Isolation Capability Matrix¶
Home practice
Reviewed on 2026-09-28: each procedure's Status and Held are derived from its Needs. Everything here is experimental home practice: read the disclaimer first.
This page records what my kitchen-table set-up can do for the process in Isolating Organisms, in one place and in a form an AI skill can read. The bottle-dregs-analysis skill plans each isolation from it. When the standard (primary) route for a step needs something marked Unavailable, the skill picks the best alternative that only uses Available items and states what that costs in selectivity, screening effort, time or confidence. The skill reads this page when it writes a plan; after a change here, an existing plan is re-checked only when I ask for a plan review.
How to read and maintain it¶
| Column | Values | Meaning |
|---|---|---|
| Status | Available / Unavailable |
Available: I have it, or can buy it off the shelf and am willing to use it. Unavailable: I can't get it, won't use it (policy), or it is unsuitable. The skill only plans with Available items. |
| Held | Yes / No / ? |
Yes: in my kit now. No: not in my kit, so buy before use. ?: listed as suggested on the equipment page, or not confirmed. |
| Access | Home / Retail / Restricted |
Home: kitchen item or home-made. Retail: sold to individuals (test: can I get it via Amazon?). Restricted: prescription-only, lab-account-only or controlled. |
| Held (procedures) | Yes / No |
Derived from Needs: Yes when every group in Needs has an Available item that is held (or a procedure that is Held). No means something must be bought or made first; Notes says what. |
| Practised (procedures) | Yes / No / ? |
Whether I already do this. The skill adds a trial run on bank strains for first-time procedures. |
| Needs (procedures) | Item IDs | A procedure is blocked if any group in its Needs has all items Unavailable. A or B means either will do; items in brackets are preferred, not required. A blocked procedure is Unavailable, and Notes names the blocking IDs. |
- Policy: no handling of pure antibiotics or cycloheximide, whatever their access. Anything that would need it stays Unavailable.
- Editing rules: change Status and Held of items freely; a procedure's Status and Held follow from its Needs, so update them when an item it needs changes. Add new rows with the next free ID in their table. Never reuse or renumber an ID: the skill refers to items by ID.
- Pre-population basis: Home and Retail items were set to Available and Restricted items to Unavailable, except where policy, cost or suitability says otherwise (see Notes). Held came from the former Equipment and Materials draft: listed = Yes, listed as suggested = ?, not listed = No.
Equipment¶
| ID | Item | Status | Held | Access | Used for | Notes |
|---|---|---|---|---|---|---|
| EQ-01 | Compound microscope, 1000x oil immersion, phase contrast | Available | Yes | Retail | Dregs, picks, purity scans | AmScope T390 with phase kit. WF10x/18 eyepieces: field number 18, so a 180 µm field at 100x. 100x phase condenser left fitted |
| EQ-02 | Brightfield set-up (non-phase condenser) | Available | Yes | Retail | Stained slides (methylene blue, Gram) | Swap the condenser; stain colours read poorly through phase rings |
| EQ-03 | Camera held at the eyepiece | Available | Yes | Home | Records | Take one full-field frame per session, field edge visible, for size calibration |
| EQ-04 | Stage micrometer (calibration slide, 0.01 mm divisions) | Available | Yes | Retail | Absolute size calibration | Replaces field-number estimates |
| EQ-05 | Haemocytometer (improved Neubauer) | Unavailable | No | Retail | Cell counts for choosing dilutions | |
