Additional file 1 of Oropharynx microbiota transitions in hypopharyngeal carcinoma treatment of induced chemotherapy followed by surgery
Creators: name: Lau, Hui-Ching
name: Hsueh, Chi-Yao
name: Gong, Hongli
name: Sun, Ji
name: Huang, Hui-Ying
name: Zhang, Ming
name: Zhou, Liang
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Molecular Biology
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Cancer

description: Additional file 1 : Figure S1. Alpha diversity and Beta diversity of advanced stage IC (as-IC) and advanced stage nIC (as-nIC) compared. Alpha diversity was based on (A) Ace index shown in violin plot, reflecting the lower richness of microbiota (p = 0.1829) and (B) Shannon index shown in violin plot, reflecting the lower evenness of microbiota in as-IC group compared to as-nIC group (p = 0.4745). Beta diversity was used to evaluate the similarity between groups and its measurements were as follows: (C) PCoA with weighted UniFrac in as-IC group presented no statistical difference compared to as-nIC group. (Adonis analysis: R2 = 0.0168; p = 0.784) (D) NMDS in as-IC group presented no statistical difference compared to as-nIC group. (Anosim analysis: R2 = 0.0433; p = 0.253). Figure S2. Pre-operative HPSCC (pre-HPSCC) and post-operative HPSCC (post-HPSCC) compared. (A) NMDS was measured through Anosim analysis, reflecting the abundance of OPM microbiota in post-HPSCC to be profoundly different compared to pre-HPSCC (Anosim: R2 = 0.3821; p = 0.001). (E) Taxa enriched in pre-HPSCC (Red) and post-HPSCC (Blue) groups are indicated with LDA scores (LDA = 3), respectively. (F) A cladogram represents the OPM microbiota in IC, nIC and CG. Taxa enriched in pre-HPSCC (Red) and post-HPSCC (Blue). The brightness of each dot is proportional to its effect size. Figure S3. IC group and post-IC group compared: (A) Ace index shown in violin plot reflected lower richness of microbiota in post-IC group (p = 0.0057). (B) Shannon index illustrated the lower evenness of microbiota in post-IC group (p = 0.0076). Comparing nIC group and post-nIC group: (A) Ace index shown in violin plot reflected lower richness of microbiota in post-nIC group (p = 0.0069). (B) Shannon index illustrated the lower evenness of microbiota in post-IC group (p &lt; 0.001). Figure S4. Taxa in post-IC and post-nIC group through LEfSe evaluated. (A) Specific taxa enriched in only post-nIC group (Blue) groups were indicated with LDA scores (LDA = 3), reflecting more accumulation of anaerobics. Post-IC group manifested no higher abundance of microbiome when compared to post-nIC group. (F) A cladogram represented the OPM microbiota in nIC group (Blue). The brightness of each dot is proportional to its effect size. Figure S5. Functional Prediction of Predominant Taxa of LSCC. (A) A colored histogram was established to visualize the predominant functional annotation clustering of KEGG (level 1) in IC, nIC, post-IC, post-nIC, and CG (EC and VCP). (B) A colored heatmap was established to visualize the predominant functional annotation clustering of KEGG (level 2) in IC, nIC, post-IC, post-nIC, and CG (EC and VCP). (C) The OPM microbiome of post-operation group had significantly lower abundance in human carcinoma signaling pathways, compared to control and pre-operation group by Mann-Whitney U test. * p &lt; 0.05, *** p &lt; 0.001. Figure S6. The Rarefaction curve. (A) OTUs versus sequences per sample (B) OTUs versus sequences between HSCC and control group.