Gastrointestinal disease is characterized by gastrointestinal dysfunction with dysbiosis of the microbiome. Probiotics may act as biological agents in treating gastrointestinal diseases through modifying gut microbiota. However, several challenges, including safety, stress resistance, postcolonization quantification, and evaluation models, may hinder the application of probiotics in gastrointestinal diseases. This review introduces the emerging methods for delivering probiotics as well as available materials. Furthermore, we elucidated bacteriocins and their role in helping probiotics obtain a competitive advantage over other strains and challenges of large-scale application. Bacteriocins produced by probiotics also showed promising efficacy in gastrointestinal diseases including the capacity of immune stimulation, intestinal barrier protection, and cytotoxicity against intestinal tumorigenesis. For the quantification of probiotics in complex microbiomes and evaluation methods of probiotic encapsulated delivery systems, recent fluorescent labeling technology and various in vitro and in vivo models were also reviewed. Given the widespread use of probiotic agents in the microecological therapy of gastrointestinal diseases, further understanding of the multiple challenges of probiotic application and the updated methods to improve the colonization and evaluation system of probiotics is of great significance for probiotics as live biotherapeutics.

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