MetagenomeSeq is designed to assess differential abundance in sparse high-throughput microbial marker-gene survey data. It uses a combination of Cumulative Sum Scaling (CSS) normalization with zero-inflated Gaussian distribution mixture or zero-inflated Log-Normal mixture model that accounts for undersampling in large-scale marker-gene studies.
For more details about its implementation please refer to the original paper by Joseph N. Paulson et al..