2.1 Nutrient Agar (NA Medium)
Nutrient agar is a general purpose non-selective medium and supports growth of a wide variety of bacteria. NA is commonly used for bacterial isolation and maintenance.
Composition of nutrient agar:
2.2 Lysogeny Broth (LB Medium)
(Also known as Luria broth, Lennox broth, or Luria–Bertani medium)
LB is also a general purpose non-selective media that supports growth of a large variety of non-fastidious bacteria. It is one of the most frequently used media for bacterial isolation and culture.
Composition of lysogeny broth:
2.3 Trypticase Soy Agar (TSA Medium)
Trypticase Soy Agar (TSA) is another general purpose non-selective media that provides nutrients to support growth of a wide variety of bacteria.
Composition of trypticase soy agar:
Tryptone: 1.5%
Soytone: 0.5%
NaCl: 0.5%
Agar: 1.5%
2.4 Reasoner's 2A (R2A) Agar Medium
R2A medium is frequently used for the isolation of slow-growing bacteria. It is also a non-selective medium but many slow-growing species that do not appear to be isolated using the above nutritionally rich media such as LB or TSA, could be isolated using R2A.
Composition of R2A agar:
3. Media for Alkaliphilic Microbes
3.1 Alkaline Nutrient Agar (ANA Medium)
Alkaline nutrient agar media is used for the enrichment, isolation and culture of alkaliphilic and alkalitolerant bacteria.
Composition of alkaline nutrient agar:
After autoclaving, adjust to desired alkaline pH with sterile 10% Na₂CO₃ solution or with the following Na-sesquicarbonate solution.
Na-sesquicarbonate solution:
NaHCO₃: 0.42%
Na₂CO₃ anhydrous: 0.53%
It is another common media for the enrichment, isolation and culture of alkaliphilic bacteria.
Composition of Horikoshi-I:
Glucose: 1%
Peptone: 0.5%
Yeast extract: 0.5%
KH₂PO₄: 0.1%
MgSO₄·7H₂O: 0.02%
Agar: 1.5–2.0%
After autoclaving, adjust to desired alkaline pH with sterile 10% Na₂CO₃ solution.
For the enrichment, isolation and growth of alkaliphilic bacteria.
Composition of Horikoshi-II:
Replace glucose with soluble starch in Horikoshi-I media described above.
4. Media for Lactic Acid Bacteria
4.1 De Man, Rogosa and Sharpe (MRS) Agar Medium
MRS is an enriched selective medium used for the isolation, cultivation and enumeration of lactic acid bacteria.
Composition of MRS agar:
Dextrose: 2%
Peptone: 1%
Beef extract: 1%
Yeast extract: 0.5%
Dipotassium hydrogen phosphate: 0.2%
Sodium acetate·3H₂O: 0.5%
Triammonium citrate: 0.2%
Magnesium sulphate·7H₂O: 0.01%
Manganese sulphate·4H₂O: 0.005%
Tween-80: 0.1%
Agar: 1–1.5%
pH: 6.2–6.5
M17 is also used for the cultivation and enumeration of lactic acid bacteria.
Composition of M17 agar:
5. Media for Antibiotic Susceptibility Testing
5.1 Mueller Hinton Agar (MHA Medium)
Mueller Hinton Agar is most commonly used for antibiotic susceptibility testing.
Composition of Mueller Hinton Agar:
6. Media for Fungal and Yeast Culture
6.1 Potato Dextrose Agar (PDA) Medium
Potato Dextrose Agar (PDA) is a common fungal culture medium used for the cultivation of yeasts and moulds.
Composition of Potato Dextrose Agar:
6.2 Sabouraud's Dextrose Agar (SDA) Medium
Sabouraud's dextrose agar (SDA) is a common fungal culture medium.
Composition of Sabouraud's Dextrose Agar:
Dextrose: 4%
Peptone: 1%
Agar: 2%
pH: 5.6
7. Media for Plant-Associated and Rhizosphere Microbes
7.1 Yeast Extract Mannitol Agar (YEMA) Medium
YEMA is used for the cultivation, isolation and enumeration of soil microorganisms such as Rhizobium species and for legume inoculant studies.
Composition of Yeast Extract Mannitol Agar:
7.2 Pikovskaya's Agar Medium
Pikovskaya's agar is used for the detection of phosphate-solubilizing soil microorganisms.
