Spatial transcriptomics of planktonic and sessile bacterial populations at single-cell resolution
- Creators
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Dar, Daniel
- Dar, Nina
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Cai, Long
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Newman, Dianne K.
Abstract
Within any community of organisms, gene expression is heterogeneous, which can manifest in genetically identical individuals having a different phenotype. One has to look at individuals in context and analyze patterns in both space and time to see the full picture. Aiming to fill a gap in current methods, Dar et al. developed a transcriptome-imaging method named parallel sequential fluorescence in situ hybridization (par-seqFISH). They applied this technique to the opportunistic pathogen Pseudomonas aeruginosa, focusing on biofilms where growth conditions can change at microscopic scale. Development of these communities, as revealed by mRNA composition, were followed in space and time. The results revealed a heterogeneous phenotypic landscape, with oxygen availability shaping the metabolism at a spatial scale of microns within a single contiguous biofilm segment. This tool should be applicable to complex microbial communities in the environment and the human microbiome.
Additional Information
© 2021 American Association for the Advancement of Science. Received 12 March 2021; accepted 25 June 2021. We thank G. A. O'Toole and M. Whiteley for help with designing the gene set, M. Bergkessel and R. Sorek for critically reading the manuscript, and members of the Newman laboratory for critically reading the manuscript and for fruitful discussions and comments, particularly M. Bergkessel for assistance with RNA-Seq analysis. This work was supported by the National Institutes of Health (grants 1R01AI127850-01A1 and 1R01HL152190-01 to D.K.N.) and the Army Research Office (grant W911NF-17-1-0024 to D.K.N.). L.C. was supported by the Allen Frontier group. D.D. was supported by the Rothschild foundation, EMBO Long-Term, and Helen Hay Whitney postdoctoral fellowships, as well as a Geobiology Postdoctoral Fellowship from the Division of Geological and Planetary Sciences, Caltech. Author contributions: D.D., N.D., L.C., and D.K.N. designed the study. D.D. led the study, designed the experiments, and performed the experiments with N.D. D.D. analyzed the data. D.K.N. and L.C. supervised the study. All authors contributed to writing the manuscript. Competing interests: L.C. is a cofounder of Spatial Genomics, Inc. A provisional patent (No. 63/153,234) has been filed by California Institute of Technology with inventors Daniel Dar, Dianne K. Newman, Kirsten Frieda, and Long Cai entitled "Multiplexing of experimental conditions and samples in spatial genomics." Data and materials availability: Custom MATLAB scripts and single-cell source data from this study are available at Zenodo (105). Imaging data obtained during this study have also been deposited at Zenodo (106). All other data are presented in the main text or the supplementary materials.Attached Files
Submitted - 2021.02.24.432792v1.full.pdf
Supplemental Material - abi4882-Dar-SM-Reproducibility_Checklist.pdf
Supplemental Material - abi4882-Dar-SM.pdf
Supplemental Material - science.abi4882_sm_table_s2.zip
Files
Additional details
- Alternative title
- In situ single-cell activities of microbial populations revealed by spatial transcriptomics
- PMCID
- PMC8454218
- Eprint ID
- 108227
- Resolver ID
- CaltechAUTHORS:20210226-074209469
- 1R01AI127850-01A1
- NIH
- 1R01HL152190-01
- NIH
- W911NF-17-1-0024
- Army Research Office (ARO)
- Allen Frontier Group
- Rothschild Foundation
- European Molecular Biology Organization (EMBO)
- Helen Hay Whitney Foundation
- Caltech Division of Geological and Planetary Sciences
- Created
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2021-02-26Created from EPrint's datestamp field
- Updated
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2021-10-04Created from EPrint's last_modified field
- Caltech groups
- Division of Geological and Planetary Sciences, Division of Biology and Biological Engineering, Division of Biology and Biological Engineering