Table 3 List of the representative databases with potential for application of the machine learning in microbiome field

BacDive

https://bacdive.dsmz.de/

BacDive offers data on 81,827 bacterial and archaeal strains, including 14,091 type strains and thereby covers approx. 90% of the validly described species

Gold

https://gold.jgi.doe.gov/

Gold is a World Wide Web resource for comprehensive access to information regarding genome and metagenome sequencing projects, and their associated metadata

NCBI Microbial Genomes

https://www.ncbi.nlm.nih.gov/genome/microbes/

Microbial Genomes resource presents public data from prokaryotic genome sequencing projects

EnsemblBacteria

http://bacteria.ensembl.org/index.html

Ensembl Bacteria is a browser for bacterial and archaeal genomes

European Nucleotide Archive

https://www.ebi.ac.uk/ena/browser/home

The European Nucleotide Archive (ENA) provides a comprehensive record of the world’s nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation

DrugBank

https://go.drugbank.com/

DrugBank, the world's most comprehensive and structured drug and molecular drug information resource

Super Natural

http://bioinf-applied.charite.de/supernatural_new/index.php?site=home

Super Natural II, a database of natural products. It contains 325,508 natural compounds (NCs), including information about the corresponding 2d structures, physicochemical properties, predicted toxicity class and potential vendors

ChEMBL

https://www.ebi.ac.uk/chembl/

ChEMBL is a manually curated database of bioactive molecules with drug-like properties

ChemSpider

http://www.chemspider.com/

ChemSpider is a free chemical structure database providing fast text and structure search access to over 100 million structures from hundreds of data sources

BindingDB

http://www.bindingdb.org/bind/index.jsp

BindingDB is a public, web-accessible database of measured binding affinities. BindingDB contains 41,328 Entries, each with a DOI, containing 2,259,122 binding data for 8,516 protein targets and 977,487 small molecules

MicrobiomeDB

https://microbiomedb.org/mbio/app/

A data-mining platform for interrogating microbiome experiments

UniProt

https://www.uniprot.org/

UniProt provides the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information

Virtual Metabolic Human

https://www.vmh.life/#home

The VMH database captures information on human and gut microbial metabolism and links this information to hundreds of diseases and nutritional data

Disbiome

https://disbiome.ugent.be/home

Disbiome® is a database covering microbial composition changes in different kinds of diseases, managed by Ghent University

eHOMD

http://www.homd.org/

eHOMD provides comprehensive curated information on the bacterial species present in the human aerodigestive tract (ADT), which encompasses the upper digestive and upper respiratory tracts, including the oral cavity, pharynx, nasal passages, sinuses and esophagus

HMDB

https://hmdb.ca/

The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body

MDB

https://db.cngb.org/microbiome/

Microbiome database involves the sequencing resource and metadata of ecological community samples of microorganisms, including both host-associated or environmental microbes

MGnify

https://www.ebi.ac.uk/metagenomics/

MGnify provides amplicon, assemblies,metabarcoding, metagenomes and metatranscriptomes data on human and environmental biomes

Human Microbiome Project

https://www.hmpdacc.org/

Genomic characterization of microbiota at five body sites (HMP1), and information on microbiota-human interactions in disease (iHMP)