Stable isotope labeling of microbial taxa of interest and their sorting provide an efficient and direct way to answer the question “who does what?” in complex microbial communities when coupled with fluorescence in situ hybridization or downstream ‘omics’ analyses. We have developed a platform for automated Raman-based sorting in which optical tweezers and microfluidics are used to sort individual cells of interest from microbial communities on the basis of their Raman spectra. This sorting of cells and their downstream DNA analysis, such as by mini-metagenomics or single-cell genomics, or cultivation permits a direct link to be made between the metabolic roles and the genomes of microbial cells within complex microbial communities, as well as targeted isolation of novel microbes with a specific physiology of interest. We describe a protocol from sample preparation through Raman-activated live cell sorting. Subsequent cultivation of sorted cells is described, whereas downstream DNA analysis involves well-established approaches with abundant methods available in the literature. Compared with manual sorting, this technique provides a substantially higher throughput (up to 500 cells per h). Furthermore, the platform has very high sorting accuracy (98.3 ± 1.7%) and is fully automated, thus avoiding user biases that might accompany manual sorting. We anticipate that this protocol will empower in particular environmental and host-associated microbiome research with a versatile tool to elucidate the metabolic contributions of microbial taxa within their complex communities. After a 1-d preparation of cells, sorting takes on the order of 4 h, depending on the number of cells required.
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The MATLAB code to operate the RACS is included in Supplementary Software 1 and 2 of this paper and is also available from GitHub (https://github.com/harubang2/MATLAB-platform-for-Raman-activated-cell-sorting-RACS).
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We acknowledge support from a US Department of Energy Joint Genome Institute Emerging Technologies Opportunity grant (DE-AC02-05CH11231 to R.S. and M.W.). R.S. acknowledges support from a Gordon and Betty Moore Foundation Marine Microbial 1775 Initiative Investigator Award (GBMF3783), a Gordon and Betty Moore Symbiosis in Aquatic Systems Initiative Investigator Award 1776 (GBMF9197), a grant from the Simons Foundation (542395) as part of the Principles of Microbial Ecosystems (PriME) Collaborative and a grant (#315230_176189) from the Swiss National Science Foundation. F.C.P. and D.B. were supported by the Austrian Science Fund (FWF; P26127-B20 and P27831-B28) and the European Research Council (Starting Grant: FunKeyGut 741623). F.C.P. was also supported by the European Union’s Horizon 2020 Framework Programme for Research and Innovation (grant no.658718). M.P. and M.W. were supported by the European Research Council via the Advanced Grant project NITRICARE 294343 and the FWF Wittgenstein award (to M.W.). L.B. was supported by grants from the Swedish Research Council (2019-04401) and the Science for Life Laboratory. We gratefully acknowledge funding from the European Molecular Biology Organization (EMBO; ALTF 1109-2016) and from the Human Frontier Science Program (HFSP; LT001209/2017) to U.A. We thank Horiba, Renishaw, and Bruker for providing their system specifications. We thank Cetoni for permission to display their software window. We thank R. Naisbit for scientific editing and M. Schmid for help with maintaining the Raman systems at the University of Vienna. We thank the M. Polz group, University of Vienna, Austria, for providing Vibrio alginolyticus 12G01 (wild type; NCBI:txid314288) and Vibrio cyclitrophicus 1F111 (wild type; NCBI:txid1136159). We thank S. Jun’s group, University of California, San Diego, for providing Escherichia coli NCM3722 ∆motA (non-motile mutant).
The authors declare no competing interests.
Peer review information Nature Protocols thanks Wei Huang and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.
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Key references using this protocol
Lee, K. S. et al. Nat. Microbiol. 4, 1035–1048 (2019): https://doi.org/10.1038/s41564-019-0394-9
Pereira, F. C. et al. Nat. Commun. 11, 5104 (2020): https://doi.org/10.1038/s41467-020-18928-1
Supplementary Figs. 1–3.
Supplementary Video 1 . The movie is composed of four sections: (i) visualization of flow in the microfluidic device; (ii) system calibration; (iii) case 1, the process for a captured and selected cell (sorted); and (iv) case 2, the process for a captured and rejected cell (not sorted). In section (i), the two separate flow streams do not interfere with each other–the sample flow traverses the analysis region and exits into the waste outlet by default, whereas the flow carries a cell released at the ‘release location’ (blue box) through the collection outlet. Section (ii) shows the Raman measurement of the working fluid (in the absence of a cell) to be used to calculate the PC values (eqn. (1) in the main text) during the RACS. For sections (iii) and (iv), the left and right panels represent the CCD image (obtained by the lower microscope) and the corresponding operation of the RACS software, respectively. The details of the sorting procedures are described in the lower panel of the movie.
Supplementary Data 1 . The CAD file is provided as a separate supplement, “Supplementary_Data_1.dxf”. Users with access to a cleanroom facility can prepare the device from scratch (i.e., fabrication from a master mold using this photomask design and creation of the PDMS microfluidic device), whereas those who do not have expertise in microfabrication can ask commercial manufacturers to fabricate the master mold and then fabricate the PDMS microfluidic device in their laboratory.
Statistical source data for Supplementary Fig. 2
Statistical source data for Supplementary Fig. 3cd
Supplementary Software 1 . ‘fig’ and ‘m’ files are bound together and thus should be identically named. See ‘README.pdf’ file that accompanies in the same zip file for system requirements and instructions to run this code.
Supplementary Software 2 K-means clustering) algorithm. ‘fig’ and ‘m’ files are bound together and thus should be identically named. See ‘README.pdf’ file that accompanies in the same zip file for system requirements and instructions to run this code.
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Lee, K.S., Pereira, F.C., Palatinszky, M. et al. Optofluidic Raman-activated cell sorting for targeted genome retrieval or cultivation of microbial cells with specific functions. Nat Protoc (2020). https://doi.org/10.1038/s41596-020-00427-8