BacDive MCP Server
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||
Instructions
Guidance the server publishes about itself, which clients place ahead of the tool catalog so the model reads it before choosing anything.
This server publishes no instructions, or was last inspected before Glama recorded them.
Capabilities
Features and capabilities supported by this server
Protocol revision2025-11-25
| Capability | Details |
|---|---|
| tools | {} |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| bacdive_search_strainA | Search for bacterial or archaeal strains in the BacDive database by species name, genus name, or both. Returns a paginated list of matching taxa with their taxon IDs, species, genus, family, order, class, phylum, and domain. Use this when looking up strains by their scientific name. |
| bacdive_search_taxonA | Perform a free-text search across the BacDive taxon database. This is useful for searching by physiological traits, morphological characteristics, or any other keywords (e.g. 'thermophilic', 'spore-forming', 'nitrogen-fixing'). Returns a paginated list of matching taxa. |
| bacdive_get_strain_by_idA | Retrieve full detailed information about a specific strain from BacDive using its numeric BacDive ID. This returns comprehensive data including: general information, name and taxonomic classification, morphology, culture and growth conditions, physiology and metabolism, enzyme activities, antibiotic resistance, safety information, applications, references, sequence information (16S rRNA gene, genome), and external links. |
| bacdive_search_by_dsm_numberB | Search for a strain in BacDive by its DSMZ strain number (e.g. 'DSM 3', 'DSM 10'). DSMZ numbers are the accession identifiers used by the German Collection of Microorganisms and Cell Cultures. Returns the matching taxon entry. |
| bacdive_browse_taxaA | Browse all taxa in the BacDive database with pagination. This is useful for systematically exploring the database or getting an overview of available strains. Each page contains up to 50 taxa. |
| bacdive_search_culture_mediumA | Search for culture media in the BacDive database by medium name. Returns details about culture media including composition, growth conditions, and citation. Useful when you need to find how to cultivate specific microorganisms. |
| bacdive_get_culture_medium_by_idA | Retrieve detailed information about a specific culture medium from BacDive using its numeric DSMZ medium ID. Returns the full medium composition, growth conditions, and citation. |
| bacdive_search_16sC | Search for 16S rRNA gene sequences in the BacDive database by species or genus name. 16S rRNA gene sequences are the gold standard for bacterial phylogenetic identification and taxonomy. |
| bacdive_search_genomeB | Search for genome sequences in the BacDive database by species or genus name. Returns genome sequence accessions and associated strain information. |
| bacdive_pingA | Check the connectivity and availability of the BacDive API. Returns a boolean indicating whether the BacDive API is currently reachable. Use this to diagnose connection issues. |
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
No resources | |
TDQS
Scored across 10 tools
Most tools are cleanly separated by resource and access path (ID lookup vs name search vs browse). However, bacdive_search_strain (by scientific name) and bacdive_search_taxon (free-text) both return taxa lists and could be confused, and search_strain/search_16s/search_genome all take species/genus names, differing only in returned content. Descriptions mitigate this well enough that selection is usually clear.
Every tool follows a consistent bacdive_ prefix plus verb_noun pattern (search_strain, get_strain_by_id, search_culture_medium, browse_taxa). The distinction between search_* and get_*_by_id is applied predictably across resources.
Ten tools is well-scoped for a read-only microbial database covering strains, taxa, media, sequences, and connectivity. Each tool clearly earns its place with no redundancy.
Strong lifecycle coverage: search and ID-based retrieval for strains and media, sequence lookups, browsing, and a ping. Minor gap: there is a bacdive_get_strain_by_id and get_culture_medium_by_id but no get_taxon_by_id, so taxon IDs surfaced by browse/search cannot be directly dereferenced—though strain detail largely compensates.