On September 26, 2022, the team of Professor Chaoyong Yang and Associate Researcher Wei Wang from the Institute of Molecular Medicine, Shanghai Jiao Tong University School of Medicine, applied the core products of HOOKE INSTRUMENTS— S3000 ultra-fast three-dimensional fluorescence imaging system and PRECI SCS, It was published in the journal mLife under the title "Integrated identification of growth pattern and taxon of bacterium in gut microbiota via confocal" fluorescence imaging oriented single‐cell sequencing "paper. The first authors of the paper are Dr. Juan Gao and Dr. Di Sun. In this study, confocal fluorescence imaging technology was combined with single-cell sorting and sequencing to directly sort and sequence the bacteria of interest that presented specific fluorescence information under confocal, so as to obtain their taxonomic information, and realize the "you can know it when you see it" of complex bacterial samples.

Abstract

Despite the fast progress in our understanding of the complex functions of gut microbiota, it is still challenging to directly investigate the in vivo microbial activities and processes on an individual cell basis. To gain knowledge of the indigenous growth/division patterns of the diverse mouse gut bacteria with a relatively high throughput, here, we propose an integrative strategy, which combines the use of fluorescent probe labeling, confocal imaging with single-cell sorting, and sequencing. Mouse gut bacteria sequentially labeled by two fluorescent d-amino acid probes in vivo were first imaged by confocal microscopy to visualize their growth patterns, which can be unveiled by the distribution of the two fluorescence signals on each bacterium. Bacterial cells of interest on the imaging slide were then sorted using a laser ejection equipment, and the collected cells were then sequenced individually to identify their taxa. Our strategy allows integrated acquirement of the growth pattern knowledge of a variety of gut bacteria and their genomic information on a single-cell basis, which should also have great potential in studying many other complex bacterial systems.

The paper links：

https://onlinelibrary.wiley.com/doi/full/10.1002/mlf2.12041