Overview
- External ontology
- TOGO:M1093 — Rumen Bacteria Medium
- Applications
-
- Microbial cultivation
- Notes
- Source: https://togomedium.org/medium/M1093 Original source: JCM - JCM_M1029 Original URL: https://www.jcm.riken.jp/cgi-bin/jcm/jcm_grmd?GRMD=1029 Original JCM1029 is unavailable. Do not transfer DSMZ330's nominal denominator to this source. Split the 960 ml main water from the 1 L mineral-stock water; retain exact mg inputs and unquantified CO2. Provider preparation text: Adjust pH to 6.7 -- 6.8; gas atmosphere: 100% CO2. Dissolve ingredients except carbohydrates, Na2CO3, cysteine and sodium sulfide in distilled water, boil for 5 min, then cool to room temperature while gassing with 100% CO2. Add Na2CO3 and equilibrate the medium with the gas to pH 6.8. Distribute under CO2 in rubber-stoppered tubes (i.e. Hungate tubes) and autoclave. Thereafter add carbohydrate mixture, cysteine and sodium sulfide from concentrated sterile stock solutions (prepared anaerobically under N2 gas and autoclaved). Complete inspected source rows define this reconstruction. Archive old flattened quantities, false LB expansions, placeholders and copied stock-solvent claims in append-only history. Unrelated annotations remain preserved, not recertified. Complete inspected source rows define this reconstruction. Archive old flattened quantities, false LB expansions, placeholders and copied stock-solvent claims in append-only history. Unrelated annotations remain preserved, not recertified.
Composition
flowchart LR
CultureMech_007610["rumen_bacteria_medium"]
ing0_Distilled_water["Distilled water"]
CultureMech_007610 --> ing0_Distilled_water
CHEBI_15377["CHEBI:15377"]
ing0_Distilled_water -.-> CHEBI_15377
ing1_Yeast_extract["Yeast extract"]
CultureMech_007610 --> ing1_Yeast_extract
ing2_K2HPO4["K2HPO4"]
CultureMech_007610 --> ing2_K2HPO4
CHEBI_131527["CHEBI:131527"]
ing2_K2HPO4 -.-> CHEBI_131527
ing3_Resazurin["Resazurin"]
CultureMech_007610 --> ing3_Resazurin
CHEBI_8806["CHEBI:8806"]
ing3_Resazurin -.-> CHEBI_8806
ing4_Na2S_9H2O["Na2S・9H2O"]
CultureMech_007610 --> ing4_Na2S_9H2O
CHEBI_76209["CHEBI:76209"]
ing4_Na2S_9H2O -.-> CHEBI_76209
ing5_Na2CO3["Na2CO3"]
CultureMech_007610 --> ing5_Na2CO3
CHEBI_29377["CHEBI:29377"]
ing5_Na2CO3 -.-> CHEBI_29377
ing6_Glycerol["Glycerol"]
CultureMech_007610 --> ing6_Glycerol
CHEBI_17754["CHEBI:17754"]
ing6_Glycerol -.-> CHEBI_17754
ing7_Cellobiose["Cellobiose"]
CultureMech_007610 --> ing7_Cellobiose
CHEBI_17057["CHEBI:17057"]
ing7_Cellobiose -.-> CHEBI_17057
ing8_Maltose["Maltose"]
CultureMech_007610 --> ing8_Maltose
CHEBI_18167["CHEBI:18167"]
ing8_Maltose -.-> CHEBI_18167
ing9_Hemin["Hemin"]
CultureMech_007610 --> ing9_Hemin
CHEBI_50385["CHEBI:50385"]
ing9_Hemin -.-> CHEBI_50385
ing10_Glucose["Glucose"]
CultureMech_007610 --> ing10_Glucose
CHEBI_17234["CHEBI:17234"]
ing10_Glucose -.-> CHEBI_17234
ing11_Starch__soluble["Starch, soluble"]
CultureMech_007610 --> ing11_Starch__soluble
ing12_Trypticase_peptone__BD_BBL_["Trypticase peptone (BD-BBL)"]
CultureMech_007610 --> ing12_Trypticase_peptone__BD_BBL_
ing13_L__Cysteine_HCl_H2O["L--Cysteine・HCl・H2O"]
CultureMech_007610 --> ing13_L__Cysteine_HCl_H2O
CHEBI_91248["CHEBI:91248"]
ing13_L__Cysteine_HCl_H2O -.-> CHEBI_91248
ing14_CO2["CO2"]
CultureMech_007610 --> ing14_CO2
CHEBI_16526["CHEBI:16526"]
ing14_CO2 -.-> CHEBI_16526
Ingredients (15)
| # | Ingredient | Concentration | Ontology | Notes |
|---|---|---|---|---|
| 1 |
Distilled water
H2O 18.015 g/mol
|
0.96 L |
CHEBI:15377
water
|
