细菌性阴道病
代谢组
医学
微生物群
普雷沃菌属
代谢物
生物标志物发现
代谢组学
生物标志物
组学
诊断生物标志物
接收机工作特性
计算生物学
微生物学
机器学习
生物信息学
蛋白质组学
内科学
细菌
计算机科学
生物
遗传学
生物化学
基因
作者
Apoorva Challa,Jaswinder Singh Maras,Sunil Nagpal,Gaurav Tripathi,Bhupesh Taneja,Garima Kachhawa,Seema Sood,Benu Dhawan,P. Arun Acharya,Ashish Datt Upadhyay,Madhu Yadav,Rakesh Sharma,Manish Kumar Bajpai,Somesh Gupta
摘要
Abstract Background Bacterial vaginosis (BV) is a common clinical manifestation of a perturbed vaginal ecology associated with adverse sexual and reproductive health outcomes if left untreated. The existing diagnostic modalities are either cumbersome or require skilled expertise, warranting alternate tests. Application of machine‐learning tools to heterogeneous and high‐dimensional multi‐omics datasets finds promising potential in data integration and may aid biomarker discovery. Objectives The present study aimed to evaluate the potential of the microbiome and metabolome‐derived biomarkers in BV diagnosis. Interpretable machine‐learning algorithms were used to evaluate the utility of an integrated‐omics‐derived classification model. Methods Vaginal samples obtained from reproductive‐age group women with ( n = 40) and without BV ( n = 40) were subjected to 16S rRNA amplicon sequencing and LC–MS‐based metabolomics. The vaginal microbiome and metabolome were characterized, and machine‐learning analysis was performed to build a classification model using biomarkers with the highest diagnostic accuracy. Results Microbiome‐based diagnostic model exhibited a ROC‐AUC (10‐fold CV) of 0.84 ± 0.21 and accuracy of 0.79 ± 0.18, and important features were Aerococcus spp., Mycoplasma hominis , Sneathia spp., Lactobacillus spp., Prevotella spp., Gardnerella spp. and Fannyhessea vaginae . The metabolome‐derived model displayed superior performance with a ROC‐AUC of 0.97 ± 0.07 and an accuracy of 0.92 ± 0.08. Beta‐leucine, methylimidazole acetaldehyde, dimethylethanolamine, L‐arginine and beta cortol were among key predictive metabolites for BV. A predictive model combining both microbial and metabolite features exhibited a high ROC‐AUC of 0.97 ± 0.07 and accuracy of 0.94 ± 0.08 with diagnostic performance only slightly superior to the metabolite‐based model. Conclusion Application of machine‐learning tools to multi‐omics datasets aid biomarker discovery with high predictive performance. Metabolome‐derived classification models were observed to have superior diagnostic performance in predicting BV than microbiome‐based biomarkers.
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