Gut Microbes Libraries: A Key Resource for Current Gut Microbiome Research

Complex microbial communities shape the dynamics of the human gut, influencing digestion, immunity, and overall health. Advances in DNA sequencing, multi-omics technologies, and data analysis have significantly improved micro-biome studies by enhancing taxonomic resolution and controlling false discovery rates. However, a major limitation remains—the lack of a cultured, representative library of human gut microbes. Existing isolate and genome collections are still limited, especially in strain-level diversity, for most microbes in the human gut. Notably, over 70% of species in the Unified Human Gastrointestinal Genome (UHGG) collection lack cultured representatives. This unknown microbial ‘dark matter’ significantly limits our understanding of the functions of the gut micro-biome and its host interactions. To advance our knowledge of the gut micro-biome through proof-of-concept research that satisfies Koch’s postulates and supports mechanistic investigations, establishing a comprehensive gut microbe library is essential. However, the scarcity of pure gut microbe cultures worldwide makes constructing a comprehensive gut microbe library challenging. Here we discuss the importance of constructing a comprehensive gut microbial library. It outlines key challenges in establishing a gut microbe library, including sample col-lection, culture media, and long-term storage. Additionally, it explores the potential applications of a comprehensive gut microbe library in microbiome research.