This Collection welcomes manuscripts that advance the scientific understanding of probiotics, prebiotics, synbiotics, postbiotics and functional foods. Emphasis is placed on strain-level characterization, comparative genomics, safety and biosafety assessment, microbial physiology, fermentation biology, and the ecological and mechanistic bases of host-microbe interactions. Submissions that bridge laboratory microbiology with functional outcomes are encouraged, including work that links specific microbial traits – such as adhesion, metabolite secretion, biofilm formation, stress tolerance, surface architecture, antimicrobial resistance determinants, mobile genetic elements and virulence-associated features – to defined effects on gastrointestinal barrier integrity, mucosal immunity, short-chain fatty acid generation and modulation of the resident microbiota.

The Collection also aims to spotlight methodological advances reshaping the field, including multi-omics profiling (metagenomics, metabolomics, proteomics), genome mining and in silico screening for novel biotic entities, extracellular vesicle biology, and the discovery of exopolysaccharides, bacteriocins and bioactive peptides produced by lactic acid bacteria and related taxa. Translational contributions are welcomed across food fermentation and reformulation, encapsulation and delivery matrices, gut–organ axes, companion-animal nutrition, and plant-associated beneficial microbes. The collection further encourages submissions addressing regulatory frameworks, quality control standards, clinical validation strategies and the translational challenges associated with next-generation probiotics and microbiome-driven interventions.

Topics of interest include, but are not limited to:

• Strain characterization: Taxonomy, comparative genomics and safety assessment of candidate probiotic, starter and adjunct strains.
• Host-microbe mechanisms: Adhesion, colonization, signaling and immunomodulatory pathways connecting microorganisms to mucosal and systemic physiology.
• Postbiotics and novel biotics: Heat-inactivated cells, cell-free supernatants, lysates, extracellular vesicles and defined microbial metabolites as functional entities.
• Fermentation science: Microbial ecology of dairy, plant-based and traditional fermentations and the bioactive compounds generated through biotransformation.
• Delivery and viability: Encapsulation chemistry, matrix design and processing strategies that preserve microbial viability and activity through shelf life and gastrointestinal transit.
• Gut barrier and metabolism: Generation of short-chain fatty acids and other metabolites, tight-junction control, and microbial modulation of lipid and glucose homeostasis.
• Gut–organ axes: Microbial contributions to the gut-brain, gut-liver and gut-skin axes, including psychobiotic candidates and neuroactive metabolites.
• Animal and plant microbiomes: Beneficial microbes for companion-animal nutrition and feed and nutritional applications, as well as plant probiotics, biocontrol agents and plant growth-promoting microorganisms.

This Collection supports and amplifies research related to SDG 2 (Zero Hunger) and SDG 3 (Good Health and Well-being).