Amelioration of neuroinflammation via modulating microglia is a promising approach for cerebral ischemia therapy. The aim of the present study was to explore gut–brain axis signals in berberine‐modulating microglia polarization following cerebral ischemia. The potential pathway was determined through analyzing the activation of the vagus nerve, hydrogen sulfide (H2S) metabolism, and cysteine persulfides of transient receptor potential vanilloid 1 (TRPV1) receptor. The cerebral microenvironment feature was explored with a metabolomics assay. The data indicated that berberine ameliorated behavioral deficiency in transient middle cerebral artery occlusion rats through modulating microglia polarization and neuroinflammation depending on microbiota. Enhanced vagus nerve activity following berberine treatment was blocked by antibiotic cocktails, capsazepine, or sodium molybdate, respectively. Berberine‐induced H2S production was responsible for vagus nerve stimulation achieved through assimilatory and dissimilatory sulfate reduction with increased synthetic enzymes. Sulfation of the TRPV1 receptor resulted in vagus nerve activation and promoted the c‐fos and ChAT in the nucleus tractus solitaries with berberine. Sphingolipid metabolism is the primary metabolic characteristic with berberine in the cerebral cortex, hippocampus, and cerebral spinal fluid disrupted by antibiotics. Berberine, in conclusion, modulates microglia polarization in a microbiota‐dependent manner. H2S stimulates the vagus nerve through TRPV1 is responsible for the berberine‐induced gut–brain axis signal transmission. Sphingolipid metabolism might mediate the neuroinflammation amelioration following vagus afferent fiber activation.

The brain is the most important organ of mammals. The infinitely complex network of special synaptic connections constitutes the main body of the brain. The neural loop is the basis of brain function. Therefore, revealing the anatomical structure of the cerebral nerve circuit contributes to an in-depth understanding of the mechanism of brain information processing. Visual labeling is a basic approach for analyzing neurons and neural loops. Undoubtedly, The development of modern molecular genetic technologies promotes virus tracer technologies, which triggers the great advance of neural circuit-tracing technology. In this paper, we reviewed the latest development of commonly used neural circuit tracers, and the basic biological characteristics of neurotropic viruses, the genetic modification of virus tracer tools and neural circuit tracking strategies. We aim to introduce novel strategies for brain science research.