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Journal of Translational Medicine
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Open Access 01-12-2024 | Research

Diagnostic potential of salivary microbiota in persistent pulmonary nodules: identifying biomarkers and functional pathways using 16S rRNA sequencing and machine learning

Authors: Xiao Zeng, Qiong Ma, Chun-Xia Huang, Jun-Jie Xiao, Xi Fu, Yi-Feng Ren, Yu-Li Qu, Hong-Xia Xiang, Mao Lei, Ru-Yi Zheng, Yang Zhong, Ping Xiao, Xiang Zhuang, Feng-Ming You, Jia-Wei He

Published in: Journal of Translational Medicine | Issue 1/2024

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Abstract

Background

The aim of this study was to explore the microbial variations and biomarkers in the oral environment of patients with persistent pulmonary nodules (pPNs) and to reveal the potential biological functions of the salivary microbiota in pPNs.

Materials and methods

This study included a total of 483 participants (141 healthy controls and 342 patients with pPNs) from June 2022 and January 2024. Saliva samples were subjected to sequencing of the V3–V4 region of the 16S rRNA gene to assess microbial diversity and differential abundance. Seven advanced machine learning algorithms (logistic regression, support vector machine, multi-layer perceptron, naïve Bayes, random forest, gradient boosting decision tree, and LightGBM) were utilized to evaluate performance and identify key microorganisms, with fivefold cross-validation employed to ensure robustness. The Shapley Additive exPlanations (SHAP) algorithm was employed to explain the contribution of these core microbiotas to the predictive model. Additionally, the PICRUSt2 algorithm was used to predict the microbial functions.

Results

The salivary microbial composition in pPNs group showed significantly lower α- and β-diversity compared to healthy controls. A high-accuracy LightGBM model was developed, identifying six core genera—Fusobacterium, Solobacterium, Actinomyces, Porphyromonas, Atopobium, and Peptostreptococcus—as pPNs biomarkers. Additionally, a visualization pPNs risk prediction system was developed. The immune responses and metabolic activities differences in salivary microbiota between the patients with pPNs and healthy controls were revealed.

Conclusions

This study highlights the potential clinical applications of the salivary microbiota for enable earlier detection and targeted interventions, offering significant promise for advancing clinical management and improving patient outcomes in pPNs.

Graphical abstract

Appendix
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Metadata
Title
Diagnostic potential of salivary microbiota in persistent pulmonary nodules: identifying biomarkers and functional pathways using 16S rRNA sequencing and machine learning
Authors
Xiao Zeng
Qiong Ma
Chun-Xia Huang
Jun-Jie Xiao
Xi Fu
Yi-Feng Ren
Yu-Li Qu
Hong-Xia Xiang
Mao Lei
Ru-Yi Zheng
Yang Zhong
Ping Xiao
Xiang Zhuang
Feng-Ming You
Jia-Wei He
Publication date
01-12-2024
Publisher
BioMed Central
Published in
Journal of Translational Medicine / Issue 1/2024
Electronic ISSN: 1479-5876
DOI
https://doi.org/10.1186/s12967-024-05802-7

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