Culturomics & Media Navigator

Media Selection

Search Organism

1Target Organism

2Isolation Objective

Indicator Key

Biosafety

Non-Pathogenic

BSL-1

BSL-2

BSL-3

Oxygen Requirement

E EOS

S Strict Anaerobe

M Microaerophile

F Facultative

A Obligate Aerobe

Gram Stain

P Gram+

N Gram−

X Archaea

Growth Environment

SCFASCFA-Dependent

ACIDAcidophile

ALKAlkaliphile

HALHalophile

E-HALExtreme Halophile

AUTOObligate Autotroph

MIXMixotroph / Fac. Autotroph

THERMThermophile

H-THMHyperthermophile

HYDHydrogenophile

METHMethanotroph

AMPHAmmoniaphile

SDPHSulphidophile

MTROMethylotroph

Organism Categories

Gut Microbiome
Culturomics / Commensal

Clinical GI Pathogens
Enteric / Foodborne

Tissue & Wound Pathogens
Implant / Surgical Site

Archaea / Methanogen
Non-bacterial colonisers

Fastidious / Dark Matter
Novel / uncultured taxa

Industrial / Bioengineering
Fermentation / Platform strains

Extreme Environments
Halophile / Alkaliphile / Lithoautotroph

Food Processing
Dairy / Cheese / Fermentation

Select a target organism and isolation objective, then click Analysis & Match to display the recommended culture medium, complete formulation, critical parameters, and authorised references.

Submit a New Organism Profile

GMExpression Media Navigator · Submission Guide V2.0

Contributor Documentation · V2.0 · 455 Organisms · 11 Groups

Propose a New Organism Profile

Use this guide to propose an organism not yet in the Navigator. Data must be traceable to peer-reviewed or authorised sources.

Before You Submit — Eligibility & Requirements ▶

Check first: Search the Navigator to confirm the organism is not already included. Use the search box or browse via Organism Taxonomy & Classification.

Authorised sources onlyAll formulations, growth parameters, and clinical data must be traceable to at least one primary reference: DSMZ type strain medium, NCBI/NIH database record, IJSEM or IJSB species description, CLSI/EUCAST guideline, ISO standard, or a peer-reviewed journal publication (PubMed-indexed). Wikipedia, textbooks, and commercial kit inserts are not accepted as primary sources.

Primary medium is mandatory — selective and enrichment are strongly recommendedThe database schema requires a Primary Isolation Medium. A Selective Medium and an Enrichment Medium / Broth are strongly recommended. If no validated selective or enrichment medium is described in the literature, state that explicitly and cite the source. All formulas must list full ingredient quantities per litre — shorthand references like "YCFA base as above" are not accepted.

BSL classification must be accurateState the correct Biosafety Level (BSL-1 / BSL-2 / BSL-3) per WHO/CDC classification. Misclassified BSL-3 organisms as BSL-2 will result in immediate rejection. Reference the WHO Laboratory Biosafety Manual (4th Ed.) or your institutional biosafety committee classification.

No proprietary or confidential dataDo not submit unpublished internal formulations, trade secrets, or confidential client data. All submitted information will be verified against public sources before integration.

DB

Database Field Reference — Required Format Structure Guide ▶

Each organism follows a consistent data structure. Match every field below when drafting your submission.

Organism Identity & Classification

Field	DB Key	Req.	Accepted Values / Format	Example
Database Key Unique ID. Lowercase, underscores, no spaces.	key	REQ	snake_case, max 30 chars	r_intestinalis
Latin Name Full binomial. Synonyms in parentheses.	latinName	REQ	String; include synonyms	Roseburia intestinalis
Category Controls badge colour in the UI. Choose the closest match.	category	REQ	`gut` · `clinical` · `tissue` · `oral` · `zoonotic` · `archaea` · `special` · `industrial` · `food` · `extremo`	oral
Traits Comma-separated. Start with Gram + O₂ class.	traits	REQ	Array of strings; 4–8 traits	Gram-Positive, Strict Anaerobe, Butyrate Producer, Lachnospiraceae
Introduction 3–5 sentences. Niche, relevance, key metabolic features.	intro	REQ	Plain text, 60–200 words	Primary butyrate-producing bacterium of the human colon…
Group / Subgroup 11 Groups: Gut Microbiome · Clinical GI · Respiratory & Wound · Zoonotic & Systemic · Oral Microbiome · Biotechnology · Food Processing · Soil & Environmental · Extremophiles · Pathogenic Fungi · Chemolithotrophs	group / subgroup	REQ	Group ID 1–11 + subgroup label (or propose new subgroup)	Group 5 · "Oral Streptococci"
BSL Level Per CDC BMBL 6th Ed. or WHO LBM 4th Ed. Must be verified by a BSL Reviewer before integration.	bsl	REQ	`0`=Non-Pathogenic/GRAS · `1`=BSL-1 · `2`=BSL-2 · `3`=BSL-3 · `null`=Unknown/Unclassified	2

