Our results support genome reconstruction as a robust process and suggest that reconstructions determined to be >90% complete are likely to effectively represent organismal function; however, population-level genotypic heterogeneity in natural populations, such as uneven distribution of plasmids, can lead to incorrect inferences.
Recommended citation: Nelson WC, Tully BJ, Mobberley JM. 2020. Biases in genome reconstruction from metagenomic data. PeerJ 8:e10119 https://doi.org/10.7717/peerj.10119