Composition of Pikovskaya's Agar:
Yeast extract: 0.05%
Dextrose: 1.0%
Calcium phosphate: 0.5%
Ammonium sulphate: 0.05%
Potassium chloride: 0.02%
Magnesium sulphate: 0.01%
Manganese sulphate: 0.00001%
Ferrous sulphate: 0.00001%
Agar: 1.5%
pH: 7.0 ± 0.2
7.3 Ashby's Mannitol Agar Medium
Ashby's mannitol agar is used for the cultivation of Azotobacter species that can use mannitol and atmospheric nitrogen as carbon and nitrogen sources, respectively.
Composition of Ashby's Mannitol Agar:
Mannitol: 2.0%
Dipotassium hydrogen phosphate: 0.02%
Magnesium sulphate: 0.02%
Sodium chloride: 0.02%
Potassium sulphate: 0.01%
Calcium carbonate: 0.5%
Agar: 1.5%
pH: 7.4 ± 0.2
7.4 N-free Malate Semi-solid Medium
N-free malate medium is used for the isolation of diazotrophic and nitrogen-fixing bacteria from soil and rhizosphere samples.
Composition of N-free Malate Semi-solid Medium:
DL-malic acid: 0.5%
K₂HPO₄: 0.05%
MgSO₄·7H₂O: 0.02%
NaCl: 0.01%
CaCl₂·2H₂O: 0.002%
Micronutrient solution: 2 mL
Bromthymol blue solution (0.5% in 0.2N KOH): 2 mL
Fe(III) EDTA (1.64%): 4 mL
Vitamin solution: 1 mL
For semisolid medium, add agar: 0.05%; for solid medium, add agar: 1.5%.
King's B agar is used for the non-selective isolation, cultivation and pigment production of Pseudomonas species from plant-associated and environmental samples.
Composition of King's B Agar:
8. Media for Marine Microbes
Marine Agar 2216 is used for the cultivation, isolation and maintenance of heterotrophic marine bacteria.
Composition of Marine Agar 2216:
Peptone: 0.5%
Yeast extract: 0.1%
Ferric citrate: 0.01%
Sodium chloride: 1.945%
Magnesium chloride: 0.88%
Sodium sulphate: 0.324%
Calcium chloride: 0.18%
Potassium chloride: 0.055%
Sodium bicarbonate: 0.016%
Potassium bromide: 0.008%
Strontium chloride: 0.0034%
Boric acid: 0.0022%
Sodium silicate: 0.0004%
Sodium fluoride: 0.00024%
Ammonium nitrate: 0.00016%
Disodium phosphate: 0.0008%
Agar: 1.5%
pH: 7.6
Marine Broth 2216 is used for the cultivation and maintenance of heterotrophic marine bacteria.
Composition of Marine Broth 2216:
Peptone: 0.5%
Yeast extract: 0.1%
Ferric citrate: 0.01%
Sodium chloride: 1.945%
Magnesium chloride: 0.59%
Sodium sulphate: 0.324%
Calcium chloride: 0.18%
Potassium chloride: 0.055%
Sodium bicarbonate: 0.016%
Potassium bromide: 0.008%
Strontium chloride: 0.0034%
Boric acid: 0.0022%
Sodium silicate: 0.0004%
Sodium fluoride: 0.00024%
Ammonium nitrate: 0.00016%
Disodium phosphate: 0.0008%
pH: 7.6
9. Selective and Differential Media for Pathogens
9.1 MacConkey Agar (MAC Medium)
MacConkey Agar is a selective and differential medium used for the isolation and differentiation of Gram-negative enteric bacteria.
Composition of MacConkey Agar:
9.2 Xylose Lysine Deoxycholate Agar (XLD Agar)
XLD Agar is a moderately selective and differential medium used for the isolation of Gram-negative enteric pathogens, including Salmonella and Shigella species.
Composition of XLD Agar:
Yeast extract: 0.3%
Lactose: 0.75%
Sucrose: 0.75%
Xylose: 0.375%
L-Lysine hydrochloride: 0.5%
Sodium chloride: 0.5%
Ferric ammonium citrate: 0.08%
Sodium thiosulfate: 0.68%
Sodium deoxycholate: 0.1%
Phenol red: 0.008%
Agar: 1.5%
pH: 7.4
9.3 Salmonella-Shigella Agar (SS Agar)
SS Agar is a selective and differential medium used for the isolation of Salmonella and Shigella species.
