The DOI matches its Crossref record; 38 of the 38 references it cites were found in a registry or an index.
Systems-level analysis of microbial community organization through combinatorial labeling and spectral imaging
Open accessAbstract
Microbes in nature frequently function as members of complex multitaxon communities, but the structural organization of these communities at the micrometer level is poorly understood because of limitations in labeling and imaging technology. We report here a combinatorial labeling strategy coupled with spectral image acquisition and analysis that greatly expands the number of fluorescent signatures distinguishable in a single image. As an imaging proof of principle, we first demonstrated visualization of Escherichia coli labeled by fluorescence in situ hybridization (FISH) with 28 different binary combinations of eight fluorophores. As a biological proof of principle, we then applied this Combinatorial Labeling and Spectral Imaging FISH (CLASI-FISH) strategy using genus- and family-specific probes to visualize simultaneously and differentiate 15 different phylotypes in an artificial mixture of laboratory-grown microbes. We then illustrated the utility of our method for the structural analysis of a natural microbial community, namely, human dental plaque, a microbial biofilm. We demonstrate that 15 taxa in the plaque community can be imaged simultaneously and analyzed and that this community was dominated by early colonizers, including species of Streptococcus , Prevotella , Actinomyces , and Veillonella . Proximity analysis was used to determine the frequency of inter- and intrataxon cell-to-cell associations which revealed statistically significant intertaxon pairings. Cells of the genera Prevotella and Actinomyces showed the most interspecies associations, suggesting a central role for these genera in establishing and maintaining biofilm complexity. The results provide an initial systems-level structural analysis of biofilm organization.
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Cites
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Self-citationBacterial competition: surviving and thriving in the microbial jungle
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Cited by
Davis, N. M., Proctor, D. M., Holmes, S. P., Relman, D. A., & Callahan, B. J. (2018) · Microbiome · doi:10.1186/s40168-018-0605-2 · Cited by 3,493
Human nutrition, the gut microbiome and the immune system
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The Oral Microbiota: Dynamic Communities and Host Interactions
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Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution
Chen, B.-C., Legant, W. R., Wang, K., Shao, L., Milkie, D. E., Davidson, M. W., Janetopoulos, C., Wu, X. S., Hammer, J. A., Liu, Z., et al. (2014) · Science · doi:10.1126/science.1257998 · Cited by 1,919
Applying systems-level spectral imaging and analysis to reveal the organelle interactome
Valm, A. M., Cohen, S., Legant, W. R., Melunis, J., Hershberg, U., Wait, E., Cohen, A. R., Davidson, M. W., Betzig, E., & Lippincott-Schwartz, J. (2017) · Nature · doi:10.1038/nature22369 · Cited by 1,113
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Metadata
- Authors
- Valm, A. M., Welch, J. L. M., Rieken, C. W., Hasegawa, Y., Sogin, M. L., Oldenbourg, R., Dewhirst, F. E., & Borisy, G. G.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2011-02-16
- Volume
- 108
- Issue
- 10
- Pages
- 4152-4157
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2053830048
- Cited by
- 344
- References
- 38
- FWCI
- 7.64
- Type
- journal article
- Language
- en
- Open access
- green
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