The α7 subtype of the nicotinic acetylcholine receptor (α7 nAChR: coded by Chrna7) is known to regulate the cholinergic ascending anti-inflammatory pathway. We previously reported that Chrna7 knock-out (KO) mice show depression-like behaviors through abnormal composition of gut microbiota and systemic inflammation. Given the role of subdiaphragmatic vagus nerve in gut-microbiota-brain axis, we investigated whether subdiaphragmatic vagotomy (SDV) could affect depression-like behaviors, abnormal composition of gut microbiota, and microbes-derived metabolites in Chrna7 KO mice. SDV blocked depression-like behaviors and reduced expression of synaptic proteins in the medial prefrontal cortex (mPFC) of Chrna7 KO mice. LEfSe (linear discriminant analysis effect size) analysis revealed that the species Lactobacillus sp. BL302, the species Lactobacillus hominis, and the species Lactobacillus reuteri, were identified as potential microbial markers in the KO + SDV group. There were several genus and species altered among the three groups [wild-type (WT) + sham group, KO + sham group, KO + SDV group]. Furthermore, there were several plasma metabolites altered among the three groups. Moreover, there were correlations between relative abundance of several microbiome and behavioral data (or synaptic proteins). Network analysis showed correlations between relative abundance of several microbiome and plasma metabolites (or behavioral data). These data suggest that Chrna7 KO mice produce depression-like behaviors and reduced expression of synaptic proteins in the mPFC through gut-microbiota-brain axis via subdiaphragmatic vagus nerve.