Machine learning and the role of the vaginal and fecal microbiome in miscarriage: a matched case-control study

TL;DR

This study explores how the vaginal and fecal microbiome, along with HPV infection, may predict miscarriage risk using machine learning and data from a Swedish cohort.

Contribution

The study introduces machine learning models for predicting miscarriage using microbiome and questionnaire data, highlighting specific microbiome types and HPV as risk factors.

Findings

Non-vaccine type HPV and specific vaginal microbiome types (CST II and CST-IVB) are associated with increased miscarriage risk.

Machine learning models achieved 81-85% accuracy in predicting miscarriage using microbiome and questionnaire data.

Combined data from vaginal and fecal microbiomes did not significantly improve prediction accuracy over individual data sources.

Abstract

Miscarriage occurs in approximately 15% of all pregnancies, and recent studies have suggested a potential role of the microbiome. A nested case-control study from the Swedish Maternal Microbiome cohort was conducted, including 34 participants who sent at least one vaginal or fecal microbiome sample and questionnaire data before miscarrying (n = 34), and matched controls (n = 105 for regression models, n = 27 for machine learning models). Non-vaccine type HPV (aOR 3.95, 95%CI 1.04–15.06) and vaginal microbiome with community state type (CST) II (aOR 6.52, 95%CI 1.58–26.98) or CST-IVB (aOR 4.18, 95%CI 1.08–16.18) in early pregnancy were associated with an increased risk of miscarriage. Furthermore, we explored six machine learning algorithms using 70% of the cohort for training and 30% for testing, for the prediction of miscarriage using vaginal (AUROC 85%), fecal (AUROC 81%) and questionnaire (AUROC 82%) data separately and combined (AUROC 82%). Our results highlight the urgency of HPV screening and vaccine development for women’s reproductive health. Despite limitations, including a small number of miscarriage cases, our results indicate the potential for both vaginal and fecal microbiomes in the prediction of miscarriage.

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