Physiological Metadata (BIOD_META)

Field	DB Key	Req.	Accepted Values	Example
O₂ Requirement	o2	REQ	`E`=EOS · `S`=Strict Anaerobe · `M`=Microaerobic · `F`=Facultative · `A`=Obligate Aerobe	S
Gram Stain	gram	REQ	`P`=Gram+ · `N`=Gram− · `X`=Variable/N/A	P
SCFA Producer	scfa	OPT	`true` if primary SCFA output	true
pH Class	ph	OPT	`AC`=Acidophile · `AL`=Alkaliphile	AC
Salinity	sal	OPT	`HL`=Halophile · `EH`=Extreme Halophile	EH
Carbon Metabolism	carbon	OPT	`AU`=Obligate Autotroph · `MX`=Mixotroph	MX
Temperature Class	temp	OPT	`TH`=Thermophile · `HT`=Hyperthermophile	TH
Gas Metabolism	h2 / ch4 / nh3 / h2s	OPT	Set any applicable flag to `true`	h2: true
Methylotrophic	methyl	OPT	`true` if C₁/methanol sole carbon source	true
Spore-Former True endospore-forming organisms only. Unlocks the Sporulation-Cultivation goal in the UI.	spore	OPT	`true` for confirmed endospore-formers (Bacillus, Clostridium, Paenibacillus, etc.)	true

Media — Three Entries Required (primary · selective · enrichment)

Field	DB Key Pattern	Req.	Format / Notes
Medium Name	media.[type].name	REQ	Full name with abbreviation and DSMZ number if applicable
Formula	media.[type].formula	REQ	Dot-aligned, per litre. Preparation notes on lines beginning with //
Atmosphere	params.Atmosphere	REQ	Specific gas composition, e.g. "< 0.5 ppm O₂ (Coy chamber)"
Incubation	params.Incubation	REQ	Temperature + duration, e.g. "37 °C, 3–5 d"
pH	params.pH	REQ	Value or range
Additional Params	params.[custom key]	OPT	Key–value pairs for inhibitors, colony features, supplements

References

Field	DB Key	Req.	Format
References Semicolon-separated. Must include DSMZ/NCBI accession or journal citation.	ref	REQ	e.g. DSMZ Medium 337; Duncan et al. (2002) IJSEM 52:1615

{}

Submission Template — Copy & Fill Plain Text ▶

Copy the template below, fill in all fields, and attach as a .txt file to your email. One file per organism. Do not alter field names. Required fields are marked with *.

## GMExpression Media Navigator — New Organism Submission Template v2.0
## One file per organism · Do not alter field names · Required fields marked *
## Submit to: submissions@gmexpression.com

────────────────────────────────────────────────
## ORGANISM IDENTITY
────────────────────────────────────────────────
KEY*:                  # snake_case, unique, no spaces — e.g. r_intestinalis
LATIN_NAME*:           # Full binomial (LPSN current nomenclature) + synonyms if any
CATEGORY*:             # gut / clinical / tissue / oral / zoonotic / archaea / special / industrial / food / extremo
TRAITS*:               # Comma-sep: Gram stain, O₂ class, key features, family — e.g. Gram-Positive, Strict Anaerobe, Butyrate Producer, Lachnospiraceae
INTRO*:                # 60–200 words plain-text scientific description (no HTML)
GROUP_ID*:             # Navigator group 1–11 (1=Gut, 2=Clinical GI, 3=Resp/Wound, 4=Zoonotic, 5=Oral, 6=Biotech, 7=Food, 8=Soil, 9=Extremo, 11=Fungi, 10=Chemolithotroph)
SUBGROUP_LABEL*:       # Existing or proposed new subgroup name within that group
BSL*:                  # 0=Non-Pathogenic/GRAS · 1=BSL-1 · 2=BSL-2 · 3=BSL-3 · null=Unknown — per CDC BMBL 6th Ed. / WHO LBM 4th Ed.

