Microbiology Manual

This lab manual has been crafted to guide you through a series of laboratory exercises designed to enhance your understanding of microbial life and its applications. The exercises within this manual not only introduce you to fundamental microbiological techniques but also challenge you to apply theoretical concepts in a practical setting.  This manual uses a Course-Based Undergraduate Research Experiences (CUREs) to introduce you to the rigorous level of research in the field. 

Overview of Laboratory Exercises

1.       Aseptic Technique and Culture Methods
The course begins with an introduction to essential aseptic techniques, which are crucial for preventing contamination in microbiological work. You will learn the proper methods for handling microbial cultures, including the use of inoculating loops and needles, as well as the preparation and sterilization of culture media. These foundational skills will set the stage for all subsequent laboratory exercises.

2.       Microscopy and Staining Techniques
The manual includes detailed instructions on using a microscope to observe microorganisms. You will perform simple stains to distinguish cellular structures and differential stains, such as the Gram stain, to differentiate between major types of bacteria. These techniques are vital for identifying and studying microorganisms at the microscopic level.

3.       Isolation of Pure Cultures
Through exercises like the streak plate method, you will learn how to isolate individual colonies from mixed microbial populations. This skill is essential for obtaining pure cultures, which are necessary for accurate identification and study of microorganisms.

4.       Biochemical Testing
The manual provides protocols for a variety of biochemical tests that are used to identify microbial species based on their metabolic activities. Tests such as the catalase test, oxidase test, and carbohydrate fermentation tests will be performed, giving you hands-on experience with techniques commonly used in clinical and research laboratories.

5.       Environmental Sampling and Microbial Ecology
You will explore the diversity of microbial life in different environments by collecting and analyzing samples from various sources, such as soil, water, and air. These exercises will demonstrate the ubiquity and adaptability of microorganisms, as well as their roles in different ecosystems.

6.       Antibiotic Sensitivity Testing
This section covers the principles and methods of testing microbial susceptibility to antibiotics. You will perform disc diffusion assays to determine the effectiveness of different antibiotics against specific bacteria, providing insight into the clinical applications of microbiology.

7.       Enumeration of Microbial Populations
Techniques such as serial dilution and plate counts will be used to estimate the number of viable microorganisms in a sample. These quantitative methods are essential for microbiological research and quality control in various industries.

Safety is a top priority in any microbiology laboratory. This manual begins with comprehensive guidelines on laboratory safety, including proper handling of biological specimens, disposal of hazardous materials, and emergency procedures. It is imperative that you familiarize yourself with these safety protocols to ensure a safe working environment for yourself and others.

Images in this manual were taken of public domain or from other open educational resources (OER) such as OpenStax (images without attribution are public domain).  

This manual is more than just a set of instructions, it is a resource that will support your journey into the fascinating world of microbiology. The skills and knowledge you gain here will be invaluable as you pursue further studies or careers in the biological sciences, healthcare, or research.

·         0.5 McFarland standard

·         8 chambered disk dispenser

·         Acid-alcohol 3%

·         Antibiotic disks

o    Penicillin

o    Tetracycline

o    Erythromycin

o    Ciprofloxacin

o    Streptomycin

o    Kanamycin

o    Chloramphenicol

o    Novobiocin

·         Autoclave

·         Bacterial Cultures

o    Bacillus cereus

o    Bacillus subtilis

o    Citrobacter freundii

o    Corynebacterium Xerosis

o    Enterococcus faecalis

o    Escherichia coli

o    Klebsiella aerogenes

o    Klebsiella pneumoniae

o    Mycobacterium species

o    Proteus mirabilis

o    Pseudomonas aeruginosa

o    Salmonella enterica

o    Shigella flexneri

o    Staphylococcus aureus

o    Staphylococcus epidermidis

o    Streptococcus pyogenes

·         Beakers

·         Bergey’s Manual

·         Biochemical Tests

o    Catalase Test

o    Coagulase Test

o    DNase Test

o    Lipase Test

o    Malonate Test

o    Oxidase Test

·         Bunsen burner

·         Carbol Fuchsin stain

·         Commercial yogurt sample

·         Crystal violet stain

·         Differential Media Types

o    Bile Esculin Agar

o    Blood Agar

o    Casease Agar

o    Citrate Agar

o    Gelatinase Agar

o    Methyl Red – Voges Proskauer Broth

o    Nitrate Reduction Broth

o    Phenol Red Broth

o    Starch Agar

o    Sulfide Indole Motility Agar

o    Triple Sugar Iron Agar

o    Urease Broth

·         Disposable gloves

·         Distilled water

·         Dropper or pipette

·         Ethanol

·         Fresh / Prepared foods

·         HCl

·         Homemade yogurt sample

·         Hot Plate

·         Hydrogen peroxide

·         Immersion oil

·         Incubator

·         Inoculating loops

·         Inoculating needles

·         Iodine solution (Gram's iodine)

