Microbial single-cell omics in situ

Abstract Metagenomics has enabled understanding of the microbial composition and functional potential in various environments. Using Laser-Induced Forward Transfer (LIFT) technology, we report high-quality microbial single-cell genome or transcriptome in complex samples such as saliva, mouse gut and human tumor sections. Neighboring cells could be separately retrieved and bacteria could be fluorescently labelled. We illustrate cell-fate commitment with sporulation. The method is scalable and precise, and would empower fundamental insight for microbial populations and single-cell interactions with the host. Competing Interest Statement The authors have declared no competing interest. Footnotes 1.Technical details including laser parameters (e.g., wavelength, pulse width, fluence), LIFT chip configuration, laser transfer setup and process parametric windows have been illustrated in Sup. Fig.1, Sup. Fig.5 and Method. 2.For physical conditions during LIFT, we have explored the impact of laser energy on cell ejection and described the configuration of LIFT chip. We have demonstrated that the cells retain viability after LIFT ejection and can be cultured. 3.To demonstrate scalability and accuracy of LIFT, we have performed LIFT ejection across different biological settings including isolating single cells of a known strain mixed with few species guided by fluorescent- and automated- modality as well as mouse colon sample. 4.For method transparency, we have supplemented the critical technical details and demonstrated the LIFT process through videos.