &lt;0.01, †P &lt;0.05) indicate statistical significance by Student’s t-test. Fig. S4. Microbial composition based on family level. Relative abundances are shown as mean ± SEM for donor (n = 13), recipient 0 (n = 13), recipient 1 (n = 13), and recipient 7 (n = 13) in successful treatments, and donor (n = 4), recipient 0 (n = 4), recipient 1 (n = 4), and for recipient 7 (n = 4) in unsuccessful treatments. P-value (*P &lt;0.05) indicates statistical significance either successful or unsuccessful treatments by one-way ANOVA followed by tukey multiple comparison test. P-values (†††P &lt;0.001, ††P &lt;0.01, †P &lt;0.05) indicate statistical significance by Student’s t-test. Fig. S5. Microbial composition based on genus level. Relative abundances are shown as mean ± SEM for donor (n = 13), recipient 0 (n = 13), recipient 1 (n = 13), and recipient 7 (n = 13) in successful treatments, and donor (n = 4), recipient 0 (n = 4), recipient 1 (n = 4), and for recipient 7 (n = 4) in unsuccessful treatments. P-values (**P &lt;0.01, *P &lt;0.05) indicate statistical significance either successful or unsuccessful treatments by one-way ANOVA followed by tukey multiple comparison test. P-value (†P &lt;0.05) indicates statistical significance by Student’s t-test. Fig. S6. Heatmap analysis based on metabolites in concentration level identified in all the groups. Each column represents a sample and each row represents a metabolite. Colors indicate fold increases or decreases in concentrations, as indicated in the key. Data are shown for donor (n = 9), recipient 0 (n = 9), recipient 1 (n = 9), and recipient 7 (n = 9) in successful treatments, and donor (n = 3), recipient 0 (n = 3), recipient 1 (n = 3), and for recipient 7 (n = 3) in unsuccessful treatments. The parameters that were used for the analysis were Euclidean distance measure and Ward cluster algorithm, using MetaboAnalyst 4.0 software. Fig. S7. Partial Least-Squares Discriminant Analysis (PLS-DA) parameter for the comparison of successful and unsuccessful treatments. (A) D-success vs D-failure (accuracy 0.75, R2: 0.66; Q2: 0.30); (B) R-0-success vs R-0-failure (accuracy=1, R2= 0.88; Q2= 0.73); (C) R-1-success vs R-1-failure (Accuracy 0.91; R2= 0.85; Q2= 0.58), and (D) R-7-success vs R-7-failure (Accuracy 0.75; R2= 0.8468; Q2= 0.19), shown for donor (n = 9), recipient 0 (n = 9), recipient 1 (n = 9), and recipient 7 (n = 9) in successful treatments, and donor (n = 3), recipient 0 (n = 3), recipient 1 (n = 3), and for recipient 7 (n = 3) in unsuccessful treatments. Fig. S8. Effect of FMT on amino acid level in successful and unsuccessful treatments. Amino acid concentration obtained from fecal sample in each group on before and after FMT. Data are shown as mean ± SEM for donor (n = 9), recipient 0 (n = 9), recipient 1 (n = 9), and recipient 7 (n = 9) in successful treatments, and donor (n = 3), recipient 0 (n = 3), recipient 1 (n = 3), and for recipient 7 (n = 3) in unsuccessful treatments and were analyzed using the unpaired t test with Welch’s correction. *P &lt;0.05; **P &lt;0.01. Fig. S9. Effect of FMT on selected metabolites in successful and unsuccessful treatments obtained from fecal sample in each group on before and after FMT. Data are shown as mean ± SEM for donor (n = 9), recipient 0 (n = 9), recipient 1 (n = 9), and recipient 7 (n = 9) in successful treatments, and donor (n = 3), recipient 0 (n = 3), recipient 1 (n = 3), and for recipient 7 (n = 3) in unsuccessful and were analyzed using the unpaired t test with Welch’s correction. *P &lt; 0.05. GABA, gamma-Aminobutyric acid. Fig. S10. Abundant metabolites in lipid and fatty acid metabolism based on their relative area obtained from fecal sample in each group on before and after FMT. Data are shown as for donor (n = 9), recipient 0 (n = 9), recipient 1 (n = 9), and recipient 7 (n = 9) in successful treatments, and donor (n = 3), recipient 0 (n = 3), recipient 1 (n = 3), and for recipient 7 (n = 3) in unsuccessful treatments. Data are shown as mean ± SEM and were analyzed using the unpaired t test with Welch’s correction. *P &lt; 0.05. Fig. S11. Effect of FMT on polyamines. Polyamines (spermidine and putresine) and diamine (cadaverine) in successful and unsuccessful treatments based on their concentration are obtained from fecal sample in each group on before and after FMT, for donor (n = 9), recipient 0 (n = 9), recipient 1 (n = 9), and recipient 7 (n = 9) in succeed treatments, and donor (n = 3), recipient 0 (n = 3), recipient 1 (n = 3), and for recipient 7 (n = 3) in unsuccessful treatments. Data are shown as mean ± SD. were analyzed using the unpaired t test with Welch’s correction. *P &lt; 0.05. Fig.S12. Microbiota-metabolome correlation based on group specific procrustes analysis. Procrustes analysis in A) D-success group (M2 = 0.2289, r = 0.8781, P = 0.0037), B) R-0-success (M2 = 0.59, r = 0.6403, P = 0.051), C) R-1-success (M2 = 0.7202, r = 0.529, P = 0.2097), D) R-7-success (M2 = 0.2155, r = 0.8857, P = 0.0022), E) D-failure (M2 = 0.3037, r = 0.8345, P = 0.66667), F) R-0-failure (M2 = 0.1437, r = 0.9254, P= 0.5), G) R-1-failure (M2 = 0.1233, r = 0.9363, P= 0.1667), H) R-7-failure (M2 = 0.0663, r = 0.9661, P= 0.1667). Fig. S13. The weighted gene co-expression network analysis (WGCNA) to identify microbiota-metabolites correlation. (A) Module trait relationship among microbiota, clinical data, metabolites and fecal immunoglobulins (IgA, IgG, and IgM). Each row corresponds to a module. Each column corresponds to a trait labeled below. Each cell at the row-column intersection contains the correlation coefficient and P-value (in brackets) between the module and that trait. A highly positive correlation between a specific module and a trait is indicated by dark red, and green indicates negative correlation. Data are shown for donor (n = 9), recipient 0 (n = 9), recipient 1 (n = 9), and recipient 7 (n = 9) in successful treatments, and for donor (n = 3), recipient 0 (n = 3), recipient 1 (n = 3), and recipient 7 (n = 3) in unsuccessful treatments. (B) Heatmap analysis from WGCNA analysis based on modules-trait relationships. Each column represents a sample and each row represents a microbial taxon from the selected modules. Colors indicate increases or decreases in abundances, as indicated in the color key (donor and recipient n numbers in successful and unsuccessful treatments as shown above). Fig. S14. Heatmap based Identification of the potential microbial taxa by module trait relationship in donor cases in WGCNA analysis. Each column represents a sample and each row represents a microbial taxon from the selected modules. Colors indicate increases or decreases in abundances, as indicated in the color key, for D-success (n = 9) in successful treatments and D-failure (n = 3) in unsuccessful treatments, respectively. Fig. S15. The weighted gene co-expression network analysis (WGCNA) to identify microbiota-metabolites correlation before FMT. (A) Module trait relationship among microbiota, and selected metabolites. Each row corresponds to a module. Each column corresponds to a trait labeled below. Each cell at the row-column intersection contains the correlation coefficient and P-values (in brackets) between the module and that trait. A highly positive correlation between a specific module and a trait is indicated by dark red, and green indicates negative correlation. (B) Heatmap analysis from WGCNA analysis based on modules-trait relationships. Each column represents a sample and each row represents a microbial taxon from the selected modules. Colors indicate increases or decreases in abundances, as indicated in the color key, shown for recipient 0 (n = 9) in successful treatments, and recipient 0 (n = 3) in unsuccessful treatments, respectively. Fig. S16. The weighted gene co-expression network analysis (WGCNA) to identify microbiota-metabolites correlation after FMT at day 1. (A) Module trait relationship among microbiota, and selected metabolites. Each row corresponds to a module. Each column corresponds to a trait labeled below. Each cell at the row-column intersection contains the correlation coefficient and P-value (in brackets) between the module and that trait. A highly positive correlation between a specific module and a trait is indicated by dark red, and green indicates negative correlation. (B) Heatmap analysis from WGCNA analysis based on modules-trait relationships. Each column represents a sample and each row represents a microbial taxon from the selected modules. Colors indicate increases or decreases in abundances, as indicated in the color key, shown for recipient 1 (n = 9) in successful treatments, and recipient 1 (n = 3) in unsuccessful treatments, respectively. Fig. S17. Heatmap based Identification of the potential microbial taxa by module trait relationship after FMT in recipient cases in WGCNA analysis. Each column represents a sample and each row represents a microbial taxon from the selected modules. Colors indicate increases or decreases in abundances, as indicated in the color key, for recipient 7 (n = 9) in successful treatments, and donor (n = 3), recipient 7 (n = 3) in unsuccessful treatments, respectively. Fig. S18. Metagenomics analysis for potential biomarker identification for a successful FMT. (A) Diarrheal score comparison between diarrheal group for diarrhea (n = 49), R-0-success (n = 14), and R-0-failure (n = 6). Data are expressed as mean±SEM and were analyzed using the 1-way ANOVA with Tukey’s post hoc multiple comparisons (*P &lt;0.05). (B) Microbial composition of overall healthy and diarrheal group for healthy (n = 105), diarrhea (n = 46), D-success (n = 13), D-failure (n = 4), R-0-success (n = 13), and R-0-failure (n = 4). Relative abundance (%) of (C) Sporobacter, (D) Camphylobactor. Data are expressed as mean ± SEM for healthy (n = 105), diarrhea (n = 46), D-success (n = 13), D-failure (n = 4), R-0-success (n = 13), and R-0-failure (n = 4).