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Bacteria: 2706 Genomes
Archaea: 112 Genomes
Taxonomy Correction Info

Highlighted Clades

(Commonly Found in Human Microbiome)

Airways Nares
Corynebacterium accolens
Propionibacterium acnes
Staphylo. epidermidis

Buccal Mucosa
Gemella haemolysans
Haemophilus influenzae
Streptococcus mitis

Supragingival Plaque
Corynebacter. matruchotii
Rothia dentocariosa
Streptococcus sanguinis

Tongue Dorsum
Neisseria flavescens
Prevotella melaninogenica
Veillonella

Gastrointestinal Tract
Bacteroides ovatus
Bacteroides vulgatus
Prevotella copri

Posterior Fornix
Lactobacillus crispatus
Lactobacillus iners
Lactobacillus jensenii

MetaRef Database v 1.0

MetaRef is a resource to comprehensively catalog and characterize clade-specific microbial genes. We identify and provide all core genes associated with all microbial species and genera with available reference genomes (final or draft). A subset of these gene families are consistently present in one or more taxonomic clades, which allows us to further indicate them as marker genes.

MetaRef paper is now available on PubMed.

Usage and Examples

For tutorials of the MetaRef website, please visit our Help page.

For example, you can have a look to the core gene families, and marker gene families of Staphylococcus aureus as well as download all genes in its pan genome, with the corresponding functional associations.

When focusing on a specific gene family in this clade (e.g. this enzyme), you can access:

Genomic Data Info

# Number of microbial genomes: 2,706 bacterial and 112 archaeal genomes
# Number of genes: 10,880,874
# Number of Non-redundant Metaref Gene Families: 5,006,295 (3,798,644 are single-gene clusters)
# Number of Core Gene Families (at species level and above): 3,600,814 (2,607,806 are single-gene clusters)
# Number of Marker Gene Families (at species level and above): 1,028,534 (880,332 are single-gene clusters)

Metagenomic Data Info

# Number of Metagenomes: 691 samples
# Number of Human Body Sites Covered: 6 sites
# Number of Human Contaminant-Screened Reads: >35 billions.









metagenomics, metaref, comparative genomics