·         Lawn creation tool

·         Malachite green stain

·         Markers and labels

·         Methylene blue

·         Metric ruler

·         Micropipette

·         Microscope

·         Microscope slides and coverslips

·         Petri Plates (various sizes)

·         Pipettes

·         Prepared mouth cell slides

·         Protective eyewear

·         Safranin

·         Selective Media Types

o    Deoxycholate Agar

o    Endo Agar

o    Eosin Methylene Blue Agar

o    Hektoen Enteric Agar

o    MacConkey Agar

o    Mannitol Salt Agar

o    Mueller-Hinton Agar

o    Phenylethyl Alcohol Agar

o    Xylose Lysine

·         Soil various types

·         Spectrophotometer

·         Sterile swabs

·         Forceps

·         Nutrient agar

·         Sterile pipette tips

·         Sterile saline

·         Stir Bars

·         Test tube

·         Test Tubes with lids

·         Timer

This laboratory safety contract is designed to ensure the safety of all individuals participating in the anatomy lab. By signing this contract, you agree to follow all safety protocols and procedures outlined below.

General Lab Safety

I understand that laboratory work involves potential hazards and risks. I agree to follow all safety procedures and protocols to minimize the risk of injury or harm to myself and others.

·         I will always wear appropriate personal protective equipment (PPE) such as gloves, lab coats, goggles, and closed-toe shoes when working in the laboratory.

·         I will follow all posted laboratory rules and regulations and adhere to the instructor's instructions.

·         I will not eat, drink, or chew gum in the laboratory.

·         I will never touch or taste any chemicals or lab materials unless instructed to do so by the instructor.

·         I will always wash my hands with soap and water before and after working in the laboratory.

·         I will keep the laboratory clean and organized at all times, including disposing of waste materials properly.

·         I will report any accidents, injuries, or spills to the instructor immediately.

·         I will not perform any experiments or procedures that are not authorized by the instructor.

·         I will not engage in horseplay, pranks, or any behavior that could distract others or compromise safety.

·         I will always use caution when handling any lab equipment, and I will never attempt to repair or modify equipment without proper authorization and training.

·         I will follow proper procedures for handling and disposing of hazardous waste, including chemicals, biological materials, and sharps.

·         I will not bring any unauthorized materials or equipment into the laboratory.

Required PPE

I hereby agree to the following terms and conditions:

·         I will wear appropriate PPE as required by the instructor, including but not limited to:

o    Lab coat or apron to protect clothing

o    Safety goggles or face shield to protect eyes and face

o    Gloves to protect hands

o    Closed-toe shoes to protect feet

o    Long pants to protect legs

·         I understand that PPE must be worn at all times while in the laboratory, regardless of the activity being performed.

·         I will follow all laboratory safety guidelines provided by the instructor, including the proper handling and disposal of hazardous materials and the use of safety equipment.

·         I will report any accidents, incidents, or near-misses to the instructor immediately.

·         I understand that failure to follow safety guidelines or wear proper PPE may result in removal from the laboratory or disciplinary action.

·         I understand that laboratory safety is a shared responsibility and that I am accountable for the safety of myself and others in the laboratory.

Microbiological Safety

·         I will follow all microbiological safety guidelines provided by the instructor.

·         I will handle microorganisms with care, following proper aseptic techniques to prevent contamination.

·         I will use biological safety cabinets and other containment devices when working with potentially hazardous microorganisms.

·         I will properly label all microbiological materials, including cultures, plates, and specimens.

·         I will promptly report any suspected contamination or unusual results to the instructor.

·         I will properly sterilize and dispose of microbiological waste according to established protocols.

 Accident Procedures

I agree to adhere to the following safety guidelines and accident procedures while working in the laboratory:

·         I will notify the supervisor or the lab manager immediately.

·         I will secure the area and prevent further harm by turning off any equipment or power sources involved in the accident.

