MOMMI-MP: A Comprehensive Database for Integrated Analysis of Metabolic and Microbiome Profiling of Mouse Pregnancy

Abstract

Pregnancy is a dynamic physiological state characterized by extensive metabolic changes. The development of insulin resistance later in gestation is a normal adaptation that supports fetal growth and a physiological response in pregnancy. However, if metabolic aberrations occur above the normal insulin resistance, gestational diabetes mellitus, a form of diabetes that appears during pregnancy, can develop. Multi-omics approaches are powerful tools to uncover the mechanisms that drive metabolic changes in different physiological and pathological states. A recent multi-omics mouse study collected pregnancy-specific physiological and metabolic profiles, 16S rRNA microbiome, and plasma untargeted LC-MS metabolome data from 3 genetically diverse strains of mice (C57BL/6J, CD1, and NIH-Swiss) over 6 timepoints: gestational days 0, 10, 15, and 19, and postpartum days 3 and 20, totaling 60 samples for each strain. To facilitate the utilization of these impactful data by other researchers, we developed Multi-omics Metabolic & Microbiome Profiling of Mouse Pregnancy (MOMMI-MP), a database that provides an easy-to-use platform to browse and search differentially abundant microbial taxa, metabolites, metabolic pathways, and predicted micro-metabolite interactions using an array of state-of-the-art statistical and machine learning models. Our analysis revealed a previously unrecognized gut microbial–host metabolic pathway involving indoleamine 2,3-dioxygenase 1 (IDO1) and kynurenine, which plays a crucial role in mediating pregnancy-related metabolic adaptations, as well as other significant microbiome and metabolic changes. The computational results are presented in various tables and plots, organized in MOMMI-MP, to empower exploratory analyses by other researchers. Representing a significant new resource, MOMMI-MP provides a tool for researchers to facilitate the investigation of novel mechanisms governing metabolic changes during pregnancy.

Received: 17 August 2025 | Revised: 9 November 2025 | Accepted: 4 January 2026

Conflicts of Interest

The authors declare that they have no conflicts of interest to this work.

Data Availability Statement

The data that support the findings of this study are openly available in the MOMMI-MP database at https://mommi-mp.github.io/Plots/index.html.

Author Contribution Statement

Kaustubh K. Pachpor: Methodology, Software, Validation, Formal analysis, Investigation, Resources, Data curation, Writing – original draft, Visualization. Julianne Jorgensen: Methodology, Formal analysis, Investigation, Resources, Data curation, Writing – review & editing, Visualization. Medha Priyadarshini: Methodology, Validation, Formal analysis, Investigation, Resources, Data curation. Derek J. Reiman: Methodology, Formal analysis, Investigation, Resources, Data curation. Brian T. Layden: Conceptualization, Investigation, Resources, Writing – review & editing, Supervision, Project administration. Yang Dai: Conceptualization, Methodology, Software, Investigation, Resources, Data curation, Writing – review & editing, Supervision, Project administration.