| EQ-06 | Plate magnifier (reversed WF10x eyepiece) and side torch | Available | Yes | Home | Inspecting and picking colonies | |
| EQ-07 | Scale, 0.001 g | Available | Yes | Retail | Indicators, selective agents, small media batches | |
| EQ-08 | Kitchen scale | Available | Yes | Home | DME, agar, larger batches | |
| EQ-09 | Probe thermometer | Available | Yes | Retail | Molten agar temperature, incubation | |
| EQ-10 | pH meter (pen type) with calibration buffers | Available | No | Retail | Acidified media, hop-tolerance broth | Strips (EQ-11) are adequate to about ±0.3 |
| EQ-11 | pH strips, narrow range (about 3.6 to 6.2) | Available | No | Retail | Acidified media, hop-tolerance broth | |
| EQ-12 | Refractometer and hydrometer | Available | Yes | Retail | Media gravity, attenuation tests | |
| EQ-13 | Graduated syringes (1, 5, 10 mL) with blunt needles | Available | Yes | Retail | Calibrated dilutions and media volumes | 1 mL syringes read to 0.01 mL |
| EQ-14 | Adjustable micropipettes (10 to 100 µL, 100 to 1000 µL) with sterile tips | Unavailable | No | Retail | Precise dilutions and plated volumes | Syringes are adequate for 0.1 mL and up |
| EQ-15 | Measuring cylinder | Available | Yes | Retail | Water for media and blanks | |
| EQ-16 | Pressure cooker, about 1 bar gauge (about 121 °C) | Available | Yes | Home | Sterilising media, tubes, water, glassware; killing waste | Time from full pressure and scale with volume |
| EQ-17 | Borosilicate Erlenmeyer flasks | Available | Yes | Retail | Media, starters | |
| EQ-18 | Stir plate and stir bars | Available | Yes | Retail | Dissolving media; propagating pure isolates | Not for mixed cultures before isolation |
| EQ-19 | Hob and microwave | Available | Yes | Home | Melting agar, hop boils | |
| EQ-20 | Water bath or sous-vide stick held at 50 °C | Available | No | Retail | Holding molten agar for heat-sensitive additions | |
| EQ-21 | Alcohol lamp (methylated spirit) | Available | Yes | Retail | Flaming wires and tube mouths | Keep it outside a plastic still air box |
| EQ-22 | Still air box (clear storage box with arm holes) | Unavailable | No | Home | Pouring, streaking and picking | Wipe with 70% ethanol; no open flame inside |
| EQ-23 | Inoculation wires and loops (nichrome, home made) | Available | Yes | Home | Streaking, picking | |
| EQ-24 | Sterile single-use loops | Unavailable | No | Retail | Flame-free work inside the still air box | |
| EQ-25 | Spreader, bent, flame-sterilisable | Available | Yes | Home | Spread plates | |
| EQ-26 | Glass Petri dishes (borosilicate, reusable) | Available | No | Retail | Plates that can be pressure-cooked and reused | |
| EQ-27 | Screw-cap borosilicate tubes (16 x 100 mm, 25 x 150 mm, 50 mL) and rack | Available | Yes | Retail | Blanks, broths, slants | |
| EQ-28 | Temperature-controlled chamber, 20 to 30 °C | Available | Yes | Retail | Incubating at a steady 25 to 28 °C | Shared with fermentation; ambient is about 21 °C |
| EQ-29 | Fridge, 4 °C | Available | Yes | Home | Plates, slants, backups | |
| EQ-30 | Domestic freezer, −18 °C | Available | Yes | Home | Glycerol stocks | Keep stocks in an insulated box to damp defrost cycles |
| EQ-31 | Ultra-low freezer, −80 °C | Unavailable | No | Retail | Long-term glycerol stocks | Not practical at home (cost, space) |
| EQ-32 | Airtight box or jar, 1 to 2 L | Available | No | Home | Anaerobic or candle-jar incubation | |
| EQ-33 | Mini centrifuge for 1.5 to 2 mL tubes | Unavailable | No | Retail | Separating yeast from bacteria by a short, low-speed spin | |
| EQ-34 | Mini-beer vessels (250 mL flask, bung, airlock) | Available | Yes | Retail | Mini-beers |
Consumables¶
| ID | Item | Status | Held | Access | Used for | Notes |
|---|---|---|---|---|---|---|
| CS-01 | Slides and cover slips (22 x 22 mm) | Available | Yes | Retail | Wet mounts | |