·         If there is a minor injury, I will provide first aid treatment as needed, such as cleaning and bandaging cuts or scrapes, or administering basic life support measures, if necessary.

·         In case of a serious injury, I will call for medical assistance immediately by dialing emergency services (911).

·         If there is a chemical spill or exposure, I will consult the instructor and the material safety data sheet (MSDS) and follow the appropriate procedures for the specific chemical.

·         If there is a fire, I will use the fire extinguisher to put out the flames, evacuate the area, and call 911.

·         I will report the incident to the lab supervisor and document the details of the accident, including the date, time, location, and nature of the incident, as well as any injuries sustained and the names of witnesses.

·         I will take corrective action to prevent incidents from occurring in the future.

Chemical Safety

·         I will not touch or taste any chemicals.

·         I will always wear appropriate personal protective equipment (PPE) such as lab coat, gloves, goggles, and face shields.

·         I will read and follow all instructions on chemical labels and Material Safety Data Sheets (MSDS) before using them.

·         I will store chemicals in appropriate containers, and label them correctly with the name of the chemical, date of receipt, expiration date, and hazard information.

·         I will not reuse pipettes, especially when transferring different chemicals.

·         I will keep chemicals in a well-ventilated area, away from sources of heat, sparks, and flame.

·         I will use fume hoods and other ventilation devices when working with volatile or toxic chemicals.

·         I will avoid working alone in the lab. Always have a lab partner or supervisor present.

·         I will dispose of chemicals and hazardous waste in accordance with local, state, and federal regulations.

·         I will know the location and proper use of emergency equipment, such as fire extinguishers, eye wash stations, and spill kits.

·         I will avoid eating or drinking in the lab, and wash hands thoroughly after working with chemicals.

·         I will report any accidents, spills, or injuries immediately to a supervisor or lab manager.

Lab Equipment Usage

·         I will not touch any equipment without the lab instructor's permission.

·         I will use equipment only for its intended purpose.

·         I will follow all operating instructions for equipment.

·         I will report any damaged equipment to the lab instructor immediately.

Here are some general procedures for using laboratory equipment commonly found in biology and anatomy labs:

·         Glassware: such as beakers, flasks, funnels, etc…

o    Cleaning: Thoroughly clean all glassware with soap and water before and after each use. Rinse with distilled water and dry using a lint-free cloth or air-dry.

o    Inspection: Inspect each piece of glassware before use for any cracks, chips, or other damage. Do not use any damaged glassware.

o    Measuring: Use graduated cylinders, pipettes, or burettes for accurate measurements of liquids. Always use the appropriate size and type of glassware for the volume of liquid you are measuring.

o    Mixing: Use a stirring rod or magnetic stir bar to mix liquids. Do not use any glassware to mix liquids that are not designed for that purpose.

o    Heating: Use a Bunsen burner or hot plate to heat glassware. Use a wire gauze mat to distribute the heat evenly and prevent direct contact between the glassware and the heat source.

o    Cooling: Use a beaker or flask filled with ice or cold water to cool glassware.

o    Transferring: Use a pipette, burette, or transfer pipette to transfer liquids between glassware. Avoid touching the glassware with the pipette tip or any other object. (DO NOT MOUTH PIPETTE)

o    Disposal: Dispose of all glassware according to your lab's protocols for hazardous waste disposal.

o    Storage: Store all glassware in a designated area, away from any heat sources or direct sunlight. Label all glassware with its intended use and keep it organized and easily accessible.

·         Microscopes: Before using a microscope, ensure that it is clean and properly adjusted. Adjust the focus and stage height as needed, and always use the lowest magnification to start. Use the stage controls to move the specimen and adjust the focus. Do not force any parts of the microscope or touch the lenses with your fingers.

·         Bunsen burner: Before lighting a Bunsen burner, ensure that the gas valve is open and the air intake is adjusted properly. Use a striker or match to light the burner, and adjust the flame as needed using the air intake. Never leave a lit Bunsen burner unattended, and always turn it off when finished.

·         Centrifuges: Load samples into centrifuge tubes or microcentrifuge tubes, being careful not to overfill them. Balance the tubes in the centrifuge and set the appropriate speed and time. Always wear appropriate personal protective equipment when using a centrifuge.

·         Balances: Calibrate the balance before use and ensure that it is properly zeroed. Place the object to be weighed on the balance and wait for the reading to stabilize. Use a clean spatula to handle the object and avoid touching it with your fingers.

