Signals of microbial growth learned from single amplicon samples

Irregularities in metagenomic whole-genome shotgun (WGS) read coverage can arise in quickly replicating microbial populations. These irregularities, summarized as peak-to-trough ratios (PTRs), are correlated with growth rates. This study seeks to explore the presence of similar coverage irregularities in 16S amplicon datasets, where multicopy diverged 16S genes provide an opportunity to explore coverage at different positions on the bacterial chromosome. To this end, we propose a model of Operational Taxonomic Unit (OTU) observations under replication and sequence similarity, from which we derive a method for simultaneous copy number correction and dynamics estimation by gradient descent. We conduct a series of benchmarks on synthetic data, determining a set of heuristics for when such methods may be applied, and compare our method with WGS-based methods on a real dataset. We find no correlation between coPTR estimates and our method, suggesting further modifications to our method may be required.