RAcolony: A Multimodal Platform Integrating Raman Spectroscopy and Automated Imaging for Efficient Construction of Personalized Gut Microbiome Biobanks

Background Gut microbiome biobanks (GMBs) serve as essential repositories for the collection, preservation, and distribution of gut microbial strains. Given that each host harbors a unique microbiome, the establishment of personalized GMBs is critical for advancing the understanding of host-microbiome interactions and the precise management of personal health. However, the construction of such biobanks has been hampered with methods of labor-intensive, low-throughput workflows that often lead to highly redundant colony picking. Results To overcome these limitations, we developed RAcolony, an intelligent and high-throughput colony screening platform that integrates Raman spectroscopy with automated colony imaging for non-destructive, efficient isolation and cultivation of gut microbiota. By prioritizing colonies based on distinct morphological and Raman spectral profiles, the platform significantly reduces redundancy while capturing gut microbial diversity. RAcolony achieves over 90% coverage of species abundance at a redundancy rate of approximately 150%, and enables discriminating colonies at the strain-level, thereby providing high-resolution profiling of gut microbial diversity. We applied RAcolony and constructed 8 personalized GMBs that are totally comprising 167 bacterial species including 27 potential novel taxa. When applied multiple media for cultivation, the personalized GMB covered 80% at species level from an individual fecal sample. Conclusions In conclusion, as a validated and scalable automated platform, RAcolony addresses critical bottlenecks in the construction of personalized GMB and in obtaining gut microbial resources, representing a significant advancement in acquisition of gut microbial diversity.