·         Autoclaves: Load the autoclave with items to be sterilized and ensure that they are properly wrapped or packaged. Set the appropriate temperature and time for the cycle and start the autoclave. Follow all safety precautions, including wearing appropriate personal protective equipment.

·         Pipettes: Select the appropriate size pipette for the volume you need to measure. Insert the pipette tip into the liquid and slowly release the plunger to draw the liquid into the pipette. Dispense the liquid into the appropriate container, being careful not to touch the pipette tip to any surfaces.

·         pH meters: Calibrate the pH meter according to the manufacturer's instructions. Immerse the electrode in the solution to be measured and wait for the reading to stabilize. Rinse the electrode with distilled water between measurements.

·         Spectrophotometers: Prepare the sample according to the manufacturer's instructions and load it into a cuvette. Set the wavelength and adjust the sample compartment as needed. Record the absorbance reading and compare it to standards or controls.

Heating Safety

·         I will use hot plates and burners only for their intended purpose.

·         I will not touch hot plates, burners, or other hot surfaces.

·         I will allow equipment to cool before touching or moving it.

·         I will use appropriate protective gear, such as oven mitts, when handling hot equipment.

·         I will never leave heating equipment unattended.

·         I will use appropriate protective equipment, such as gloves, lab coats, and safety goggles, when working with heating equipment.

·         I will ensure that all heating equipment is in good working condition and properly grounded.

·         I will avoid overheating by regulating temperature and carefully monitoring the equipment.

·         I will keep flammable materials and liquids away from heating equipment.

·         I will follow all manufacturer instructions for operating and maintaining heating equipment.

·         I will familiarize yourself with the emergency procedures in case of accidents, such as fire or burns.

·         I will always turn off heating equipment after use and unplug it from the outlet.

·         I will store heating equipment in a safe and secure location when not in use.

·         I will keep the work area clean and organized to prevent accidents and ensure safe use of heating equipment.

If there are physical, medical, mental, emotional, religious, or other concern about a chemical, lab practice, experiment, etc. notify the instructor as soon as possible.  Health issues are taken seriously, to avoid harm to the student.  You are not required to volunteer personal information, but it may improve the assistance received (i.e.: if a student is pregnant but doesn’t relay this information to the instructor, they may not be alerted to certain chemicals that could to harmful during pregnancy.  Or, if a student is allergic to penicillin and doesn’t inform the instructor they may not be aware of the usage of penicillin in some labs). 

Biosafety is of paramount importance in any microbiology laboratory setting, as it encompasses a range of practices and protocols designed to protect individuals, the community, and the environment from potential risks associated with the handling of microorganisms. In a microbiology laboratory, where students engage in hands-on activities with potentially hazardous microorganisms, understanding and practicing biosafety measures are crucial to ensure a safe and productive learning environment.

Biosafety measures safeguard the health and well-being of individuals working in the laboratory. Microorganisms used in lab settings can pose a variety of risks, including infections, allergic reactions, and exposure to hazardous materials. By adhering to proper biosafety protocols, students and instructors can minimize these risks and protect themselves from harm.

Proper biosafety practices help prevent the accidental release of microorganisms into the environment. Some microorganisms used in laboratories may have the potential to cause harm if they enter ecosystems outside the controlled setting. By implementing containment measures, the spread of these organisms can be effectively controlled and mitigated.

Biosafety protocols also contribute to safeguarding public health. Ensuring that potentially harmful microorganisms are handled safely within a laboratory environment prevents the accidental release or dissemination of these organisms into the community, thereby reducing the risk of disease transmission and outbreaks.

Protective Measures in a Microbiology Lab

Laboratory personnel should wear appropriate Personal Protective Equipment (PPE), including lab coats, gloves, protective eyewear, and closed-toe shoes. PPE acts as a physical barrier, preventing direct contact between microorganisms and the skin, eyes, or respiratory system.

Proper hand hygiene is essential in a microbiology lab. Hands should be washed thoroughly before entering the lab, after handling microorganisms, and before leaving the lab. Handwashing with soap and water or using hand sanitizers effectively reduces the risk of cross-contamination.

Adhering to Good Laboratory Practices (GLP) is crucial for maintaining a safe environment. This includes proper handling, storage, and disposal of microorganisms, as well as keeping the workspace clean and organized to minimize the risk of accidents and contamination.

