On Dryad:

16S rRNA gene amplicon sequencing data
Fastq files from S1B-0 to S1E20 are 16S rRNA gene amplicon sequencing data. representing the bacteria composition in human stool samples and related ex vivo communities in fig. S1B, fig. S1D and fig.S1E. Library strategy: AMPLICON, library building type: single, sequencing platform: ILLUMINA, sequencing instrument: Illumina HiSeq 1500.

The metagenomic data of human and animal samples.
Fastq files from 1-1 to A6-6 are the metagenomic data including 57 human stool samples and 36 mouse faces samples. The human samples ID (1-57) correspond to the ID in supplementary table 4. The mouse samples (A1-1 to 16-6) were fecal microbiota transplant experiments in fig. S12 D to F. Each sample contains two sequencing data from paired-end sequencing. Library strategy: METAGENOMIC, library building type: paired, sequencing platform: ILLUMINA, sequencing instrument: Illumina HiSeq 1500.

On Zenodo:

Source data of Figure 1-6 and supplementary figure 1-21.
The source data are presented in 27 separate Excel files and each sheet represent one panel of each figure.

Phylo-tree
Phylo-tree is the raw data of phylogenetic analysis of microbial DPP4 protein sequences in fig. S4C.

Supplementary methods
Supplementary methods file is the process for isoenzyme activity detection, related to Fig 1.