Composition of Salmonella-Shigella Agar:
Peptones: 1.0%
Lactose: 1.0%
Ox bile: 0.85%
Sodium citrate: 1.0%
Sodium thiosulfate: 0.85%
Ferric ammonium citrate: 0.1%
Brilliant green: 0.00003%
Neutral red: 0.0025%
Agar: 1.2%
pH: 7.0
10. Preparation of Culture Media
Step‑by‑step (for 1 liter):
Weigh and dissolve all ingredients in ~800 mL distilled water.
Adjust pH using 1 M HCl or 1 M NaOH (use a calibrated pH meter).
For solid or semi‑solid media, add agar (1–2% w/v).
Bring volume to 1 liter with distilled water.
Sterilize by autoclaving at 121 °C, 15 psi for 15 min.
For heat‑sensitive components (e.g., antibiotics, vitamins), filter‑sterilize and add after autoclaving (when medium cooled to ~50 °C).
Always prepare a media preparation log (date, batch, pH, sterilization run).
11. Storage of Culture Media
Most of the prepared media can be stored for a few months at 2–8 °C, preferably away from light. Many liquid broths can also be stored at room temperature (25 °C) for weeks to months. However, storage conditions should be validated for each medium; in general, refrigerated storage is preferred unless a medium has been specifically tested for room-temperature stability. It is, however, better to use freshly prepared media if possible. Agar plates should be stored in inverted position.
12. Preparation and Preservation of Glycerol Stocks
We prepare glycerol stocks of our cultures for long-term preservation. Here are the steps we use for preparing and preserving glycerol stocks:
Growing the culture:
Preparing the glycerol stock:
In a sterile cryogenic vial or microfuge tube, combine an equal volume of the microbial culture and sterile 50% glycerol solution. For example, mix 500 μL of culture with 500 μL of 50% glycerol so that the final glycerol concentration reaches 25%. We usually use a final glycerol concentration of ~20%.
Gently mix the contents by inverting the tube a few times to ensure thorough mixing.
Freezing the glycerol stock:
Storage and retrieval:
To retrieve a culture, remove the glycerol stock from the freezer, thaw it quickly on ice, and then streak a small amount of the thawed culture onto an appropriate solid growth medium using a sterile toothpick or inoculation loop.
It is recommended to prepare multiple glycerol stocks for each culture to ensure backup samples in case of freezer failure or other issues.
13. Quality Control & Troubleshooting
13.1 Routine Quality Control
Test each new batch of media with positive and negative control strains (e.g., E. coli ATCC 25922, S. aureus ATCC 25923).
Record the following for every batch:
Maintain a media preparation log noting date, batch number, pH, and sterilization run.
13.2 Common Problems and Solutions
Problem: No growth or poor growth
Possible causes: Wrong pH, expired ingredients, incorrect sterilization.
Solutions: Re‑check pH with a calibrated meter, use fresh components, verify autoclave temperature and pressure (121 °C, 15 psi, 15 min).
Problem: Contamination of plates
Possible causes: Autoclave failure, poor aseptic technique.
Solutions: Run a sterility test (autoclave water + media without inoculum). Retrain personnel on aseptic handling.
Problem: Media too soft or too hard
Possible causes: Incorrect agar concentration.
Solutions: Re‑prepare using the correct agar percentage (usually 1.0–1.5% for plates, 0.5–0.7% for semi‑solid).
Problem: Precipitation after autoclaving
Possible causes: pH drift, insoluble components.
Solutions: Adjust pH before autoclaving. For stubborn components, filter‑sterilize instead of autoclaving.
Problem: Inconsistent pH across batches
Possible causes: Old buffers, inaccurate measurement.
Solutions: Calibrate pH meter before each use. Use fresh buffer solutions. Measure pH after adding all ingredients (except agar) but before autoclaving.
13.3 Documentation Best Practice
Keep a digital or physical logbook with:
Medium name and date of preparation.
Lot numbers of all raw ingredients.
Measured pH before and after autoclaving.
Results of sterility and control strain tests.
This log is essential for troubleshooting and for reproducible research.
14. Safety, Sterility, and Waste Disposal
Proper safety and waste management protect every member of HOPE Lab, preserve the environment, and ensure reproducible research. The following protocols apply to all activities involving microbial cultures, media preparation, chemical reagents, and autoclave operation. Every student and researcher must read and follow these guidelines before starting any lab work.
14.1 Personal Protective Equipment (PPE)
Before entering the working area, put on a clean lab coat, safety goggles that fully shield the eyes, and nitrile gloves. Wear closed‑toe shoes and tie back long hair. Gloves must be changed immediately if they come into contact with live cultures, spilled chemicals, or contaminated surfaces. Never wear the same gloves when leaving the lab or touching personal items such as phones or notebooks.