When working with infectious agents, it is important to utilize Biological Safety Cabinets (BSCs), which provide a controlled environment for handling hazardous materials. BSCs prevent the release of microorganisms into the surrounding environment while protecting the worker from exposure.

Bio-Safety Levels

Bio-safety levels (BSL) categorize laboratories based on the degree of risk associated with the microorganisms being handled.

Biosafety is of utmost importance in a microbiology laboratory. It serves to protect individuals, prevent environmental contamination, and ensure public health. By adhering to proper biosafety practices, including the use of PPE, good laboratory hygiene, and understanding and implementing the appropriate bio-safety level for the microorganisms being handled, students and instructors can create a safe and conducive learning environment while working with potentially hazardous microorganisms.

BSL-1

This level represents the lowest risk and is suitable for handling well-characterized microorganisms that are not known to cause disease in healthy individuals. Standard laboratory practices are sufficient for safety.

Microorganisms Allowed:

·         Well-characterized microorganisms not known to cause disease in healthy individuals.

Laboratory Practices:

·         Basic aseptic techniques.

·         Handwashing and proper hygiene.

·         No eating, drinking, or applying cosmetics in the laboratory.

Personal Protective Equipment:

·         Lab coats and gloves are recommended.

Facility Requirements:

·         Standard microbiological laboratory facilities.

·         Adequate ventilation.

Waste Management:

·         Routine disposal of non-infectious waste following standard laboratory protocols.

BSL-2

This level is designed for moderate-risk agents that pose a potential hazard through ingestion, inhalation, or direct contact. Additional safety measures, such as the use of PPE, biological safety cabinets, and waste management protocols, are implemented.

Microorganisms Allowed:

·         Moderately hazardous agents that pose a risk through ingestion, inhalation, or direct contact.

Laboratory Practices:

·         BSL-1 practices plus additional precautions.

·         Restricted access to authorized personnel.

·         Awareness of potential hazards.

Personal Protective Equipment:

·         Lab coats, gloves, eye protection.

Facility Requirements:

·         Designated work areas.

·         Use of biological safety cabinets for procedures that may generate aerosols.

Waste Management:

·         Decontamination of waste before disposal.

·         Use of autoclaves for sterilization.

BSL-3

BSL-3 labs are used for handling indigenous or exotic agents that can cause serious or potentially lethal diseases through respiratory transmission. Strict containment measures, including controlled access, negative airflow, and decontamination procedures, are enforced.

Microorganisms Allowed:

·         Indigenous or exotic agents causing serious diseases through respiratory transmission.

Laboratory Practices:

·         BSL-2 practices plus additional precautions.

·         Controlled access to the laboratory.

·         Specialized training for personnel.

Personal Protective Equipment:

·         All BSL-2 PPE plus respiratory protection.

Facility Requirements:

·         Negative airflow systems.

·         Strict entry and exit protocols.

·         Dedicated facilities or areas.

Waste Management:

·         Decontamination of waste.

·         Autoclaving or incineration for disposal.

BSL-4

This highest level of containment is reserved for highly dangerous and exotic agents that pose a severe threat to public health, often without known treatments or vaccines. BSL-4 laboratories have the highest level of security and include complex engineering controls and procedures to ensure maximum containment.

Microorganisms Allowed:

·         Highly dangerous and exotic agents without known treatments or vaccines.

Laboratory Practices:

·         BSL-3 practices plus additional precautions.

·         Complete personnel protective suits.

·         Shower-in, shower-out procedures.

Personal Protective Equipment:

·         All BSL-3 PPE plus full-body suits, including positive pressure respirators.

Facility Requirements:

·         Highly controlled access with security measures.

·         Separate building or isolated zone within a facility.

·         Complex engineering controls for maximum containment.

Waste Management:

·         Decontamination of all waste.

·         Incineration or specialized disposal methods.

Good documentation practices (GDP) are essential in a microbiology laboratory to ensure accurate and reliable record-keeping, traceability, and compliance with regulatory requirements. Proper documentation is vital for maintaining the integrity of experimental data, facilitating reproducibility, and supporting quality control and assurance processes. Here are some key principles and guidelines for implementing good documentation practices in a microbiology laboratory:

·         Clear and Legible Records: All documentation should be legible, written in permanent ink or using electronic systems, and free from alterations or unauthorized modifications. Use clear and concise language, avoiding jargon or abbreviations that may cause confusion. Illegible or unclear records can lead to errors or misinterpretations, compromising the integrity of the data.

