Chronic stress remodels gut bacterial ecology and polysaccharide metabolism with neuroendocrine consequences despite unchanged behavior

The gut-microbiome-brain axis (GMBA) links the gut and brain through metabolic, immunological, and neuroendocrine pathways, and can become dysregulated during psychological stress (PS). While previous studies primarily infer microbial function and use physical stressors that incompletely model human PS, here, functional multi-omics was applied to a chronic social-isolation mouse model. Although isolation caused no measurable behavioral changes, brain proteomics revealed stress-associated molecular responses. Taxonomic and short-chain fatty acid analyses suggested limited microbiome changes; however, metaproteomics uncovered sex-specific restructuring of bacterial ecology and carbohydrate-active enzymes. In females, isolation increased Petralouisia muris proteins involved in bacterial microcompartment metabolism and β-glucuronidases across Lachnospiraceae taxa. Enriched β-glucuronidase abundance coincided with reduced circulating glucuronides and altered brain estrogen-receptor activity, suggesting a microbial deconjugation-host estrogen-signaling interaction. These findings demonstrate that functional GMBA alterations may precede or occur independently of overt behavioral phenotypes and highlight the value of direct functional profiling in PS.