Role: Solvating media; Properties: Inorganic compound, Defined component, Simple component [Merged 2 duplicates: 960.0, 1.0] Source input only; not final volume or volume percentage; keep main water 960 ml separate from mineral-stock water 1 L; restore stock doses 38 and 3.1 ml, not g/L; original JCM source access remains unresolved Source input: 960 ml; stage=main solution 1. |
| 2 | Yeast extract | Role: Nutrient source; Properties: Undefined component Keep literal source mass and preparation stage in evidenced notes; no assumed receiving-medium denominator; keep main water 960 ml separate from mineral-stock water 1 L; restore stock doses 38 and 3.1 ml, not g/L; original JCM source access remains unresolved Source input: 0.5 g; stage=main solution 1. | ||
| 3 |
K2HPO4
HO4P.2K 174.174 g/mol
|
CHEBI:131527
dipotassium hydrogen phosphate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component Keep literal source mass and preparation stage in evidenced notes; no assumed receiving-medium denominator; keep main water 960 ml separate from mineral-stock water 1 L; restore stock doses 38 and 3.1 ml, not g/L; original JCM source access remains unresolved Source input: 0.3 g; stage=main solution 1. | |
| 4 |
Resazurin
C12H7NO4 229.191 g/mol
|
CHEBI:8806
Resazurin
|
Role: pH dependent redox indicator; Properties: Organic compound, Defined component, Simple component Keep literal source mass and preparation stage in evidenced notes; no assumed receiving-medium denominator; keep main water 960 ml separate from mineral-stock water 1 L; restore stock doses 38 and 3.1 ml, not g/L; original JCM source access remains unresolved Source input: 1 mg; stage=main solution 1. | |
| 5 |
Na2S・9H2O
9H2O.2Na.S 240.182 g/mol
|
CHEBI:76209
sodium sulfide nonahydrate
|
Role: Reducing agent; Properties: Inorganic compound, Defined component, Simple component Keep literal source mass and preparation stage in evidenced notes; no assumed receiving-medium denominator; keep main water 960 ml separate from mineral-stock water 1 L; restore stock doses 38 and 3.1 ml, not g/L; original JCM source access remains unresolved Source input: 0.25 g; stage=main solution 1. | |
| 6 |
Na2CO3
CO3.2Na 105.988 g/mol
|
CHEBI:29377
sodium carbonate
|
Role: Buffer; Properties: Inorganic compound, Defined component, Simple component Keep literal source mass and preparation stage in evidenced notes; no assumed receiving-medium denominator; keep main water 960 ml separate from mineral-stock water 1 L; restore stock doses 38 and 3.1 ml, not g/L; original JCM source access remains unresolved Source input: 4 g; stage=main solution 1. | |
| 7 |
Glycerol
C3H8O3 92.094 g/mol
|
CHEBI:17754
glycerol
|
Role: Carbon source; Properties: Organic compound, Defined component, Simple component Keep literal source mass and preparation stage in evidenced notes; no assumed receiving-medium denominator; keep main water 960 ml separate from mineral-stock water 1 L; restore stock doses 38 and 3.1 ml, not g/L; original JCM source access remains unresolved Source input: 0.5 g; stage=main solution 1. | |
| 8 |
Cellobiose
C12H22O11 342.297 g/mol
|
CHEBI:17057
cellobiose
|
Role: Carbon source; Properties: Organic compound, Defined component, Simple component Keep literal source mass and preparation stage in evidenced notes; no assumed receiving-medium denominator; keep main water 960 ml separate from mineral-stock water 1 L; restore stock doses 38 and 3.1 ml, not g/L; original JCM source access remains unresolved Source input: 0.5 g; stage=main solution 1. | |
| 9 |
Maltose
C12H22O11 342.297 g/mol
|
CHEBI:18167
alpha-maltose
|
Role: Carbon source; Properties: Organic compound, Defined component, Simple component Keep literal source mass and preparation stage in evidenced notes; no assumed receiving-medium denominator; keep main water 960 ml separate from mineral-stock water 1 L; restore stock doses 38 and 3.1 ml, not g/L; original JCM source access remains unresolved Source input: 0.5 g; stage=main solution 1. | |