| CS-02 | Immersion oil, lens paper, isopropyl alcohol | Available | Yes | Retail | 100x objective | |
| CS-03 | Sterile single-use Petri dishes, 90 mm | Available | Yes | Retail | Plates | Use new; washed and alcohol-rinsed dishes are not sterile |
| CS-04 | Disposable pipettes | Available | Yes | Retail | Transfers | |
| CS-05 | Plate sealing film (cling film; Parafilm) | Available | Yes | Home | Sealing plates from day 0 | Parafilm not confirmed |
| CS-06 | Foil, autoclave tape, labels, permanent marker | Available | Yes | Retail | Sterilising and labelling | |
| CS-07 | Autoclavable screw-cap microtubes or cryovials, 1.5 to 2 mL | Unavailable | No | Retail | Glycerol stocks, small blanks | |
| CS-08 | Durham tubes | Unavailable | No | Retail | Gas test (heterofermentative bacteria) | |
| CS-09 | Mineral oil for slants | Available | Yes | Retail | Slant overlay | |
| CS-10 | Distilled water | Available | Yes | Retail | Media, blanks | |
| CS-11 | Iron-based food oxygen absorbers | Unavailable | No | Retail | Anaerobic box | Rated capacity at least 1.5x the box's oxygen volume (about 0.21 x box volume) |
| CS-12 | Oxygen indicator tablets | Unavailable | No | Retail | Confirming the box is oxygen-free | |
| CS-13 | Anaerobic gas-generating sachets (laboratory type) | Unavailable | No | Retail | Anaerobic jar with CO2 | Lab webshops; check they sell to individuals |
| CS-14 | Nitrile gloves, safety glasses | Available | Yes | Retail | Acids, stains, hot liquids |
Media and nutrients¶
| ID | Item | Status | Held | Access | Used for | Notes |
|---|---|---|---|---|---|---|
| MD-01 | Dried malt extract (DME) | Available | Yes | Retail | Wort media, starters | |
| MD-02 | Agar-agar, food grade | Available | Yes | Retail | Solid media | |
| MD-03 | Yeast extract powder | Available | Yes | Retail | Nutrient supplement; home MRS-like medium | |
| MD-04 | Dextrose (glucose) | Available | Yes | Retail | Minimal and MRS-like media | |
| MD-05 | Hop pellets | Available | Yes | Retail | Hopped media, hop-tolerance tests | |
| MD-06 | Isomerised hop extract (iso-α-acids) | Available | No | Retail | Dosing IBU precisely | Availability varies; a hop boil works |
| MD-07 | Peptone (bacteriological or soy) | Available | No | Retail | Richer bacterial media | Optional |
| MD-08 | Polysorbate 80 (Tween 80) | Available | No | Retail | Growth factor for lactic acid bacteria (MRS component) | |
| MD-09 | Manganese sulfate | Available | No | Retail | Growth factor for lactic acid bacteria (MRS component) | |
| MD-10 | Magnesium sulfate (Epsom salt) | Available | Yes | Retail | Minimal and MRS-like media | |
| MD-11 | Sodium acetate | Available | No | Retail | MRS-like medium | Anhydrous or trihydrate: adjust the weight |
| MD-12 | Potassium phosphates (monopotassium "MKP", dipotassium) | Available | No | Retail | Minimal and MRS-like media | Hydroponic grades are fine |
| MD-13 | Ammonium sulfate (or diammonium phosphate) | Available | No | Retail | Sole nitrogen source in minimal medium | DAP raises pH: correct after sterilising |
| MD-14 | B-complex tablets containing biotin; inositol powder | Available | Yes | Retail | Vitamins for minimal media | |
| MD-15 | Zinc sulfate stock, 0.1 mg/mL | Available | Yes | Retail | Trace zinc | |
| MD-16 | Calcium carbonate (precipitated chalk) | Available | Yes | Retail | Acid-halo plates; stab cultures for bacteria | |
| MD-17 | Table salt, calcium chloride | Available | Yes | Home | Saline blanks; minimal medium | |
| MD-18 | Vodka (40% neutral ethanol) | Available | Yes | Home | Ethanol-carbon medium; acetic acid bacteria plates | |
| MD-19 | L-lysine hydrochloride, pure supplement powder | Available | No | Retail | Home lysine medium (non-Saccharomyces yeasts) | Check for fillers |
