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.