Analysis of Couples’ Microbiomes and Health Outcomes v1

Background: Cohabiting partners share more similar microbiomes across gut, oral, skin, and genital sites than unrelated individuals, with metagenomic studies demonstrating measurable strain sharing (median ~12% gut; ~32% oral) and convergence that scales with duration of cohabitation. This “social microbiome” may influence reproductive, metabolic, and child health outcomes. Objective: In-silico workflow for exploratory, couple-level, multi-site microbiome analysis using only public datasets (shotgun metagenomics, 16S supported), with emphasis on strain-resolved transmission, functional convergence, and associations with fertility, pregnancy, fetal development, and child health. Methods: We harmonize public multi-site datasets with identifiable partner/household links (e.g., gut, oral, skin, genital) and rich metadata. Amplicon reads are reprocessed with a uniform QIIME 2/DADA2 pipeline; metagenomes undergo host depletion, species profiling (MetaPhlAn 4), and pathway profiling (HUMAnN 3). Strain sharing is quantified with StrainPhlAn/inStrain across prioritized taxa using stringent ANI/breadth thresholds to reduce false positives. Dyadic analytics include partner-vs-non-partner beta-diversity contrasts, permutation tests, mixed-effects models, and actor-partner interdependence models; functional similarity and resistomes are compared within couples; transmission and cross-site co-occurrence networks are reconstructed. Outcome-linked analyses integrate fertility and perinatal phenotypes when available. Expected results: We anticipate (i) elevated partner similarity and strain sharing in gut and oral microbiomes; (ii) strong partner convergence on skin and measurable oral transfer tied to intimate behaviors and (iii) couple-level functional convergence, with exploratory links to reproductive and family health. Significance: This protocol operationalizes a reproducible framework to study the couple as the analytical unit-advancing hypotheses on person-to-person microbial transmission, co-adaptation, and their relevance for preconception care, BV recurrence prevention, fertility optimization, and early-life microbiome seeding.