Additional file 2 of A fiber-deprived diet causes cognitive impairment and hippocampal microglia-mediated synaptic loss through the gut microbiota and metabolites
Creators: name: Shi, Hongli
name: Ge, Xing
name: Ma, Xi
name: Zheng, Mingxuan
name: Cui, Xiaoying
name: Pan, Wei
name: Zheng, Peng
name: Yang, Xiaoying
name: Zhang, Peng
name: Hu, Minmin
name: Hu, Tao
name: Tang, Renxian
name: Zheng, Kuiyang
name: Huang, Xu-Feng
name: Yu, Yinghua
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Neuroscience
subject: Physiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Mental Health
subject: Hematology

description: Additional file 1: Fig. S1. Dietary fiber deficiency for 15 weeks impaired cognition and increased colonic and systemic inflammation. Total object exploration time in the object location test (A) and temporal order memory tests (B). (C) Deacon nest score in nest building tests (n=15). (D) Average energy intake (n=15). (E) Body weight at 15 week (n=15). (F) Fat pad weight (n=9). (G) mRNA expression levels of TNFα, IL-1β and IL-6 in the colon (n=5). (H) TNF-α, IL-1β, and IL-6 levels in the serum (n=10). Values are mean ± SEM. *p &lt; 0.05 fiber deficiency (FD) group vs. control (Con) group. Fig. S2. Dietary fiber deficiency altered gut microbiota. (A-D) The α-diversity of the cecal microbiome among two groups depicted according to Chao1 index (A), Ace index (B), Sob index (C) and Shannon index (D). (E) Cladogram generated from linear discriminant analysis (LDA) (n=5-6). (F) Predicted KEGG functional pathway differences at level 3 inferred from 16S rRNA gene sequences using PICRUSt. Values are mean ± SEM. *p &lt; 0.05 fiber deficiency (FD) group vs. control (Con) group. Fig S3. Dietary fiber deficiency for 7 days altered gut microbiota, but not colon tight junctions and inflammation. (A) Predicted KEGG functional pathway differences at level 3 inferred from 16S rRNA gene sequences using PICRUSt (n=5-6). (B-D) Protein levels of occludin and ZO-1 in the colon (n=6). (E) The quantification of colon length was statistically analyzed (n=9) with representative images of colons. (F-H) mRNA expression levels of TNFα, IL-1β and IL-6 in the colon (n=6). (I) Average energy intake (n=15). (J) Body weight at 1 week (n=15). Values are mean ± SEM. *p &lt; 0.05 fiber deficiency for short-term (FD-ST) group vs. control (Con) group. Fig. S4. The cognitive behavior in the GPR41-/- and GPR43-/-mice. Total object exploration time in the object location test (A) and temporal order memory tests (B). (C) Deacon nest score in nest building tests (n=8-10). Values are mean ± SEM. *p &lt; 0.05 vs. wild type (WT) mice. Fig. S5. SCFAs supplementation prevented FD-induced cognitive decline and microglia activation. Total object exploration time in the object location test (A) and temporal order memory tests (B). (C) Deacon nest score in nest building tests (n=15). (D) The immunofluorescent staining of Iba1 (Scale bar: 50μm), the image capture from the box marked with a dotted line (Scale bar: 10μm). (E) Quantification of Iba1+cells numbers in CA1, CA3 and DG of the hippocampus (2 images per mouse, n=6). (F) The protein level of Iba1 in the hippocampus (n=6). (G and H) The circularity and ramification index of Iba1+ cells (2 images per mouse, n=3). (I) mRNA expression level of CD68 (n=6). (J) The representative immunofluorescent staining of CD68 in the hippocampus, Scale bar: 25μm. (K) The orthogonal view of the high-resolution confocal image shows the colocalization of Iba1 (green) and PSD95 (red) (Scale bar: 5μm). Values are mean ± SEM. *p &lt; 0.05 vs. control (Con) group. #p &lt; 0.05 vs. fiber deficiency (FD) group. The FD mice with SCFAs supplementation: FDS. Fig. S6. SCFAs supplementation prevented FD-induced intestinal integrity impairment, endotoxemia and systemic inflammation. (A) Immunofluorescence images of colonic sections stained with Anti-MUC2 antibody and DAPI. Opposing white arrows with shafts delineates the mucus layer. Scale bar: 50μm (B) FISH analysis of sections of the colon using the general bacterial probe EUB338-Alexa Fluor 488 (green), and nuclear staining DAPI (blue). Arrows indicate the distance between bacteria and epithelium. Scale bar: 20μm. (C) Fecal albumin concentrations (n=8). (D) Serum LPS endotoxin level (n=10). (E) mRNA expression levels of TNFα, IL-1β and IL-6 in the colon (n=5). (F) The quantification of colon length was statistically analyzed (n=9) and representative images of colons. (G) TNF-α, IL-1β and IL-6 levels in the serum (n=10). Values are mean ± SEM. *p &lt; 0.05 vs. control (Con) group. #p &lt; 0.05 vs. fiber deficiency (FD) group. The FD mice with SCFAs supplementation: FDS. Table S1. Composition of the control (Con) and fiber deficient (FD) diets. Table S2. Pearson correlations between energy intake and metabolic and behavior parameters