mic_cit_herriott_et_al

CultureMech:007183 bacterial DEFINED LIQUID
Original name: Mic-Cit; Herriott et al

Overview

External ontology
MEDIADB:282 (source link unavailable) — Mic-Cit; Herriott et al
Applications
  • Cultivation of genome-sequenced organisms
  • Metabolic modeling
  • Systems biology research
Notes
Source: MediaDB (Chemically-defined media for genome-sequenced organisms) Reference: https://mediadb.systemsbiology.net/

Composition

flowchart LR
    CultureMech_007183["mic_cit_herriott_et_al"]
    ing0_NAD_["NAD+"]
    CultureMech_007183 --> ing0_NAD_
    CHEBI_15846["CHEBI:15846"]
    ing0_NAD_ -.-> CHEBI_15846
    ing1_L_Glutamate["L-Glutamate"]
    CultureMech_007183 --> ing1_L_Glutamate
    CHEBI_16015["CHEBI:16015"]
    ing1_L_Glutamate -.-> CHEBI_16015
    ing2_Glycine["Glycine"]
    CultureMech_007183 --> ing2_Glycine
    CHEBI_15428["CHEBI:15428"]
    ing2_Glycine -.-> CHEBI_15428
    ing3_L_Lysine["L-Lysine"]
    CultureMech_007183 --> ing3_L_Lysine
    CHEBI_18019["CHEBI:18019"]
    ing3_L_Lysine -.-> CHEBI_18019
    ing4_L_Aspartate["L-Aspartate"]
    CultureMech_007183 --> ing4_L_Aspartate
    CHEBI_29991["CHEBI:29991"]
    ing4_L_Aspartate -.-> CHEBI_29991
    ing5_L_Serine["L-Serine"]
    CultureMech_007183 --> ing5_L_Serine
    CHEBI_17115["CHEBI:17115"]
    ing5_L_Serine -.-> CHEBI_17115
    ing6_L_Methionine["L-Methionine"]
    CultureMech_007183 --> ing6_L_Methionine
    CHEBI_16643["CHEBI:16643"]
    ing6_L_Methionine -.-> CHEBI_16643
    ing7_L_Tyrosine["L-Tyrosine"]
    CultureMech_007183 --> ing7_L_Tyrosine
    CHEBI_17895["CHEBI:17895"]
    ing7_L_Tyrosine -.-> CHEBI_17895
    ing8_L_Cysteine["L-Cysteine"]
    CultureMech_007183 --> ing8_L_Cysteine
    CHEBI_17561["CHEBI:17561"]
    ing8_L_Cysteine -.-> CHEBI_17561
    ing9_Glycerol["Glycerol"]
    CultureMech_007183 --> ing9_Glycerol
    CHEBI_17754["CHEBI:17754"]
    ing9_Glycerol -.-> CHEBI_17754
    ing10_L_Leucine["L-Leucine"]
    CultureMech_007183 --> ing10_L_Leucine
    CHEBI_15603["CHEBI:15603"]
    ing10_L_Leucine -.-> CHEBI_15603
    ing11_L_Histidine["L-Histidine"]
    CultureMech_007183 --> ing11_L_Histidine
    CHEBI_15971["CHEBI:15971"]
    ing11_L_Histidine -.-> CHEBI_15971
    ing12_Hypoxanthine["Hypoxanthine"]
    CultureMech_007183 --> ing12_Hypoxanthine
    CHEBI_17368["CHEBI:17368"]
    ing12_Hypoxanthine -.-> CHEBI_17368
    ing13_EDTA["EDTA"]
    CultureMech_007183 --> ing13_EDTA
    CHEBI_4735["CHEBI:4735"]
    ing13_EDTA -.-> CHEBI_4735
    ing14_Inosine["Inosine"]
    CultureMech_007183 --> ing14_Inosine
    CHEBI_17596["CHEBI:17596"]
    ing14_Inosine -.-> CHEBI_17596
    ing15_L_Citrulline["L-Citrulline"]
    CultureMech_007183 --> ing15_L_Citrulline
    CHEBI_16349["CHEBI:16349"]
    ing15_L_Citrulline -.-> CHEBI_16349
    ing16_Thiamine["Thiamine"]
    CultureMech_007183 --> ing16_Thiamine
    CHEBI_18385["CHEBI:18385"]
    ing16_Thiamine -.-> CHEBI_18385
    ing17_Polyvinyl_alcohol["Polyvinyl alcohol"]
    CultureMech_007183 --> ing17_Polyvinyl_alcohol
    ing18_Triethanolamine["Triethanolamine"]
    CultureMech_007183 --> ing18_Triethanolamine
    CHEBI_28621["CHEBI:28621"]
    ing18_Triethanolamine -.-> CHEBI_28621
    ing19_Magnesium_chloride["Magnesium chloride"]
    CultureMech_007183 --> ing19_Magnesium_chloride
    CHEBI_86345["CHEBI:86345"]
    ing19_Magnesium_chloride -.-> CHEBI_86345
    ing20_Calcium_chloride_anhydrous["Calcium chloride anhydrous"]
    CultureMech_007183 --> ing20_Calcium_chloride_anhydrous
    CHEBI_3312["CHEBI:3312"]
    ing20_Calcium_chloride_anhydrous -.-> CHEBI_3312
    ing21_Tween_80["Tween 80"]
    CultureMech_007183 --> ing21_Tween_80
    CHEBI_53426["CHEBI:53426"]
    ing21_Tween_80 -.-> CHEBI_53426
    ing22_Potassium_sulfate["Potassium sulfate"]
    CultureMech_007183 --> ing22_Potassium_sulfate
    CHEBI_32036["CHEBI:32036"]
    ing22_Potassium_sulfate -.-> CHEBI_32036
    ing23_Potassium_dibasic_phosphate["Potassium dibasic phosphate"]
    CultureMech_007183 --> ing23_Potassium_dibasic_phosphate
    CHEBI_131527["CHEBI:131527"]
    ing23_Potassium_dibasic_phosphate -.-> CHEBI_131527
    ing24_Sodium_chloride["Sodium chloride"]
    CultureMech_007183 --> ing24_Sodium_chloride
    CHEBI_26710["CHEBI:26710"]
    ing24_Sodium_chloride -.-> CHEBI_26710
    ing25_Calcium_pantothenate["Calcium pantothenate"]
    CultureMech_007183 --> ing25_Calcium_pantothenate
    CHEBI_31345["CHEBI:31345"]
    ing25_Calcium_pantothenate -.-> CHEBI_31345
    ing26_Potassium_dihydrogen_phosphate["Potassium dihydrogen phosphate"]
    CultureMech_007183 --> ing26_Potassium_dihydrogen_phosphate
    CHEBI_63036["CHEBI:63036"]
    ing26_Potassium_dihydrogen_phosphate -.-> CHEBI_63036
    ing27_Hemin["Hemin"]
    CultureMech_007183 --> ing27_Hemin
    CHEBI_50385["CHEBI:50385"]
    ing27_Hemin -.-> CHEBI_50385
    ing28_Sodium_L_lactate["Sodium L-lactate"]
    CultureMech_007183 --> ing28_Sodium_L_lactate
    CHEBI_232798["CHEBI:232798"]
    ing28_Sodium_L_lactate -.-> CHEBI_232798

