Signatures within esophageal microbiota with progression of esophageal squamous cell carcinoma - PubMed (original) (raw)
Signatures within esophageal microbiota with progression of esophageal squamous cell carcinoma
Minjuan Li et al. Chin J Cancer Res. 2020.
Abstract
Objective: Esophageal squamous cell carcinoma (ESCC) is one of the dominant malignances worldwide, but currently there is less focus on the microbiota with ESCC and its precancerous lesions.
Methods: Paired esophageal biopsy and swab specimens were obtained from 236 participants in Linzhou, China. Data from 16S ribosomal RNA gene sequencing were processed using quantitative insights into microbial ecology (QIIME2) and R Studio to evaluate differences. The Wilcoxon rank sum test and Kruskal-Wallis rank sum test were used to compare diversity and characteristic genera by specimens and participant groups. Ordinal logistic regression model was used to build microbiol prediction model.
Results: Microbial diversity was similar between biopsy and swab specimens, including operational taxonomic unit (OTU) numbers and Shannon index. There were variations and similarities of esophageal microbiota among different pathological characteristics of ESCC. Top 10 relative abundance genera in all groups include Streptococcus, Prevotella, Veillonella, Actinobacillus, Haemophilus, Neisseria, Alloprevotella, Rothia, Gemella and Porphyromonas. Genus Streptococcus, Haemophilus, Neisseria and Porphyromonas showed significantly difference in disease groups when compared to normal control, whereas Streptococcus showed an increasing tendency with the progression of ESCC and others showed a decreasing tendency. About models based on all combinations of characteristic genera, only taken Streptococcus and Neisseria into model, the prediction performance was the ideal one, of which the area under the curve (AUC) was 0.738.
Conclusions: Esophageal biopsy and swab specimens could yield similar microbial characterization. The combination of Streptococcus and Neisseria has the potential to predict the progression of ESCC, which is needed to confirm by large-scale, prospective cohort studies.
Keywords: 16S rRNA; Esophageal squamous cell carcinoma; Neisseria; Streptococcus; precancerous lesions.
Copyright © 2020 Chinese Journal of Cancer Research. All rights reserved.
Figures
1
Microbial comparison for β diversity. β diversity based on (A) the weighted UniFrac distance (P<0.05) and (B) the unweighted UniFrac distance (P<0.05) was compared with PCoA for swab and biopsy specimens. β diversity based on (C) the weighted UniFrac distance (P<0.05) and (D) the unweighted UniFrac distance (P<0.05) was compared with PCoA for participant groups. PCoA, principal coordinates analysis; ESCC, esophageal squamous cell carcinoma; HGIN, high-grade intraepithelial neoplasia; LGIN, low-grade intraepithelial neoplasia.
2
Comparison for α diversity of participants with different diagnosis in swab and biopsy specimens. α diversity was assessed by observed OTUs (Swab, P<0.01; Biopsy, P=0.13) (A) and Shannon index (Swab, P=0.26; Biopsy, P=0.09) (B). OTU, operational taxonomic unit; LGIN, low-grade intraepithelial neoplasia; HGIN, high-grade intraepithelial neoplasia; ESCC, esophageal squamous cell carcinoma.
3
Microbial composition at phylum and genus level for participants in different participant groups in swab and biopsy specimens respectively. (A) Microbial composition for all participants in swab specimens at the phylum and genus level; (B) Microbial composition for all participants in biopsy specimens at the phylum and genus level. LGIN, low-grade intraepithelial neoplasia; HGIN, high-grade intraepithelial neoplasia; ESCC, esophageal squamous cell carcinoma.
4
Comparison of relative abundance of microbial genera among participant groups. (A) Mean relative abundance of top 10 high-relative abundance genera in swab specimens; (B) Mean relative abundance of top 10 high-relative abundance genera in biopsy specimens. LGIN, low-grade intraepithelial neoplasia; HGIN, high-grade intraepithelial neoplasia; ESCC, esophageal squamous cell carcinoma; *, P<0.05; **, P<0.01.
5
Microbial models based on characteristic genera. (A) Each characteristic genus was tested by a ROC analysis; (B) Combinations of any two genera were tested by ROC analysis; (C) Combinations of any three genera were tested by ROC analysis; (D) Combination of four genera was tested by ROC analysis. S, Streptococcus; N, Neisseria; P, Porphyromonas; H, Haemophilus; ROC, receiver operating characteristic; AUC, area under the curve.
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