────────────────────────────────────────────────
## PHYSIOLOGICAL METADATA (BIOD_META)
────────────────────────────────────────────────
O2*:                   # E=Extreme anaerobe / S=Strict anaerobe / M=Microaerophile / F=Facultative / A=Aerobe / X=Variable
GRAM*:                 # P=Gram+ / N=Gram− / X=Variable or N/A (Archaea, Fungi)
SPORE:                 # true — confirmed endospore-former (Bacillus, Clostridium, Paenibacillus etc.); unlocks Sporulation goal
SCFA:                  # true — primary short-chain fatty acid producer
PH_CLASS:              # AC=Acidophile (opt pH <5) / AL=Alkaliphile (opt pH >9) / (leave blank if mesophilic pH)
SALINITY:              # HL=Halophile / EH=Extreme halophile / (leave blank if non-halophilic)
CARBON:                # AU=Obligate autotroph / MX=Mixotroph / (leave blank if heterotroph)
TEMP_CLASS:            # TH=Thermophile (opt 45–80 °C) / HT=Hyperthermophile (opt >80 °C) / (leave blank if mesophile)
GAS_H2:                # true — H₂ metabolism (production or consumption)
GAS_CH4:               # true — methanogenesis
GAS_NH3:               # true — ammonification
GAS_H2S:               # true — sulfide production
METHYL:                # true — methylotrophy (C₁ / methanol as sole carbon source)

────────────────────────────────────────────────
## PRIMARY ISOLATION MEDIUM  [REQUIRED]
────────────────────────────────────────────────
PM_NAME*:              # Full name, e.g. "YCFA Medium + 30 mM Sodium Acetate"
PM_FORMULA*:
  [Component] .................. [Amount / L]
  [Component] .................. [Amount / L]
  // Preparation notes (pH, atmosphere, autoclave conditions, supplements)
PM_ATMOSPHERE*:       # e.g. "< 0.5 ppm O₂ (Coy anaerobic chamber)" or "Aerobic" or "5% CO₂"
PM_INCUBATION*:       # Temperature + duration, e.g. "37 °C, 3–5 d"
PM_PH*:                # Value or range, e.g. "6.8–7.0"
PM_ID_FEATURE:        # Colony morphology, diagnostic features, colour reactions

────────────────────────────────────────────────
## SELECTIVE MEDIUM  [Strongly recommended — if no validated medium exists, state explicitly]
────────────────────────────────────────────────
SM_NAME*:
SM_FORMULA*:
  [Component] .................. [Amount / L]
  // Notes on inhibitors, selective agents, rationale
SM_ATMOSPHERE*:
SM_INCUBATION*:
SM_PH*:
SM_INHIBITORS:        # e.g. Vancomycin 7.5 µg/mL + Kanamycin 75 µg/mL

────────────────────────────────────────────────
## ENRICHMENT MEDIUM / BROTH  [Strongly recommended — if none, state explicitly]
────────────────────────────────────────────────
EM_NAME*:
EM_FORMULA*:
  [Component] .................. [Amount / L]
  // Notes on inoculation source, dilution series, transfer timing
EM_FORMAT*:           # e.g. "Liquid enrichment broth — 5 d then plate on primary medium"
EM_ATMOSPHERE*:
EM_INCUBATION*:
EM_PH*:

────────────────────────────────────────────────
## REFERENCES  (semicolon-separated; must include DSMZ/NCBI accession or PubMed-indexed citation)
────────────────────────────────────────────────
REF*:                  # e.g. DSMZ Medium 337; Duncan et al. (2002) IJSEM 52:1615; ATCC 29149

────────────────────────────────────────────────
## SUBMITTER INFORMATION
────────────────────────────────────────────────
SUBMITTER_NAME:
SUBMITTER_EMAIL:
SUBMITTER_AFFIL:
SUBMISSION_DATE:

✉

How to Submit Submission Method ▶

📧

Email Submission Recommended

Send your completed template or Excel file to the submissions address. Accepted formats: .txt (template above), .xlsx (download at gmexpression.com/navigator/submission-template.xlsx), or inline email with fields clearly labelled. Attach primary reference PDFs where available.

submissions@gmexpression.com

Subject line: [SUBMISSION] Organism · Category · Your Name