Journal: bioRxiv

Article Title: Saccharomyces boulardii attenuates obesity-associated inflammation and weight gain through coordinated gut ecosystem remodeling

doi: 10.64898/2026.04.01.715546

Figure Lengend Snippet: (A) Alpha diversity metrics including observed richness, Berger–Parker dominance, and Shannon diversity index in PBS- and S. boulardii –treated mice. (B) Relative abundance of microbial phyla in PBS- and S. boulardii –treated mice. (C) Principal coordinate analysis (PCoA) of beta diversity based on Bray–Curtis dissimilarity. Each point represents an individual mouse. Statistical significance was assessed using PERMANOVA. (D) Differentially abundant microbial species identified using linear discriminant analysis effect size (LEfSe), displayed as LDA scores indicating enrichment in PBS- or S. boulardii –treated groups. Group differences were assessed using two-sided Kruskal–Wallis and Wilcoxon rank-sum tests with Benjamini–Hochberg false discovery rate (FDR) correction ( p < 0.05). Taxa with LDA scores > 2.0 were considered enriched.

Article Snippet: Cryopreserved S. boulardii (ATCC MYA-796 ura3 Δ was streaked on yeast extract peptone dextrose (YPD) agar and incubated to obtain single colonies.

Techniques:

Journal: bioRxiv

Article Title: Saccharomyces boulardii attenuates obesity-associated inflammation and weight gain through coordinated gut ecosystem remodeling

doi: 10.64898/2026.04.01.715546

Figure Lengend Snippet: (A) Principal coordinate analysis (PCoA) of predicted microbial pathway profiles. Statistical significance was assessed using PERMANOVA. (B) Differentially enriched microbial pathways identified using linear discriminant analysis effect size (LEfSe), displayed as LDA scores indicating enrichment in PBS- or S. boulardii –treated mice. Group differences were tested using two-sided Kruskal–Wallis and Wilcoxon rank-sum tests with Benjamini–Hochberg false discovery rate (FDR) correction ( p < 0.05); pathways with LDA > 2.0 were considered enriched. (C) UpSet plot showing pathway presence–absence relationships derived from HUMAnN3 MetaCyc annotations, indicating the number of pathways shared between or unique to treatment groups. Bar heights represent intersection sizes, and horizontal bars indicate total pathway counts per group. (D) Principal component analysis (PCA) of cecal metabolomic profiles. Percentage of variance explained by each principal component is indicated; statistical significance was assessed using PERMANOVA. (E) Volcano plot of cecal metabolites showing log 2 fold change in S. boulardii –treated mice relative to PBS-treated controls versus −log 10 FDR-adjusted p values. Differential abundance was defined as |log 2 fold change| ≥ 0.5 and FDR-adjusted p < 0.1.

Article Snippet: Cryopreserved S. boulardii (ATCC MYA-796 ura3 Δ was streaked on yeast extract peptone dextrose (YPD) agar and incubated to obtain single colonies.

Techniques: Derivative Assay, Metabolomic

Journal: bioRxiv

Article Title: Saccharomyces boulardii attenuates obesity-associated inflammation and weight gain through coordinated gut ecosystem remodeling

doi: 10.64898/2026.04.01.715546

Figure Lengend Snippet: (A) Volcano plot of colonic gene expression derived from DESeq2 analysis showing S. boulardii –treated log 2 fold change relative to PBS-treated mice versus −log 10 false discovery rate (FDR)–adjusted p-values. Differential expression was defined as |log₂ fold change| ≥ 0.5 and FDR-adjusted p < 0.1. (B) Gene set enrichment analysis (GSEA) of MSigDB Hallmark pathways performed on ranked gene lists. Normalized enrichment scores (NES) are shown for pathways significantly enriched at FDR-adjusted p < 0.05. Dot size reflects gene set size. Positively enriched pathways indicate relative upregulation, and negatively enriched pathways indicate relative downregulation in S. boulardi i–treated mice compared with controls.

Article Snippet: Cryopreserved S. boulardii (ATCC MYA-796 ura3 Δ was streaked on yeast extract peptone dextrose (YPD) agar and incubated to obtain single colonies.

Techniques: Gene Expression, Derivative Assay, Quantitative Proteomics

Journal: bioRxiv

Article Title: Saccharomyces boulardii attenuates obesity-associated inflammation and weight gain through coordinated gut ecosystem remodeling

doi: 10.64898/2026.04.01.715546

Figure Lengend Snippet: (A) Fasting portal vein concentrations (pg/mL) of metabolic hormones, including ghrelin, GLP-1, glucagon, insulin, leptin, and PYY. (B) Principal component analysis (PCA) of cytokine profiles. Percentage of variance explained by each principal component is indicated; statistical significance was assessed using PERMANOVA. (C) Volcano plot of fasting portal vein cytokines showing S. boulardii –treated log 2 fold change relative to PBS-treated mice versus –log 10 false discovery rate (FDR)–adjusted p-values. Differential abundance was defined as |log₂ fold change| ≥ 0.5 and FDR-adjusted P < 0.1. (D) Fasting portal vein concentrations (pg/mL) of IL-6. (E) Fasting portal vein concentrations (pg/mL) of selected cytokines, including IL-6, CXCL1, CXCL2, CCL22, CSF2, IL22 and IL-17A. Data are presented as mean ± SEM (n = 9). Statistical significance was assessed using the Wilcoxon rank-sum (Mann–Whitney U) test, with multiple testing correction applied using the Benjamini–Hochberg false discovery rate. * P < 0.05.

Article Snippet: Cryopreserved S. boulardii (ATCC MYA-796 ura3 Δ was streaked on yeast extract peptone dextrose (YPD) agar and incubated to obtain single colonies.

Techniques: MANN-WHITNEY

Journal: bioRxiv

Article Title: Saccharomyces boulardii attenuates obesity-associated inflammation and weight gain through coordinated gut ecosystem remodeling

doi: 10.64898/2026.04.01.715546

Figure Lengend Snippet: (A) DIABLO component score plots for individual data blocks (metabolomics, microbial pathways, physiological variables, proteomics (Olink), RNA-seq, and taxa) showing separation between PBS- and S. boulardii –treated mice along component 1 and component 2. Ellipses represent 95% confidence intervals. (B) Pairwise agreement (absolute correlation, |r|) between component 1 scores across data blocks. Color intensity reflects correlation strength. (C) Network representation of DIABLO-selected features (|ρ| ≥ 0.65) across omics layers. Nodes represent selected features colored by data type (metabolomics, pathways, physiological, proteomics, RNA-seq, taxa). Edge color indicates direction of correlation (red, positive; blue, negative), and edge thickness reflects correlation strength. Node size corresponds to degree (number of connections). (D) Boxplots of representative DIABLO-selected hub features across treatment groups. Data are shown as individual points with median and interquartile range.

Article Snippet: Cryopreserved S. boulardii (ATCC MYA-796 ura3 Δ was streaked on yeast extract peptone dextrose (YPD) agar and incubated to obtain single colonies.

Techniques: RNA Sequencing