| MD-20 | Potassium nitrate | Available | No | Retail | Home nitrate medium | UK reportable explosives precursor: legal to buy, sellers may report unusual purchases |
| MD-21 | Corn starch | Available | Yes | Home | Starch-iodine plates | |
| MD-22 | Plain tomato juice | Available | Yes | Home | Growth factors for lactic acid bacteria (optional) | |
| MD-23 | Pasteurised pale lager | Available | No | Home | Forcing test; hop-tolerance medium | |
| MD-24 | MRS agar or broth premix | Unavailable | No | Retail | Lactic acid bacteria medium | On Amazon (US) and from UK education suppliers |
| MD-25 | WL Nutrient premix | Unavailable | No | Retail | Differential yeast medium | Home version (wort agar with bromocresol green) is adequate |
| MD-26 | WL Differential premix (contains cycloheximide) | Unavailable | No | Retail | Brett-selective plates | Policy: no cycloheximide handling; bulk packs only on Amazon |
| MD-27 | Sabouraud dextrose agar with chloramphenicol (pre-poured plates or powder) | Available | No | Retail | Yeast plates free of bacteria | Antibiotic already in the medium, no pure powder handled. Set to Unavailable to stay antibiotic-free. Check UK suppliers sell to individuals |
| MD-28 | Lab-only premixes (YGC, DRBC, lysine medium, Lin's cupric sulfate, Raka-Ray, NBB) | Unavailable | No | Restricted | Brewing-lab selective media | Home equivalents: PR-18, PR-19, PR-23 |
| MD-29 | Reference cultures: banked Saccharomyces and Brett; a probiotic LAB capsule | Available | Yes | Home | Positive and negative controls for home-made media |
Selective and differential agents¶
| ID | Item | Status | Held | Access | Used for | Notes |
|---|---|---|---|---|---|---|
| SA-01 | Bromocresol green | Available | Yes | Retail | Acid indicator in plates (22 mg/L, as in WL Nutrient) | |
| SA-02 | p-Coumaric acid stock, 10 mg/mL | Available | Yes | Retail | 4-vinylphenol and 4-ethylphenol tests | |
| SA-03 | Ferulic acid stock, 10 mg/mL | Available | Yes | Retail | POF (4-vinylguaiacol) and 4-ethylguaiacol tests | |
| SA-04 | Lactic acid, 80 to 88% | Available | Yes | Retail | Acidifying media after sterilising | |
| SA-05 | Phosphoric acid | Available | Yes | Retail | Acidifying media | |
| SA-06 | Potassium sorbate (wine stabiliser) | Available | No | Retail | Holding back yeasts on bacterial plates | |
| SA-07 | Natamycin (E235), food grade | Unavailable | No | Retail | Removing yeasts and moulds, Brett included, from bacterial plates | Amazon (US, DE). Often 50% on lactose: double the weight |
| SA-08 | Copper sulfate | Available | Yes | Retail | Lin-type suppression of Saccharomyces | Narrow window: has killed Brett here before |
| SA-09 | Cycloheximide, pure | Unavailable | No | Restricted | Suppressing Saccharomyces | Policy and access |
| SA-10 | Chloramphenicol, pure | Unavailable | No | Restricted | Suppressing bacteria | Prescription-only |
| SA-11 | Chloramphenicol eye drops, 0.5% | Unavailable | No | Retail | None | Unsuitable: contains phenylmercuric nitrate, an antifungal preservative |
| SA-12 | Penicillin-streptomycin | Unavailable | No | Restricted | None | Prescription-only (POM-V). Also unsuitable: penicillin breaks down at wort pH; lactic acid bacteria resist streptomycin |
| SA-13 | Doxycycline and other tetracyclines | Unavailable | No | Restricted | None | Prescription-only. Also unsuitable: they only pause bacteria, wort calcium and magnesium bind them, and resistance is common in lactic acid bacteria |
Reagents and stains¶
| ID | Item | Status | Held | Access | Used for | Notes |
|---|---|---|---|---|---|---|
| RG-01 | Methylene blue | Available | No | Retail | Yeast viability; simple stain | |
