A cursory google search suggests that cohabitating couples converge on the same gut biome among various other things like good habits but also bad habits.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6458105/

The paper also points out that because of all the concordances, couples tend to share the same downfalls, not just the good things: disease risks, bad diet, bad sleep, emotional turmoil.

Seems to defeat your theory.