14.2 Safe Handling of Microorganisms
Handle non‑pathogenic organisms – such as lactic acid bacteria, beneficial microbes, and safe extremophiles – using standard aseptic technique. However, for potential pathogens including Salmonella, Shigella, unknown clinical isolates, or any microorganism with uncertain biosafety status, always work inside a Class II biosafety cabinet. After each use, disinfect the cabinet surfaces and all exposed bench areas with 1% sodium hypochlorite followed by 70% ethanol.
Never pipette any culture by mouth. Use only mechanical pipettes with sterile tips. Label every culture tube, flask, or plate clearly with the name of the organism, the date of inoculation, and your initials. Unlabelled cultures are considered hazardous and must be autoclaved immediately.
The autoclave is the most effective sterilisation tool but also a source of serious injury if used improperly. Before opening the autoclave door, always check that the pressure gauge reads zero and that the temperature has dropped below 100°C. Wear heat‑resistant gloves and a face shield when removing hot items. Use only autoclavable polypropylene or borosilicate glass containers; never seal them completely – loosen caps or use vented closures. Do not overfill bags or containers, as this prevents proper steam penetration. Once a month, run a biological indicator such as a Geobacillus stearothermophilus spore strip to verify that the autoclave reaches the required 121°C for 15 minutes.
All waste must be segregated and treated according to its type.
Solid biohazard waste – including used agar plates, culture tubes, contaminated pipette tips, and disposable loops – must be collected in orange or yellow autoclavable bags. Run a full autoclave cycle at 121°C for 30 minutes, then seal the bag and place it into the regular solid waste bin.
Liquid microbial cultures can be either autoclaved directly in their original containers (with loose caps) or treated with household bleach (sodium hypochlorite) to a final concentration of 1%. After 30 minutes of contact time, the inactivated liquid may be poured down the laboratory sink with copious running water.
Non‑contaminated laboratory waste such as clean paper towels, wrapping materials, and unused gloves goes to the ordinary trash. If you are unsure whether an item is contaminated, treat it as biohazardous.
Chemical waste requires special care. Never pour antibiotic solutions, stains (such as crystal violet or neutral red), heavy metal solutions, or concentrated acids or bases down the sink. Collect these in clearly labelled hazardous waste containers – plastic carboys for liquids, sturdy boxes for solids. Arrange for institutional hazardous waste pickup or follow your local environmental safety guidelines.
Broken glass – including cracked culture tubes, shattered Petri dishes, and broken glass bottles – must never be placed in regular trash. Use a rigid, puncture‑proof sharps container clearly marked "Broken Glass". When the container is three‑quarters full, seal it and dispose of it according to your lab's glass waste protocol.
Act quickly but calmly when a spill occurs.
For a small spill of a few millilitres on the bench, cover the area with paper towels, then pour 1% sodium hypochlorite over the towels until they are saturated. Wait 15 minutes, then wipe up the liquid and discard the towels as biohazard waste.
For a large spill – especially inside a biosafety cabinet – keep the cabinet running to contain aerosols. Cover the spill with absorbent material (such as paper towels or spill pads), carefully pour disinfectant over the spill area, and allow at least 30 minutes of contact time before cleaning. If the spill occurred on the floor, restrict access to the area and wear waterproof boots or overshoes during cleanup.
If a spill contacts your skin, wash immediately with soap and warm water for at least 15 minutes. Report the incident to the lab supervisor. If a spill splashes into your eyes, use the eyewash station continuously for 15 minutes and seek medical attention.
14.6 Sterility Checks for Media
Every batch of sterilised medium must be tested for sterility before use. For solid media, incubate one uninoculated plate from each batch at 30°C or 37°C (depending on the target organism) for 48 hours. For liquid media, aseptically transfer 5 to 10 millilitres into a sterile tube and incubate under the same conditions. If any growth appears, discard the entire batch and re‑prepare the medium.
14.7 Training and Documentation
No student or new researcher may work independently in the lab until they have completed a safety training session and signed a lab safety acknowledgement form. Keep a written or digital logbook that records every autoclave run (date, time, temperature, pressure), each batch of prepared media (sterility test result), and all waste disposal activities including autoclave cycles for biohazard bags. This documentation is not bureaucracy – it protects you, your colleagues, and the integrity of your research.
When in doubt about any safety procedure, stop and ask the lab supervisor.
HOPE Lab Internal Training Document
Laboratory for Health, Omics and Pathway Exploration (HOPE Lab)
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