Ingredients (29)

# Ingredient Concentration Ontology Notes
1 NAD+
C21H28N7O14P2 664.438 g/mol
0.00603 MILLIMOLAR CHEBI:15846
NAD(+)
 Restored from MediaDB compound row C00003; the archived leading compound labels are corrupt, while the row sequence preserves the KEGG identity.
2 L-Glutamate
C5H9NO4 147.13 g/mol
8.83572 MILLIMOLAR CHEBI:16015
L-glutamic acid
 Cross-references: KEGG:glu-L
3 Glycine
C2H5NO2 75.067 g/mol
0.39963 MILLIMOLAR CHEBI:15428
glycine
 Cross-references: KEGG:gly
4 L-Lysine
C6H14N2O2 146.19 g/mol
0.34202 MILLIMOLAR CHEBI:18019
L-lysine
 Cross-references: KEGG:lys-L
5 L-Aspartate
C4H6NO4 132.095 g/mol
3.75657 MILLIMOLAR CHEBI:29991
L-aspartate(1-)
 Cross-references: KEGG:asp-L
6 L-Serine
C3H7NO3 105.093 g/mol
0.95157 MILLIMOLAR CHEBI:17115
L-serine
 Cross-references: KEGG:ser-L
7 L-Methionine
C5H11NO2S 149.215 g/mol
0.6702 MILLIMOLAR CHEBI:16643
L-methionine
 Cross-references: KEGG:met-L
8 L-Tyrosine
C9H11NO3 181.191 g/mol
1.10381 MILLIMOLAR CHEBI:17895
L-tyrosine
 Cross-references: KEGG:tyr-L
9 L-Cysteine
C3H7NO2S 121.161 g/mol
0.83229 MILLIMOLAR CHEBI:17561
L-cysteine
 Cross-references: KEGG:cys-L
10 Glycerol
C3H8O3 92.094 g/mol
32.5768 MILLIMOLAR CHEBI:17754
glycerol
 Cross-references: KEGG:glyc
11 L-Leucine
C6H13NO2 131.175 g/mol
2.28711 MILLIMOLAR CHEBI:15603
L-leucine
 Cross-references: KEGG:leu-L
12 L-Histidine
C6H9N3O2 155.157 g/mol
0.06445 MILLIMOLAR CHEBI:15971
L-histidine
 Cross-references: KEGG:his-L
13 Hypoxanthine
C5H4N4O 136.114 g/mol
0.14693 MILLIMOLAR CHEBI:17368
hypoxanthine
 Cross-references: KEGG:hxan
14 EDTA
C10H16N2O8 292.244 g/mol
0.01369 MILLIMOLAR CHEBI:4735
ethylenediaminetetraacetic acid
15 Inosine
C10H12N4O5 268.229 g/mol
7.45434 MILLIMOLAR CHEBI:17596
inosine
 Cross-references: KEGG:ins
16 L-Citrulline
C6H13N3O3 175.188 g/mol
0.85621 MILLIMOLAR CHEBI:16349
L-citrulline
 Cross-references: KEGG:citr-L
17 Thiamine
C12H17N4OS 265.362 g/mol
0.0133 MILLIMOLAR CHEBI:18385
thiamine(1+)
 Cross-references: KEGG:thm
18 Polyvinyl alcohol 0.45401 MILLIMOLAR
19 Triethanolamine
C6H15NO3 149.19 g/mol
2.68118 MILLIMOLAR CHEBI:28621
triethanolamine
20 Magnesium chloride
2Cl.6H2O.Mg 203.301 g/mol
2.1006 MILLIMOLAR CHEBI:86345
magnesium dichloride hexahydrate
21 Calcium chloride anhydrous
Ca.2Cl 110.984 g/mol
0.19823 MILLIMOLAR CHEBI:3312
calcium dichloride
22 Tween 80
(C2H4O)w.(C2H4O)x.(C2H4O)y.(C2H4O)z.C24H44O6 604.822 g/mol
0.01527 MILLIMOLAR CHEBI:53426
polysorbate 80
23 Potassium sulfate
2K.O4S 174.259 g/mol
5.73858 MILLIMOLAR CHEBI:32036
potassium sulfate
24 Potassium dibasic phosphate
HO4P.2K 174.174 g/mol
20.0918 MILLIMOLAR CHEBI:131527
dipotassium hydrogen phosphate
25 Sodium chloride
Cl.Na 58.443 g/mol
99.2471 MILLIMOLAR CHEBI:26710
sodium chloride
26 Calcium pantothenate
2C9H16NO5.Ca 476.536 g/mol
0.00839 MILLIMOLAR CHEBI:31345
Calcium pantothenate
27 Potassium dihydrogen phosphate
H2O4P.K 136.084 g/mol
19.8404 MILLIMOLAR CHEBI:63036
potassium dihydrogen phosphate
28 Hemin
C34H32ClFeN4O4 651.952 g/mol
0.01534 MILLIMOLAR CHEBI:50385
hemin
29 Sodium L-lactate
C3H5O3.Na 112.06 g/mol
7.13903 MILLIMOLAR CHEBI:232798
sodium L-lactate

