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Robust estimation of bacterial cell count from optical density

Beal, Jacob and Farny, Natalie G. and Haddock-Angelli, Traci and Selvarajah, Vinoo and Baldwin, Geoff S. and Buckley-Taylor, Russell and Gershater, Markus and Kiga, Daisuke and Marken, John and Sanchania, Vishal and Sison, Abigail and Workman, Christopher T. (2019) Robust estimation of bacterial cell count from optical density. Communications Biology, 3 . Art. No. 512. ISSN 2399-3642. https://resolver.caltech.edu/CaltechAUTHORS:20191014-134916544

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Abstract

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1038/s42003-020-01127-5DOIArticle
https://doi.org/10.1101/803239DOIDiscussion Paper
ORCID:
AuthorORCID
Beal, Jacob0000-0002-1663-5102
Farny, Natalie G.0000-0003-1143-4560
Haddock-Angelli, Traci0000-0002-0683-807X
Baldwin, Geoff S.0000-0003-4800-023X
Marken, John0000-0001-9696-088X
Workman, Christopher T.0000-0002-2210-3743
Additional Information:© The Author(s) 2020. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. Received 24 October 2019; Accepted 03 July 2020; Published 17 September 2020. Partial support for this work was provided by NSF Expeditions in Computing Program Award #1522074 as part of the Living Computing Project, and by the Engineering and Physical Sciences Research Council [EP/R034915/1] and EU H2020 [820699]. This document does not contain technology or technical data controlled under either the U.S. International Traffic in Arms Regulations or the U.S. Export Administration Regulations. Data availability: All data generated or analyzed during this study are included in this published article (and its Supplementary Information files). Author Contributions: Conceptualization: J.B., N.G.F., T.H-A., V.S.-1, G.S.B., R.B-T., M.G., D.K., J.M., and C.T.W. Data curation: J.B., N.G.F., T.H-A., and V.S.-1. Formal analysis: J.B. Investigation: Experimental data gathered by iGEM Interlab Study Contributors Methodology: J.B., N.G.F., T.H-A., V.S.-1, G.S.B., R.B-T., M.G., D.K., J.M., V.S.-2, A.S., and C.T.W. Project administration: J.B., N.G.F., and T.H-A. Resources: T.H-A., V.S.-1, and A.S. Software: J.B. Writing (original draft): J.B. and N.G.F. Writing (review & editing): J.B., N.G.F., T.H-A., G.S.B., J.M., C.T.W., and V.S.-2. The authors declare no competing interests.
Funders:
Funding AgencyGrant Number
NSFCCF-1522074
Engineering and Physical Sciences Research Council (EPSRC)EP/R034915/1
European Research Council (ERC)820699
Subject Keywords:Biological techniques; Data acquisition
Record Number:CaltechAUTHORS:20191014-134916544
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20191014-134916544
Official Citation:Beal, J., Farny, N.G., Haddock-Angelli, T. et al. Robust estimation of bacterial cell count from optical density. Commun Biol 3, 512 (2020). https://doi.org/10.1038/s42003-020-01127-5
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:99256
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:14 Oct 2019 21:06
Last Modified:21 Sep 2020 22:48

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