Additional file 2 of Metagenome-wide analysis uncovers gut microbial signatures and implicates taxon-specific functions in end-stage renal disease
Creators: name: Zhang, Pan
name: Wang, Xifan
name: Li, Shenghui
name: Cao, Xuesen
name: Zou, Jianzhou
name: Fang, Yi
name: Shi, Yiqin
name: Xiang, Fangfang
name: Shen, Bo
name: Li, Yixuan
name: Fang, Bing
name: Zhang, Yue
name: Guo, Ruochun
name: Lv, Qingbo
name: Zhang, Liwen
name: Lu, Yufei
name: Wang, Yaqiong
name: Yu, Jinbo
name: Xie, Yeqing
name: Wang, Ran
name: Chen, Xiaohong
name: Yu, Jiawei
name: Zhang, Zhen
name: He, Jingjing
name: Zhan, Jing
name: Lv, Wenlv
name: Nie, Yuxin
name: Cai, Jieru
name: Xu, Xialian
name: Hu, Jiachang
name: Zhang, Qi
name: Gao, Ting
name: Jiang, Xiaotian
name: Tan, Xiao
name: Xue, Ning
name: Wang, Yimei
name: Ren, Yimei
name: Wang, Li
name: Zhang, Han
name: Ning, Yichun
name: Chen, Jing
name: Zhang, Lin
name: Jin, Shi
name: Ren, Fazheng
name: Ehrlich, Stanislav Dusko
name: Zhao, Liang
name: Ding, Xiaoqiang
Publisher: name: figshare
Year: 2024
Subjects: subject: Microbiology
subject: FOS: Biological sciences

description: Additional file 2: Figure S1. Genome-wide phylogeny of 1,303 gut microbial species. Figure S2. Species boundary and reads mappability of the 1,303 gut species in this study. Figure S3. Comparison of microbial diversity between ESRD patients and healthy controls. Figure S4. Distribution of samples in the five primary PCs. Figure S5. Random forest models for discriminating ESRD patients and healthy controls based on gut species profile. Figure S6. Identification of ESRD-associated species from two independent cohorts. Figure S7. Comparison of functional profiles between ESRD patients and healthy controls. Figure S8. Identification of ESRD-associated functional signatures from two independent cohorts. Figure S9. Comparison of antibiotic resistance genes between ESRD patients and healthy controls. Figure S10. Effect of the bacterial phylogeny on the functional composition. Figure S11. Occurrence of several types of enzymes in Firmicutes species. Figure S12. Modules differing in completeness between ESRD-enriched and HC-enriched non-Firmicutes species. Figure S13. Analysis of polysaccharide utilization for ESRD-associated Bacteroidetes species. Figure S14. Relationship between individuals’ dietary pattern and their metagenomic polysaccharide utilization and Prevotellaceae/Muribaculaceae level. Figure S15. Presence of several important enzymes in the ESRD-associated species. Figure S16. Distribution of the key synthetases involved in the biosynthesis of uremic toxins in fecal metagenomes. Figure S17. Predicting the concentrations of toxins in ESRD patients, based on the gut microbial species. Figure S18. Predicting the concentrations of toxins in healthy subjects based on the gut microbial species. Figure S19. Heatmap presented below illustrates the relative abundance variations of ESRD-associated species in healthy controls, as well as patients with CKD stage 3-4, CKD5N, and ESRD. Figure S20. Random forest models for discriminating CKD patients from the healthy controls based on gut species profile of ESRD patients. Figure S21. Flow diagram of recruitment of individuals in the Shanghai cohort.