Additional file 1 of A synbiotic mixture of selected oligosaccharides and bifidobacteria assists murine gut microbiota restoration following antibiotic challenge
Creators: name: Hoedt, Emily C.
name: Hueston, Cara M.
name: Cash, Nora
name: Bongers, Roger S.
name: Keane, Jonathan M.
name: van Limpt, Kees
name: Ben Amor, Kaouther
name: Knol, Jan
name: MacSharry, John
name: van Sinderen, Douwe
Publisher: name: figshare
Year: 2023
Subjects: subject: Space Science
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Developmental Biology
subject: Cancer
subject: Science Policy

description: Additional file 1: Table S1. Strains used in this study. Table S2. Diet formulation manufactured by SSNIFF (www.ssniff.com). Table S3. Primers used in this study. Table S4. PERMANOVA statistics between microbiota sequence timepoints of beta diversity matrices for each treatment group. N=5/group. Figure S1. Ileum content HPLC VFA results for A) groups culled on Day 29, and B) Replicate groups culled on Day 35. Figure S2. Cecum content HPLC VFA results for A) groups culled on Day 29, and B) replicate groups culled on Day 35. Figure S3. Relative abundance of the top 25 genera at Day -7, 5, 13, 25 and 35 across the 3 intervention groups supplemented with A)scGOS/lcFOS/2’-FL and B.breve NRBB01 B) scGOS/lcFOS/2’-FL and the Bifidobacterium strain Mix and C) scGOS/lcFOS/2’-FL diet only, without clindamycin treatment. Groups treated with clindamycin between Day 7-14 include groups supplemented with D) scGOS/lcFOS/2’-FL and B. breve NRBB01 E) scGOS/lcFOS/2’-FL and the Bifidobacterium strain Mix and F) scGOS/lcFOS/2’-FL diet only. N=5/group. Figure S4. Line plot of the relative abundance of key genera A) Akkermansia, B) Bacteroides, C) Citrobacter, D) Clostridioides, E) Enterococcus, F) Escherichia, G) Lactobacillus, H) Parabacteroides at Days -7, 5, 13, 25 and 35. Each line represents a treatment group with and without antibiotic treatment (clindamycin) between Day 7-14 (B. breve NRBB01, Bifidobacterium strain Mix and scGOS/lcFOS/2’-FL diet only), without clindamycin treatment. Clindamycin treatment occurred between Day 7-14; n=5/group. Figure S5. Cecum dimensions for replicate groups A (29 Day) and B (35 Day) demonstrate a difference between groups treated with and without antibiotics. Cecums of animals receiving clindamycin treatment are larger in length, which is more noticeable for Group A (cull Day 29) which was culled 2 weeks post antibiotic treatment (n = 5). Group B (cull Day 35) had an n=1 and PBS+ABX control was not imaged. Therefore, these results are only observational and not appropriate for statistical analysis. Figure S6. Histological scoring found no significant differences, at Day 35 (3 weeks post antibiotic), of the colonic folds number (glands), edema, neutral mucin staining, and goblets cells (I-L) were measured with at least 5 per mouse. Data are expressed as means ± SD. n= 4 per group. Mean values were significantly different between the groups: *P&lt;0.05, **P&lt;0.01, *** P&lt;0.001. Figure S7. Immune markers A) IL-1b, B) lL-6, and C) IL-10 qPCR relative expressions at Day 29 and D) IL-1b, E) lL-6, and F) IL-10 at Day 35. Data are expressed as Log 2 transformed ± SD; n= 5 per group. Mean values were significantly different between the groups: *P&lt;0.05, **P&lt;0.01, *** P&lt;0.001. Figure S8. Immune markers A) TNF-α and B) IFN-g qPCR relative expressions at Day 29 and C) TNF-α D) IFN-g at Day 35. Data are Log 2 transformed ± SD; n= 5 per group. Mean values were significantly different between the groups: *P&lt;0.05, **P&lt;0.01, *** P&lt;0.001. Figure S9. Epithelial barrier markers A) Muc2, and B) DEFA5 at Day 29 qPCR relative expressions and C) Muc2, D) DEFA5 at Day 35. Data is Log 2 transformed ± SD; n= 5 per group. Mean values were significantly different between the groups: *P&lt;0.05, **P&lt;0.01, *** P&lt;0.001. Figure S10. Epithelial barrier markers A) CLDN-1 and A) CLDN-2 qPCR relative expressions at Day 29 and C) CLDN-1, D) CLDN-2 at Day 35. Log 2 transformed data as ± SD; n= 5 per group. Mean values were significantly different between the groups: *P&lt;0.05, **P&lt;0.01, *** P&lt;0.001.