| 10 |
Hemin
C34H32ClFeN4O4 651.952 g/mol
|
CHEBI:50385
hemin
|
Role: Growth factor; Properties: Organic compound, Defined component, Simple component Keep literal source mass and preparation stage in evidenced notes; no assumed receiving-medium denominator; keep main water 960 ml separate from mineral-stock water 1 L; restore stock doses 38 and 3.1 ml, not g/L; original JCM source access remains unresolved Source input: 1 mg; stage=main solution 1. | |
| 11 |
Glucose
C6H12O6 180.156 g/mol
|
CHEBI:17234
glucose
|
Role: Carbon source; Properties: Organic compound, Defined component, Simple component Keep literal source mass and preparation stage in evidenced notes; no assumed receiving-medium denominator; keep main water 960 ml separate from mineral-stock water 1 L; restore stock doses 38 and 3.1 ml, not g/L; original JCM source access remains unresolved Source input: 0.5 g; stage=main solution 1. | |
| 12 | Starch, soluble | Role: Carbon source; Properties: Undefined component Keep literal source mass and preparation stage in evidenced notes; no assumed receiving-medium denominator; keep main water 960 ml separate from mineral-stock water 1 L; restore stock doses 38 and 3.1 ml, not g/L; original JCM source access remains unresolved Source input: 0.5 g; stage=main solution 1. | ||
| 13 | Trypticase peptone (BD-BBL) | Properties: Undefined component Keep literal source mass and preparation stage in evidenced notes; no assumed receiving-medium denominator; keep main water 960 ml separate from mineral-stock water 1 L; restore stock doses 38 and 3.1 ml, not g/L; original JCM source access remains unresolved Source input: 2 g; stage=main solution 1. | ||
| 14 |
L--Cysteine・HCl・H2O
C3H7NO2S.H2O.HCl 175.637 g/mol
|
CHEBI:91248
L-cysteine hydrochloride hydrate
|
Properties: Defined component, Simple component, Organic compound Keep literal source mass and preparation stage in evidenced notes; no assumed receiving-medium denominator; keep main water 960 ml separate from mineral-stock water 1 L; restore stock doses 38 and 3.1 ml, not g/L; original JCM source access remains unresolved Source input: 0.25 g; stage=main solution 1. | |
| 15 |
CO2
CO2 44.009 g/mol
|
CHEBI:16526
carbon dioxide
|
Properties: Gas No numeric source dose; missing is not zero; keep main water 960 ml separate from mineral-stock water 1 L; restore stock doses 38 and 3.1 ml, not g/L; original JCM source access remains unresolved Source input: None None; stage=main solution 1. |
Solutions
Mineral solution (see below)
Dose: 0.038 L
| Ingredient | Concentration | Notes |
|---|---|---|
| Distilled water | 1 L | Role: Solvating media; Properties: Inorganic compound, Defined component, Simple component [Merged 2 duplicates: 960.0, 1.0] Source input only; not final volume or volume percentage; keep main water 960 ml separate from mineral-stock water 1 L; restore stock doses 38 and 3.1 ml, not g/L; original JCM source access remains unresolved Source input: 1 L; stage=Mineral solution. |
| MgSO4・7H2O | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Keep literal source mass and preparation stage in evidenced notes; no assumed receiving-medium denominator; keep main water 960 ml separate from mineral-stock water 1 L; restore stock doses 38 and 3.1 ml, not g/L; original JCM source access remains unresolved Source input: 2.5 g; stage=Mineral solution. | |
