Reference-based Enterotype Classification Tool

Enterotypes describe clustering patterns across samples from the human intestinal microbiome that are associated with disease, medication, diet, and lifestyle. The Enterotyper is a computational tool designed for the scientific community to classify human fecal metagenomes into established enterotypes. Using a robust XGboost machine learning model, this tool provides accurate enterotype classification based on a large global dataset of fecal metagenomes.

Step 1: Upload a taxonomic profile.

Step 2: Choose the enterotype model.
PAM clustering Fuzzy clustering

Step 3: Choose number of enterotypes.
2 3 4

Predict Show example

Please cite when you use Enterotyper: Keller et al.

Usage

Input

Please upload a taxonomic profile generated either by one of the following taxonomic profiler:

• mOTUs
• MetaPhlAn
• Kraken
• Kraken2
• Bracken
• Kaiju
• Krakenuniq

Alternatively, you can also upload a GTDB taxonomic profile at genus level with genera as rownames and sample names as columns. An example file is shown here.

Output

• EnterotypeAssignment_EnterotypeModel.tsv contains the enterotype classification. In case of FKM clustering, a classification strength for each enterotype for each sample is also reported. The enterotype with the highest classification strength determines the hard classification. In addition, the Enterotype Dysbiosis Score, which is the inverted, z-score normalised and scaled between 0 and 1 maximum classification strength, is reported in the FKM 3-enterotype model.
• GTDB_genus_level_taxonomy.tsv contains the GTD genus-level taxonomy profiles for the uploaded data which is used as a basis for the Enterotyper.
• Visualizations displayed on the web page for a first assessment of the predicted enterotype classification of the input data and comparison with the enterotype landscape in the global dataset used to build the Enterotyper.