The aim of the present study was to provide a theoretical basis for the selection of standard sampling methods in the study of the esophageal microbiota in patients with esophageal squamous cell carcinoma (ESCC) by comparing the differences in bacterial communities between surgical and endoscopic esophageal mucosal tissues. A total of 72 patients with ESCC who were diagnosed at Taihe Hospital (Shiyan, China) between July 2018 and July 2019 were selected to participate in the present study. The sequence V4 hypervariable region was amplified, and Illumina HiSeq sequencing was performed to analyze the differences between the two groups. The Shannon and Chao1 indices of the postoperative esophageal cancer tissue group samples (Group A) were higher than those of the esophageal mucosa tissue samples (Group B), and the difference was statistically significant (P<0.05). The Simpson index of Group A was higher than that of Group B, but the difference was not significant (P>0.05). The β diversity analysis demonstrated that the overall composition of the flora of the two groups was not significantly different. Linear discriminant analysis effect size analysis showed that the abundance of Megasphaera, Actinobacteria, Enterobacteriaceae and Enterobacteriales in Group A was significantly higher than that in Group B, but the abundance of Mogibacteriaceae in Group B was significantly higher than that in Group A. The top 60 species were selected using the random forest method to establish a model. The error rate of the prediction model constructed using the random forest method was 22.59%. The receiver operating characteristic (ROC) curve analysis confirmed that the present model was reliable and could effectively distinguish between the two groups of samples (area under the curve, 0.86). The source of the sample should be considered in studies investigating the esophageal flora. Considering the increased richness and improved uniformity of postoperative tissue microbiota compared with the mucosal group, it was predicted that postoperative tissue may be more conducive to the study of esophageal cancer microbiota.

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