Preparation

  1. Dissolve all ingredients in distilled water to specified concentrations
  2. Adjust pH if specified in original formulation
  3. Sterilize by filtration (0.22 μm) to preserve heat-sensitive components

Target organisms

No target organisms are recorded.

Provenance

TimestampCuratorActionNotes
2026-06-14T05:58:58.561437+00:00 idnf-grounding-fix-v1.0 Fixed ID_NOT_FOUND term groundings Absent/obsolete CHEBI term ids fixed - 2 re-grounded to the correct CHEBI, 0 de-grounded (mixture or unverifiable).
2026-01-27T07:21:45.211189Z mediadb-import Imported from MediaDB Source: MediaDB (Institute for Systems Biology), Medium ID: 282, Reference: Mazumdar et al. (2014) PLOS One
2026-01-28T19:48:18.452004Z chebi-enrichment Added CHEBI ontology terms to ingredients Enriched using MicrobeMediaParam and MediaDive chemical mappings
2026-03-13T06:19:46.647372Z culturemech-id-assigner-v1.0 Assigned CultureMech ID Assigned stable identifier: CultureMech:007183
2026-03-17T06:30:04.000000Z mediaingredientmech-enrichment-v1.0 Added MediaIngredientMech links Linked ingredients to MediaIngredientMech identifiers
2026-03-17T19:46:04.823796+00:00 normalize_media_names_to_snake_case.py NAME_NORMALIZED Normalized name from "Mic-Cit; Herriott et al" to "mic_cit_herriott_et_al" for consistent matching
2026-06-05T07:41:33.719695+00:00 mim-legacy-to-chebi-migration-v1.0 Refreshed legacy MediaIngredientMech links to CHEBI keying Replaced 18 legacy mediaingredientmech_term link(s) with mediaingredientmech_chebi_term (id-safe: ingredient's own CHEBI + label). MIM deprecated the MediaIngredientMech:NNNNNN id scheme.
2026-08-20T19:02:53.859106+00:00 apply_mim_groundings.py Adopted MIM published grounding Grounded 1 ingredient(s) from MIM's ingredient_mappings.sssom.tsv (2026-08-18), exactMatch only, where this record carried no CHEBI term (#308).
2026-08-25T00:00:00-07:00 fix_mediadb_leading_compounds.py RESTORED_CORRUPT_SOURCE_COMPOUND Restored C00003 as NAD+ (CHEBI:15846) from the MediaDB row sequence; resolves the 2026-08-24 EMPTY_INGREDIENT_NAME review finding.