Microbiome databases are collections of data on microorganism. These are repositories that involve the sequencing resource and metadata of ecological community samples of microorganisms, including both host-associated and environmental microbes. They provide detailed and accurate metadata of these metagenomics samples, as well as gene catalogs for host-associated microbiome.
See also:
What is the difference between microbiota and microbiome?
An NCBI Guide to Finding & Analyzing Metagenomic Data
Microbiome databases are a valuable resource for researchers studying the microbiome. They can be used to identify patterns in the distribution of microorganisms, to study the function of the microbiome, and to identify potential new therapies for diseases that are associated with the microbiome.
There are several different microbiome databases available, each with its own strengths and weaknesses. Hereinbelow is a list of some of the most popular microbiome databases found online.
General microbiome databases
MDB (Microbiome Database) of China National Gene Bank involves the sequencing resource and metadata of ecological community samples of microorganisms, including both host-associated and environmental microbes. This database provides detailed and accurate metadata of these metagenomics samples, as well as gene catalogs for host-associated microbiome, and moreover, well-characterized isolated strains can be found in the database too.
Meta-Storms 2 is the standalone implementation of the Microbiome Search Engine (MSE). MSE is a search engine designed to efficiently search a database of microbiome samples and identify similar samples based on phylogenetic or functional relatedness.
MG-RAST, is a metagenomics analysis server. It provides a wide range of functionalities for analyzing microbiome data, including sequence preprocessing, gene prediction, and functional annotation.
MicrobiomeDB (Microbiome Database), a data-mining platform for interrogating microbiome experiments. This is a comprehensive resource for exploring microbiome data from a variety of studies, including human, animal, and environmental microbiomes. This database provides detailed and accurate metadata of metagenomics samples, as well as gene catalogs for host-associated microbiome. It allows users to search for studies by various criteria, including body site, disease, and treatment.
MSE (Microbiome Search Engine) is a search-able database of microbiome for in-depth data mining of microbial community studies by data integration and data selection. It contains large scale of microbial community samples with sequences, meta-data, and analysis results. Based on the query sample(s), Microbiome Search Engine will provide the matched entry sample(s) in the database with very similar community structures in an ultra-fast speed. In addition, samples in the database can also be sorted, selected, exported and downloaded by their sampling meta-data information.
NMDC (National Microbiome Data Collaborative) supports microbiome multi-omics data exploration and access through an integrated, distributed data framework aligned with the FAIR (Findable, Accessible, Interoperable and Reusable) data principles. The NMDC Data Portal offers download capabilities and several search components.
QIIME 2™ (pronounced as “chime”, originally coined as an acronym for Quantitative Insights Into Microbial Ecology) is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. It is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. QIIME 2 enables researchers to start an analysis with raw DNA sequence data and finish with publication-quality figures and statistical results.
Qiita (pronounced cheetah), a user-friendly platform for sharing, analyzing and visualizing microbiome data. It keeps track of multiple studies with multiple omics data. Additionally, Qiita is capable of supporting multiple analytical pipelines through a 3rd-party plugin system, allowing the user to have a single entry point for all their analyses. Qiita’s main site provides database and compute resources to the global community, alleviating the technical burdens, such as familiarity with the command line or access to compute power, that are typically limiting for researchers studying microbial ecology.
SRA (Sequence Read Archive) data, available through multiple cloud providers and NCBI servers, is the largest publicly available repository of high throughput sequencing data. The archive accepts data from all branches of life as well as metagenomic and environmental surveys. SRA stores raw sequencing data and alignment information to enhance reproducibility and facilitate new discoveries through data analysis.
Human microbiome databases
Disbiome® is a database covering microbial composition changes in different kinds of diseases, managed by Ghent University. Disease names, detection methods or organism names can be used as search queries giving you all information related to the experiment (related disease/bacteria, abundancy subject/control, control type, detection method and related literature).
GMrepo (data repository for Gut Microbiota) is a database of curated and consistently annotated human gut metagenomes. It groups samples/runs according to their associated human phenotypes (i.e., health and diseases).
Gut Microbiome Metabolome Curated Data includes curated data from multiple studies where both metagenomic and metabolomic profiles were obtained from human fecal samples.
GutMeta is a one-stop web server of human gut whole-genome shotgun metagenomics data analysis and visualization with build-in curated processed human gut microbiome database (HGMD).
gutMGene is a comprehensive database for target genes of gut microbes and microbial metabolites. It is a manually curated database that aims at providing a comprehensive resource of target genes of gut microbes and microbial metabolites in humans and mice.
HOMD (Human Oral Microbiome Database) provides comprehensive taxonomic and genomic curated information on bacteria in the human mouth and aerodigestive tract, including the pharynx, nasal passages, sinuses, and esophagus.
HumanMetagenomeDB is a public repository of curated and standardized metadata for human metagenomes. It simplifies the identification and use of public human metagenomes of interest.
HumGut – the healthy human gut genomes is a comprehensive human gut prokaryotic genomes collection filtered by metagenome data.
MetaGeneBank database is a unique bioinformatics resource for whole-genome sequencing metagenomes in human gut. It provides not only raw sequencing files, but also readily usable multiple-level processed data.
MiMeDB (The Human Microbial Metabolome Database) is a freely available, web-enabled database. It is a comprehensive, multi-omic, microbiome resource that connects microbes to microbial genomes, microbial genomes to microbial metabolites, microbial metabolites to the human exposome, and all of these ‘omes’ to human health.
NIH Human Microbiome Project (HMP) Data Analysis and Coordination Center (DACC) and the HMP integrated portal provide access to all publicly available HMP data sets from both phases of the program. The HMP was supported by the National Institutes of Health (NIH) Common Fund from 2007 through 2016. Since the HMP is no longer supported by the Common Fund, the program website is being maintained as an archive and will not be updated on a regular basis.
SKIOME Project is a curated collection of skin microbiome datasets enriched with study-related metadata. It is accompanied by a state-of-the-art analysis of the last 10 years of the skin microbiome field.
Animal metagenome databases
AnimalMetagenome DB current version of the data contains 5 Excel files, which are the metagenome metadata of pigs, horse, bovines, sheep and wild animals.
MMDB (Murine Microbiome Database) contains microbiome taxonomic profiles (MTPs) of the healthy mouse gut with manually curated metadata. This database provides researchers with information about not only which bacterial species are predominant in the specific mouse condition, including types of sampling locations, genotypes or vendors but also which mouse environment harbors high levels of the specific bacteria.
Environmental microbiome databases
Earth Microbiome Project (EMP) is a massively collaborative effort to characterize microbial life on this planet.
FungalRoot database accumulates information about plant mycorrhizal status and root colonization intensity. The current version of the database is published through GBIF (Global Biodiversity Information Facility).
Global ocean microbiome study aims to generate an ocean microbial reference gene catalog.
Global soil microbiomes is a new frontline of biome-ecology research that aimed to define large-scale structure in the diversity of soil microbiomes, pinpoint the environmental drivers shaping it and identify resemblance and mismatch with existing terrestrial biome schemes. It is published through GBIF (Global Biodiversity Information Facility).
MetaSUB (Metagenomics and Metadesign of Subways and Urban Biomes) International Consortium is pioneering an unprecedented study of urban mass-transit systems and cities around the world.
MGnify resource offers an automated pipeline for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all the analyzed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis.
UNITE (User-friendly Nordic ITS Ectomycorrhiza Database) is a fungal database and sequence management environment centered on the eukaryotic nuclear ribosomal ITS (internal transcribed spacer) region.
These are just a few of the many online microbiome databases that are available. The choice of database will depend on the specific research question or application.
See various Databases