| RG-02 | Gram stain kit | Available | No | Retail | Gram status | |
| RG-03 | Hydrogen peroxide, 3% | Available | No | Retail | Catalase test | |
| RG-04 | Potassium hydroxide (for a 3% solution) | Available | Yes | Retail | KOH string test | Caustic: gloves and glasses |
| RG-05 | Lugol's iodine | Available | No | Retail | Starch-iodine test | Included in Gram kits |
| RG-06 | Glycerol, pharmaceutical grade | Available | No | Retail | Freezer stocks | |
| RG-07 | 70% ethanol, isopropyl alcohol, methylated spirit | Available | Yes | Retail | Surfaces, lamp fuel | |
| RG-08 | Household bleach | Available | Yes | Home | Killing cultures before disposal | |
| RG-09 | Sterile saline, 0.9% (salt and distilled water, pressure-cooked) | Available | Yes | Home | Dilution blanks, picks |
Procedures¶
| ID | Procedure | Status | Held | Practised | Needs | Used for | Notes |
|---|---|---|---|---|---|---|---|
| PR-01 | Pressure-cooker sterilisation, timed from full pressure | Available | Yes | Yes | EQ-16 | Media, tubes, water | Caps loosened a quarter turn; time scaled to volume |
| PR-02 | Sterility check of each pressure-cooker run | Available | Yes | No | PR-01, EQ-27 | Catching failed runs | One un-inoculated tube, 5 days at 25 to 30 °C |
| PR-03 | Pouring plates in a still air box; 48 h pre-incubation check | Unavailable | No | No | EQ-22, CS-03 or EQ-26 | Mould-free plates | Discard any plate that grows anything. Blocked by EQ-22 |
| PR-04 | Quadrant streak | Available | Yes | Yes | EQ-23 or EQ-24 | Isolation | |
| PR-05 | Calibrated 10-fold serial dilution | Available | Yes | No | EQ-13 or EQ-14, RG-09, EQ-27 | Reproducible plate density | 0.5 mL into 4.5 mL saline |
| PR-06 | Spread plate of a fixed volume (0.1 mL) | Available | Yes | Yes | EQ-25, PR-05 | Census and counts | |
| PR-07 | Wet-mount field count | Available | Yes | No | EQ-01, CS-01, EQ-13 | Estimating cells per mL | |
| PR-08 | Haemocytometer count | Unavailable | No | No | EQ-05 | Cells per mL | Blocked by EQ-05 |
| PR-09 | Size calibration | Available | Yes | No | EQ-01 (EQ-04 preferred) | Measuring cells | |
| PR-10 | Settle-and-wash fractionation | Available | Yes | No | EQ-27, RG-09 | Enriching yeast or bacteria before plating | |
| PR-11 | Low-speed centrifugation | Unavailable | No | No | EQ-33, CS-07 | Sharper yeast/bacteria separation | Blocked by CS-07, EQ-33 |
| PR-12 | Anaerobic incubation in an absorber box | Unavailable | No | No | EQ-32, CS-11, CS-12 | Bacterial and Pedio plates | Blocked by CS-11, CS-12 |
| PR-13 | Candle jar | Available | No | No | EQ-32 | Low-oxygen incubation | About 17% O2 and 3% CO2 remain. Buy or make first: EQ-32 |
| PR-14 | Agar overlay | Available | Yes | No | PR-01 | Low-oxygen colonies without a jar | |
| PR-15 | Direct plating from the dregs on day 0 | Available | Yes | No | PR-05, PR-06 | Representative census | |
| PR-16 | Short static revival (24 to 48 h in 1.020 to 1.030 wort) | Available | Yes | Yes | MD-01, EQ-27 | Backup when dregs are weak | Plate at 24 h and 48 h, not later |
| PR-17 | Mother culture (unfractionated dregs, hopped wort, static) | Available | Yes | No | MD-01, MD-05, EQ-17 | Reference consortium | One step from the bottle only |
| PR-18 | Home minimal (amino-acid-free) yeast agar | Available | No | No | MD-02, MD-04, MD-10, MD-12, MD-13, MD-14, MD-15, MD-17 | Yeast plates without bacteria | Check on bank controls first. Buy or make first: MD-12, MD-13 |
| PR-19 | Home lysine agar | Available | No | No | PR-18, MD-19, MD-29 | Non-Saccharomyces yeasts | Check on banked Brett first: uptake varies by strain. Buy or make first: MD-19, PR-18 |
| PR-20 | Home nitrate agar | Available | No | No | PR-18, MD-20, MD-29 | Nitrate-using yeasts (some Brett) | Check on banked Brett first. Buy or make first: MD-20, PR-18 |