| NaCl | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Keep literal source mass and preparation stage in evidenced notes; no assumed receiving-medium denominator; keep main water 960 ml separate from mineral-stock water 1 L; restore stock doses 38 and 3.1 ml, not g/L; original JCM source access remains unresolved Source input: 12 g; stage=Mineral solution. | |
| CaCl2・2H2O | Role: Mineral source; Properties: Inorganic compound, Defined component, Simple component Keep literal source mass and preparation stage in evidenced notes; no assumed receiving-medium denominator; keep main water 960 ml separate from mineral-stock water 1 L; restore stock doses 38 and 3.1 ml, not g/L; original JCM source access remains unresolved Source input: 1.6 g; stage=Mineral solution. | |
| KH2PO4 | Role: Buffer; Properties: Inorganic compound, Defined component, Simple component Keep literal source mass and preparation stage in evidenced notes; no assumed receiving-medium denominator; keep main water 960 ml separate from mineral-stock water 1 L; restore stock doses 38 and 3.1 ml, not g/L; original JCM source access remains unresolved Source input: 6 g; stage=Mineral solution. | |
| (NH4)2SO4 | Role: Nitrogen source; Properties: Inorganic compound, Defined component, Simple component Keep literal source mass and preparation stage in evidenced notes; no assumed receiving-medium denominator; keep main water 960 ml separate from mineral-stock water 1 L; restore stock doses 38 and 3.1 ml, not g/L; original JCM source access remains unresolved Source input: 6 g; stage=Mineral solution. |
Source input only; not final volume or volume percentage; keep main water 960 ml separate from mineral-stock water 1 L; restore stock doses 38 and 3.1 ml, not g/L; original JCM source access remains unresolved Source input: 38 ml; stage=main solution 1.
VFA solution (see Medium [M124])
Dose: 0.0031 L
| Ingredient | Concentration | Notes |
|---|---|---|
| DL--α--Methyl butyric acid | 0.001 L | VFA-stock input only. No density, volume additivity or receiving-medium concentration inferred. M1093 explicitly links M124; M124 identifies original JCM133. Import only the VFA subsection. |
| n--Butyric acid | 0.004 L | VFA-stock input only. No density, volume additivity or receiving-medium concentration inferred. M1093 explicitly links M124; M124 identifies original JCM133. Import only the VFA subsection. |
| Acetic acid | 0.017 L | VFA-stock input only. No density, volume additivity or receiving-medium concentration inferred. M1093 explicitly links M124; M124 identifies original JCM133. Import only the VFA subsection. |
| n--Valeric acid | 0.001 L | VFA-stock input only. No density, volume additivity or receiving-medium concentration inferred. M1093 explicitly links M124; M124 identifies original JCM133. Import only the VFA subsection. |
| iso--Valeric acid | 0.001 L | VFA-stock input only. No density, volume additivity or receiving-medium concentration inferred. M1093 explicitly links M124; M124 identifies original JCM133. Import only the VFA subsection. |
| iso--Butyric acid | 0.001 L | VFA-stock input only. No density, volume additivity or receiving-medium concentration inferred. M1093 explicitly links M124; M124 identifies original JCM133. Import only the VFA subsection. |
| Propionic acid | 0.006 L | VFA-stock input only. No density, volume additivity or receiving-medium concentration inferred. M1093 explicitly links M124; M124 identifies original JCM133. Import only the VFA subsection. |
Source input only; not final volume or volume percentage; keep main water 960 ml separate from mineral-stock water 1 L; restore stock doses 38 and 3.1 ml, not g/L; original JCM source access remains unresolved Source input: 3.1 ml; stage=main solution 1.
