Integrating Microbial Genomics and Neurotranscriptomics to Understand the Impact of Probiotic Strains on Neurological Health

Xiaolan JinHuaying CaiZhengwei Li^*

• affiliated with Zhejiang University School of Medicine, Hangzhou, China

Background: The gut–brain axis is increasingly recognized as a key regulator of neurological health, with microbial metabolites influencing neurotransmission, synaptic plasticity, and neuroinflammation. Probiotics such as Lactobacillus rhamnosus GG and Bifidobacterium longum 1714 have been associated with neuroactive effects, yet the molecular mechanisms linking microbial genomic potential to host neuronal responses remain poorly defined. Objective: This study aimed to integrate microbial genomics, neurotranscriptomics, and in vitro validation to unravel the neuromodulatory effects of L. rhamnosus GG and B. longum 1714. Methods: Whole-genome functional annotation, metabolic pathway prediction, and biosynthetic gene cluster analysis were performed to identify neuroactive potential. Neuronal RNA-seq datasets (n = 3 biological replicates per condition) were analyzed using differential expression, WGCNA, and GSEA to capture transcriptomic responses. Multi-omics integration (CCA, DIABLO, SPIEC-EASI) linked microbial pathways with neuronal gene modules. In vitro assays using SH-SY5Y and iPSC-derived neurons validated predictions through measurements of cell viability, oxidative stress, neurotransmitter release (ELISA), qPCR of synaptic and inflammatory genes, and extracellular vesicle characterization including EV transcript profiling. Results: Genomic analysis revealed that L. rhamnosus GG was enriched in γ-aminobutyric acid (GABA) and SCFA pathways, while B. longum 1714 carried tryptophan–indole metabolism genes. Transcriptomic profiling demonstrated upregulation of synaptic genes (BDNF, SYN1), showed upregulation of synaptic genes (BDNF, SYN1), serotonergic transporters (SLC6A4, TPH2), and suppression of inflammatory mediators (IL-6, TNF-α). Integration analyses identified two major subnetworks: a "neurotransmission module" driven by L. rhamnosus GG and a "serotonin–immune module" driven by B. longum 1714. In vitro validation confirmed increased GABA (1.7-fold) and serotonin (1.5-fold) release, reduced ROS (–18 to –22%), and EV transcript enrichment for synaptic and anti-inflammatory markers. Conclusion: This multi-omics study demonstrates mechanistic evidence that probiotics exert complementary neuromodulatory effects: L. rhamnosus GG primarily enhances GABAergic and SCFA-mediated synaptic pathways, whereas B. longum 1714 regulates the tryptophan–serotonin– immune axis. Together, these findings support the therapeutic potential of precision probiotics for neurological health and establish a systems-level framework for probing host–microbe interactions.