*This archive contains code for analyses and necessary additional files in our manuscript* Additional file 2.xlsx: Reference list of datasets included in this study All public raw sequences and metadatas can be accessed through the Additional file 2 ChinaMetadata.xlsx: Metadata for the dataset from Wenzhou, China in this study Enterotypes_tutorial.sanger.R: Code for enterotype clustering MetaHIT_SangerSamples.genus.txt: An example test data for enterotype clustering MarkovChain.R: Code for calcualting transition probability and Markov chain MarkovList.txt: Data for Markov chain