Multi-omics analysis identifies potential microbial and metabolite diagnostic biomarkers of bacterial vaginosis.

Autor: Challa A; Department of Dermatology and Venereology, All India Institute of Medical Sciences, New Delhi, India., Maras JS; Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India., Nagpal S; TCS Research, Tata Consultancy Services Ltd, Pune, India.; CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India., Tripathi G; Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India., Taneja B; CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India., Kachhawa G; Department of Obstetrics and Gynaecology, All India Institute of Medical Sciences, New Delhi, India., Sood S; Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India., Dhawan B; Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India., Acharya P; Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India., Upadhyay AD; Department of Biostatistics, All India Institute of Medical Sciences, New Delhi, India., Yadav M; Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India., Sharma R; CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India., Bajpai M; Department of Transfusion Medicine, Institute of Liver and Biliary Sciences, New Delhi, India., Gupta S; Department of Dermatology and Venereology, All India Institute of Medical Sciences, New Delhi, India.
Jazyk: angličtina
Zdroj: Journal of the European Academy of Dermatology and Venereology : JEADV [J Eur Acad Dermatol Venereol] 2024 Jun; Vol. 38 (6), pp. 1152-1165. Date of Electronic Publication: 2024 Jan 29.
DOI: 10.1111/jdv.19805
Abstrakt: 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.
(© 2024 European Academy of Dermatology and Venereology.)
Databáze: MEDLINE
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