Quantifying and comparing bacterial growth dynamics in multiple metagenomic samples

Nat Methods. 2018 Dec;15(12):1041-1044. doi: 10.1038/s41592-018-0182-0. Epub 2018 Nov 12.


The accurate quantification of microbial growth dynamics for species without complete genome sequences is biologically important, but computationally challenging in metagenomics. Here we present dynamic estimator of microbial communities (DEMIC; https://sourceforge.net/projects/demic/ ), a multi-sample algorithm based on contigs and coverage values, to infer the relative distances of contigs from the replication origin and to accurately compare bacterial growth rates between samples. We demonstrate robust performances of DEMIC for various sample sizes and assembly qualities using multiple synthetic and real datasets.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms*
  • Bacteria / classification
  • Bacteria / genetics*
  • Bacteria / growth & development*
  • Contig Mapping
  • Genome, Bacterial*
  • Metagenomics / methods*
  • Molecular Sequence Annotation
  • Sequence Analysis, DNA / methods*