Understanding the Passport

A stable, unique identifier for each taxon entry following the format MCA-[DOMAIN]-[NNNNNN].

[DOMAIN] prefixes indicate the organism type:

• BAC: Bacteria
• FUN: Fungi
• VIR: Viruses
• ARC: Archaea

[NNNNNN] is a unique six-digit numeric identifier that ensures permanent reference regardless of taxonomic updates.

The official NCBI Taxonomy database identifier, linking each entry to a globally recognised taxonomic record. Clicking the TaxID opens the corresponding NCBI Taxonomy page.

Identifier linking to the BacDive entry for this taxon's type strain. BacDive is a standardised microbiological culture collection database maintained by DSMZ, providing curated microbiological metadata including culture conditions, physiology, and isolation sources. Available at species level and below.

The taxonomic level of the entry, such as family, genus, species, or strain.

The full taxonomic hierarchy from domain down to the specific rank of the entry.

Alternative scientific names and historical nomenclature sourced from NCBI Taxonomy.

Gram stain classification (positive, negative, or variable) for bacterial taxa. Sourced from BacDive.

Classification of metabolic oxygen requirements (e.g., aerobe, obligate anaerobe, facultative anaerobe). Sourced from BacDive.

Typical physical cell structure and shape (e.g., rod, coccus, spiral). Sourced from BacDive.

Biologically relevant features such as spore formation, biofilm production, or toxin production. Sourced from BacDive.

The specific body sites or environments where the organism is most commonly found (e.g., gut, oral cavity, skin). Sourced from BacDive.

The natural hosts or environments where the taxon persists: human, animal, or environment. Sourced from BacDive.

The routes through which the organism is typically acquired (e.g., contact, foodborne, waterborne). Sourced from the curated literature.

Whether this taxon is considered a pathobiont — a resident commensal that can cause disease under specific conditions. Values:

• Yes — organism is a recognised pathobiont
• Context dependent — pathobiont status depends on host factors, clinical setting, or taxonomic level
• No — organism is not considered a pathobiont
• Unknown — insufficient evidence to classify

The clinical characterisation of this taxon, such as opportunistic pathogen, protective commensal, or commensal. Extracted from curated literature.

Common specimen types in which the organism is identified in a clinical context (e.g., stool, blood, respiratory). Extracted from curated literature.

Clinical settings or patient populations where this taxon is most likely to cause harm (e.g., ICU, post-antibiotic, immunocompromised). Extracted from curated literature.

Notable resistance phenotypes that impact clinical management (e.g., ESBL, CRE, VRE). Extracted from curated literature. Where available, linked to the CARD Antibiotic Resistance Ontology (ARO):

Conditions that enable this taxon to expand to clinically relevant abundance (e.g., antibiotic exposure, immunosuppression). Extracted from curated literature. Specific drugs are linked to KEGG Drug (D numbers):

Molecular factors that contribute to pathogenicity (e.g., toxins, adhesins, capsule). Linked to the Virulence Factor Database (VFDB) where available:

Documented metabolic interactions between this taxon and specific compounds. Each entry describes the relationship type:

• Produces — taxon synthesises this metabolite
• Consumes — taxon degrades or consumes this metabolite
• Modifies — taxon chemically transforms this metabolite

Compounds are linked to KEGG Compound (C numbers) and ChEBI IDs (CHEBI:XXXXXX) where available. IDs are displayed as clickable badges linking to their respective databases.

An individual, evidence-graded claim linking this taxon to a specific clinical condition or outcome, extracted from a peer-reviewed publication. Each association is supported by at least one PMID and assigned an evidence grade:

Standardised Medical Subject Headings (MeSH) terms assigned by NLM to the source paper, filtered to those directly relevant to the association. Clicking a badge opens the NLM MeSH Browser entry.

KEGG Disease identifiers mapping the associated clinical condition to KEGG's disease classification. Clicking a badge opens the corresponding KEGG Disease entry.

A chronological summary of the papers that contributed clinical associations to this passport. Each card shows the publication year and study design. Clicking a card opens the source paper on PubMed.

Other taxa in the MCA database that share at least one annotated attribute with this entry. Two match types are shown:

• Shared Niche — both taxa occupy the same primary body site or environment
• Shared Risk — both taxa are associated with the same clinical risk context or vulnerable population

Clicking a related taxon card opens its passport in a new tab.