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Temporal encoding of bacterial identity and traits in growth dynamics.

Publication ,  Journal Article
Zhang, C; Song, W; Ma, HR; Peng, X; Anderson, DJ; Fowler, VG; Thaden, JT; Xiao, M; You, L
Published in: Proc Natl Acad Sci U S A
August 18, 2020

In biology, it is often critical to determine the identity of an organism and phenotypic traits of interest. Whole-genome sequencing can be useful for this but has limited power for trait prediction. However, we can take advantage of the inherent information content of phenotypes to bypass these limitations. We demonstrate, in clinical and environmental bacterial isolates, that growth dynamics in standardized conditions can differentiate between genotypes, even among strains from the same species. We find that for pairs of isolates, there is little correlation between genetic distance, according to phylogenetic analysis, and phenotypic distance, as determined by growth dynamics. This absence of correlation underscores the challenge in using genomics to infer phenotypes and vice versa. Bypassing this complexity, we show that growth dynamics alone can robustly predict antibiotic responses. These findings are a foundation for a method to identify traits not easily traced to a genetic mechanism.

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Published In

Proc Natl Acad Sci U S A

DOI

EISSN

1091-6490

Publication Date

August 18, 2020

Volume

117

Issue

33

Start / End Page

20202 / 20210

Location

United States

Related Subject Headings

  • Time Factors
  • Species Specificity
  • Polymorphism, Single Nucleotide
  • Gene Expression Regulation, Bacterial
  • Environmental Microbiology
  • Enterobacteriaceae
  • Drug Resistance, Multiple, Bacterial
  • DNA, Bacterial
  • Anti-Bacterial Agents
 

Citation

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Zhang, C., Song, W., Ma, H. R., Peng, X., Anderson, D. J., Fowler, V. G., … You, L. (2020). Temporal encoding of bacterial identity and traits in growth dynamics. Proc Natl Acad Sci U S A, 117(33), 20202–20210. https://doi.org/10.1073/pnas.2008807117
Zhang, Carolyn, Wenchen Song, Helena R. Ma, Xiao Peng, Deverick J. Anderson, Vance G. Fowler, Joshua T. Thaden, Minfeng Xiao, and Lingchong You. “Temporal encoding of bacterial identity and traits in growth dynamics.Proc Natl Acad Sci U S A 117, no. 33 (August 18, 2020): 20202–10. https://doi.org/10.1073/pnas.2008807117.
Zhang C, Song W, Ma HR, Peng X, Anderson DJ, Fowler VG, et al. Temporal encoding of bacterial identity and traits in growth dynamics. Proc Natl Acad Sci U S A. 2020 Aug 18;117(33):20202–10.
Zhang, Carolyn, et al. “Temporal encoding of bacterial identity and traits in growth dynamics.Proc Natl Acad Sci U S A, vol. 117, no. 33, Aug. 2020, pp. 20202–10. Pubmed, doi:10.1073/pnas.2008807117.
Zhang C, Song W, Ma HR, Peng X, Anderson DJ, Fowler VG, Thaden JT, Xiao M, You L. Temporal encoding of bacterial identity and traits in growth dynamics. Proc Natl Acad Sci U S A. 2020 Aug 18;117(33):20202–20210.
Journal cover image

Published In

Proc Natl Acad Sci U S A

DOI

EISSN

1091-6490

Publication Date

August 18, 2020

Volume

117

Issue

33

Start / End Page

20202 / 20210

Location

United States

Related Subject Headings

  • Time Factors
  • Species Specificity
  • Polymorphism, Single Nucleotide
  • Gene Expression Regulation, Bacterial
  • Environmental Microbiology
  • Enterobacteriaceae
  • Drug Resistance, Multiple, Bacterial
  • DNA, Bacterial
  • Anti-Bacterial Agents