Target organisms
No target organisms are recorded.
Provenance
| Timestamp | Curator | Action | Notes |
|---|---|---|---|
| 2026-01-27T06:35:53.899955Z | togo-import | Imported from TOGO Medium | Source: JCM, ID: M1093 |
| 2026-01-28T19:48:17.407611Z | chebi-enrichment | Added CHEBI ontology terms to ingredients | Enriched using MicrobeMediaParam and MediaDive chemical mappings |
| 2026-02-03T00:00:00+00:00 | schema-defaulter-v1.0 | Applied schema defaults and normalizations | Added default concentration for ingredient: CO2 |
| 2026-03-09T08:04:28.836541+00:00 | solution-migrator-v1.0 | Migrated solutions from ingredients to solutions array | Moved 2 solution(s) from ingredients |
| 2026-03-13T03:08:57.647135Z | data-quality-cleanup-v1.0 | Data quality fixes | Merged 1 duplicate ingredient(s) |
| 2026-03-13T06:19:50.032954Z | culturemech-id-assigner-v1.0 | Assigned CultureMech ID | Assigned stable identifier: CultureMech:007610 |
| 2026-03-14T00:00:00+00:00 | schema-defaulter-v1.0 | Applied schema defaults and normalizations | Added default solution name; Added default solution name |
| 2026-03-17T06:30:02.000000Z | mediaingredientmech-enrichment-v1.0 | Added MediaIngredientMech links | Linked ingredients to MediaIngredientMech identifiers |
| 2026-03-17T19:46:08.391464+00:00 | normalize_media_names_to_snake_case.py | NAME_NORMALIZED | Normalized name from "Rumen Bacteria Medium" to "rumen_bacteria_medium" for consistent matching |
| 2026-05-16T09:03:07.483480+00:00 | migrate_legacy_fields.py | MIGRATED_LEGACY_FIELDS | curation_history.date->timestamp=2 |
| 2026-06-05T07:40:30.338035+00:00 | mim-legacy-to-chebi-migration-v1.0 | Refreshed legacy MediaIngredientMech links to CHEBI keying | Replaced 12 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme. |
| 2026-06-08T23:19:29.865286+00:00 | chebi-regrounding-v1.0 | Corrected CHEBI ingredient grounding (audit G21/G22) | Re-grounded 2 term reference(s) to the correct CHEBI (see reports/chebi_grounding_audit.md). Label-conditional fixes for pyridoxine/pyridoxamine, glycerol, MnSO4, Ca(NO3)2, selenate; casamino acids de-grounded (mixture, no single CHEBI). |
| 2026-06-10T06:57:21.148923+00:00 | mgso4-heptahydrate-term-fix-v1.0 | Corrected MgSO4·7H2O primary term grounding to heptahydrate | Re-grounded 1 heptahydrate-labelled ingredient(s) from CHEBI:32599 (generic magnesium sulfate) to CHEBI:31795 (magnesium sulfate heptahydrate). Generic/hexahydrate labels untouched. |
| 2026-06-10T07:46:46.879682+00:00 | primary-term-label-canonicalization-v1.0 | Canonicalized primary term label to OBO canonical (OAK) | 4 primary term(s); ingredient name resolved by OAK sqlite:obo:chebi. |
| 2026-10-09T08:40:02.418657+00:00 | codex | RESTORED_RUMEN_BACTERIA_SOURCE_FORMULATIONS_WITH_EVIDENCE | Restore source-specific medium330 ingredients, stock scopes and input units with literal evidence. Preserve prior supported entries, provider nulls, unknown original bases and the JCM1029 access gap. No growth association added. |