| PR-21 | Ethanol-carbon differential agar (DBDM-like, no cycloheximide) | Available | No | No | PR-18, MD-18, SA-01, SA-02 | Flagging Brett among yeasts | Buy or make first: PR-18 |
| PR-22 | Home MRS-like agar or broth | Available | No | No | MD-01 or MD-04, MD-02, MD-03, MD-08, MD-09, MD-10, MD-11, MD-12 | Lactic acid bacteria | Buy or make first: MD-08, MD-09, MD-11, MD-12 |
| PR-23 | Sorbate bacterial agar (MRS-S principle) | Available | No | No | PR-22, SA-06, SA-04, EQ-11 | Bacterial plates with yeasts held back | Buy or make first: EQ-11, PR-22, SA-06 |
| PR-24 | Natamycin bacterial agar | Unavailable | No | No | PR-22 or MD-24, SA-07 | Bacterial plates without yeasts | Blocked by SA-07 |
| PR-25 | Chloramphenicol yeast agar (premix) | Available | No | No | MD-27 | Yeast plates without bacteria | Buy or make first: MD-27 |
| PR-26 | Cycloheximide Brett agar | Unavailable | No | No | MD-26 or SA-09 | Brett without Saccharomyces | Blocked by policy (MD-26, SA-09) |
| PR-27 | Calcium carbonate acid-halo plates | Available | Yes | No | MD-16 | Acid producers (Brett, bacteria) | |
| PR-28 | Bromocresol green plates (home WL Nutrient) | Available | Yes | Yes | SA-01 | Differentiating colonies | |
| PR-29 | Forcing enrichment in pasteurised lager | Unavailable | No | No | MD-23, SA-06 or SA-07, PR-12 | Beer-spoiling bacteria and Pedio | Blocked by PR-12 |
| PR-30 | Methylene blue viability (yeast) | Available | No | ? | RG-01, EQ-02 | Yeast viability | Buy or make first: RG-01 |
| PR-31 | Gram stain | Available | No | No | RG-02, EQ-02 | Gram status | Buy or make first: RG-02 |
| PR-32 | KOH string test | Available | Yes | No | RG-04 | Gram status, quick proxy | |
| PR-33 | Catalase test | Available | No | No | RG-03 | Lactic acid bacteria (negative) vs yeast and acetic acid bacteria (positive) | Buy or make first: RG-03 |
| PR-34 | Motility check in a fresh wet mount | Available | Yes | No | EQ-01 | Flagging rods that are not lactic acid bacteria | |
| PR-35 | Gas test (Durham tube) | Unavailable | No | No | CS-08, PR-22 | Hetero- vs homofermentative bacteria | Blocked by CS-08 |
| PR-36 | POF test (ferulic acid) | Available | Yes | Yes | SA-03 | Phenolic Saccharomyces | |
| PR-37 | Brett phenol test (p-coumaric, ferulic) | Available | Yes | Yes | SA-02, SA-03 | 4-ethylphenol, 4-ethylguaiacol | |
| PR-38 | Forced attenuation test | Available | Yes | No | EQ-12 | Screening for diastatic Saccharomyces | |
| PR-39 | Starch-iodine plate | Available | No | No | MD-21, RG-05 | Screening for diastatic Saccharomyces | Buy or make first: RG-05 |
| PR-40 | Hop-tolerance test | Available | No | No | MD-05 or MD-06, SA-04, EQ-11 | Bacterial hop tolerance before banking | Buy or make first: EQ-11 |
| PR-41 | Counter-selective purity check | Unavailable | No | No | PR-12, PR-22, PR-18 (PR-23 or PR-24 preferred) | Hidden contaminants in picks | Blocked by PR-12 |
| PR-42 | Full-slide scan at 1000x | Available | Yes | Yes | EQ-01 | Final purity check | |
| PR-43 | Mini-beer (200 mL) | Available | Yes | Yes | EQ-34 | Character of an isolate | |
| PR-44 | Slants under mineral oil at 4 °C (yeasts) | Available | Yes | Yes | EQ-27, CS-09, EQ-29 | Banking yeasts | |
| PR-45 | Stab cultures with calcium carbonate at 4 °C (bacteria) | Available | No | No | PR-22, MD-16 | Banking lactic acid bacteria | Subculture every 4 to 6 weeks. Buy or make first: PR-22 |
| PR-46 | Glycerol stocks at −18 °C | Unavailable | No | No | RG-06, CS-07, EQ-30 | Backup banking | Blocked by CS-07 |
| PR-47 | Killing cultures and plates before disposal | Available | Yes | ? | EQ-16 or RG-08 | Waste | |
| PR-48 | Traceable labels (journey, round, plate, tube) | Available | Yes | Yes | CS-06 | Traceability |