Topic: Probiotics–Gut Microbiome Interactions: From Mechanisms to Health Outcomes

Interactions between probiotics and the gut microbiome represent a dynamic component of host–microbe relationships that contribute to intestinal and systemic homeostasis. Probiotics can modulate indigenous microbial communities through microbial competition, metabolite production, community restructuring, and host–microbe signaling, thereby influencing microbial stability, intestinal barrier integrity, and immune and metabolic functions. However, probiotic effects are highly strain-specific and can be shaped by the composition of the gut microbiome, dietary factors, and host characteristics. These complex and context-dependent interactions highlight the importance of understanding probiotics within the broader ecological landscape of the gut microbiome and their implications for host health.

This Special Issue aims to bring together cutting-edge research on the mechanistic and causal basis of probiotic–gut microbiome interactions. Particular emphasis will be placed on strain-specific interactions with resident microbial communities, ecological and metabolic mechanisms, microbial networks, metabolite exchange, and host–microbiome signaling. Studies investigating probiotic-derived or probiotic-modulated metabolites, microbial cross-feeding, and causal links between microbial interactions and host phenotypes are especially encouraged. Research employing experimental perturbation, gnotobiotic or defined microbial communities, multi-omics, metabolomics, and microbial genetics to dissect mechanisms and establish causality is also welcomed. This Special Issue seeks to advance mechanistic understanding of how probiotics function within the gut microbiome and how these interactions translate into specific host outcomes.

Topics of interest include, but are not limited to:

● Strain-specific probiotic–gut microbiome interactions;

● Molecular and cellular mechanisms governing probiotic–microbe interactions;

● Probiotic colonization, persistence, niche occupation, and microbial competition;

● Probiotic-mediated remodeling of microbial communities and functional networks;

● Probiotic-derived and probiotic-modulated metabolites;

● Mechanistic links between probiotic–microbiome interactions and host signaling;

● Causal relationships between probiotic-induced microbial changes and host phenotypes;

● Experimental and computational approaches for dissecting probiotic–microbiome interactions.