Additional file 1 of Bacteroides salyersiae is a potent chondroitin sulfate-degrading species in the human gut microbiota

Abstract

Additional file 1: Figure S1. TLC showing the degradation of CS by the human gut microbiota. The degradation was monitored at 12 hours (A), 24 hours (B), 36 hours (C), 48 hours (D), and 72 hours (E). Figure S2. Degradation of CS by the human gut microbiota. Relative CS content in the culture medium at 72 hours (A). UPLC-MS/MS analysis of CSOSs in the culture medium of donor T25 (B). Total ion chromatograms showing the elution profiles of CSOSs in the culture medium of donor T25 at different time points (C). Figure S3. Mass spectrum showing the signals of udp2 (A), udp4 (B), and udp6 (C) according to their m/z ratios. The CSOSs, including udp2, udp4, and udp6 were produced in the culture medium as a result of CS degradation by the human gut microbiota. Figure S4. Changes in the structure of the human gut microbiota before and after fermentation. Venn diagram showing the differences of the operational taxonomic units (OTUs) (A). Observed species (B). Chao1 index (C). Shannon index (D). Heatmap of the abundance of gut bacteria at the genus level (E). Figure S5. Differences in the composition of the human gut microbiota before and after fermentation. Wilcoxon rank-sum test analysis of the gut microbiota at the species level (A). Linear discriminant analysis (LDA) Effect Size (LEfSe) analysis of the gut microbiota at the species level (B). Only bacterial taxa with an LDA score of above 3.0 were listed. Figure S6. Isolation of CS-degrading bacteria from the human gut microbiota. Different species of bacteria were obtained from different human fecal samples (A-W). Figure S7. B. salyersiae CSP6 was identified as a potent bacterium for CS-degradation in the present study. Heatmap of the relative abundance of the consumed CS (A). Phylogenetic tree analysis of the CS-degrading bacteria based on the 16S rRNA gene (B). Figure S8. TLC showing the degradation of CS by different human fecal isolates. The results were presented from B. thetaiotaomicron E1-7 to H. porci E13-26 (A-I). Figure S9. TLC showing the degradation of CS by different human fecal isolates. The results were presented from E. durans E13-16 to S. oneidensis P30-2-30 (A-H). Figure S10. Degradation and fermentation of CS by B. finegoldii B36-12, B. thetaiotaomicron E1-7, B. xylanisolvens B33-17, and B. ovatus B33-4. Concentrations of different SCFAs in the culture medium of B. finegoldii B36-12 (A), B. thetaiotaomicron E1-7 (B), B. xylanisolvens B33-17 (C), and B. ovatus B33-4 (D). * p < 0.05; ** p < 0.01. Figure S11. CS degradation by B. finegoldii B36-12, B. thetaiotaomicron E1-7, B. xylanisolvens B33-17, and B. ovatus B33-4. UPLC-MS/MS analysis of CSOSs produced by B. finegoldii B36-12 (A), B. thetaiotaomicron E1-7 (B), B. xylanisolvens B33-17 (C), and B. ovatus B33-4 (D). Total ion chromatograms showing the elution profiles of CSOSs in the culture medium of B. finegoldii B36-12 (E), B. thetaiotaomicron E1-7 (F), B. xylanisolvens B33-17 (G), and B. ovatus B33-4 (H) at different time points. * p < 0.05. Figure S12. Mass spectrum showing the signals of udp4 (A), udp6 (B), and udp8 (C) according to their m/z ratios. The CSOSs, including udp4, udp6, and udp8 were produced in the culture medium as a result of CS degradation by B. salyersiae CSP6, B. finegoldii B36-12, B. xylanisolvens B33-17, B. thetaiotaomicron E1-7, and B. ovatus B33-4. Figure S13. Degradation of CS by different strains of B. salyersiae. TLC showing the degradation of CS by B. salyersiae CSP6 and B. salyersiae FL17 (A). Relative carbohydrate content in the culture medium at different time points (B). B. salyersiae FL17 was previously isolated from the fecal sample of a healthy individual. This individual has not participated in the present study. Figure S14. Genome analysis of B. salyersiae CSP6. COG function classification (A). KEGG pathway analysis (B). Figure S15. Screening of candidate bacteria that could utilize udp4 using the spent medium assay. TLC showing the utilization of udp4 by different human gut bacteria. (A). List of the tested bacteria (B). Figure S16. Cross-feeding interactions between B. salyersiae and B. stercoris identified using the spent medium assay. Relative carbohydrate content in the culture medium (A). Growth curve (B) and CFU analysis (C). Concentrations of total SCFAs (D), acetate (E), and propionate (F) in the culture medium of B. salyersiae and B. stercoris. * p < 0.05; ** p < 0.01; *** p < 0.001. Figure S17. Mass spectrum showing the signal of udp4 according to the m/z ratio. The udp4 concentration in the spent medium was analyzed using UPLC-MS/MS. Table S1. Summary of CS-degrading bacteria isolated from the human fecal samples. Table S2. Summary of the potential enzymes for CS degradation in B. salyersiae CSP6 based on the genomic analysis. Supplementary Table S3. Genome annotation of B. salyersiae CSP6. Supplementary Table S4. CAZyme annotation of B. salyersiae CSP6