·         Document Everything: It is crucial to document all relevant information associated with an experiment or procedure. This includes experimental protocols, procedures, observations, calculations, results, and any deviations or unexpected events. Recording details of reagents, equipment, lot numbers, and expiration dates ensures traceability and aids in troubleshooting or future replication of experiments.

·         Timely and Contemporaneous Entries: Document information in real-time, as the work is being performed. Delayed or retrospective documentation increases the risk of errors or omissions. Make entries immediately after completing a task or making an observation, and include the date, time, and signature or initials. This practice ensures accuracy and avoids confusion or loss of critical information.

·         Use Standardized Forms and Templates: Utilize standardized forms, templates, or electronic systems for recording data and observations. These tools provide structure and consistency, making it easier to locate and interpret information. Standardized formats also facilitate data analysis and reporting.

·         Version Control and Signatures: Whenever changes are made to a document, maintain version control by indicating the revision number or date. Ensure that each version has appropriate authorization and sign-off by the relevant personnel. Clearly indicate who made the changes and the reason for the modification. This practice ensures accountability and helps in tracking the evolution of documents.

·         Record Keeping and Retention: Establish a record retention policy in compliance with applicable regulations and institutional guidelines. Clearly define the duration for which records should be retained and ensure proper storage and accessibility of documents. Proper archiving allows for future reference, audits, and regulatory inspections.

·         Data Integrity and Security: Protect the integrity and security of data through appropriate measures. This includes safeguarding electronic records with secure backup systems, implementing user access controls, and using password-protected accounts. Regularly validate and verify electronic systems to ensure data integrity and prevent unauthorized access or tampering.

·         Training and Documentation Awareness: Provide training to laboratory personnel on the importance of good documentation practices and the specific guidelines and requirements of the laboratory. Ensure that all staff members understand the significance of accurate and complete documentation and are familiar with the laboratory's documentation procedures and protocols.

By adhering to these good documentation practices, microbiology laboratories can maintain accurate and reliable records, ensure data integrity, and meet regulatory requirements. Good documentation practices enhance the quality and transparency of laboratory work, supporting scientific integrity, and facilitating effective communication and collaboration among researchers. 

Acid-Fast Staining: A differential staining technique used to identify bacteria with waxy cell walls, such as Mycobacterium species, by their resistance to decolorization by acids.

Acne: A common skin condition characterized by clogged hair follicles, leading to pimples, blackheads, and cysts, often caused by hormonal changes and bacteria.

Aerobic: Referring to processes or organisms that require oxygen for growth and metabolism.

Agar: A gelatinous substance derived from seaweed, used as a solidifying agent in microbiological culture media.

Airborne Transmission: The spread of pathogens through the air, typically via respiratory droplets or dust particles.

Alkaliphiles: Microorganisms that thrive in highly alkaline environments (pH above 9).

Anaerobic: Referring to processes or organisms that do not require oxygen for growth and may even be harmed by it.

Anaerobic Media: Culture media designed to support the growth of anaerobic microorganisms by excluding oxygen.

Antibiotics: Drugs used to kill or inhibit the growth of bacteria.

Antifungals: Medications used to treat fungal infections.

Antivirals: Drugs used to treat viral infections by inhibiting the development of the virus.

Aseptic Technique: A set of practices used to prevent contamination by pathogens during medical or laboratory procedures.

Autoclaving: A sterilization method that uses high-pressure steam at high temperatures to kill microorganisms.

Bacillus: A genus of rod-shaped bacteria, some of which are known to form endospores and are important in agriculture and industry.

Bacterial Sampling: The process of collecting samples from various environments to detect and identify bacterial species.

Bacteroides Bile Esculin Agar: A selective and differential medium used to isolate and identify Bacteroides species based on their ability to hydrolyze esculin in the presence of bile.

Basic Reproduction Number: A measure of the number of secondary infections produced by an infected individual in a completely susceptible population.

Benzoyl Peroxide: An antibacterial agent commonly used in the treatment of acne.

Bergey's Manual: A comprehensive reference for the classification and identification of bacteria.

Bile Esculin Agar: A selective and differential medium used to identify enterococci and some other bacteria based on their ability to hydrolyze esculin.

Biological Safety Cabinets (BSCs): Enclosures designed to protect laboratory workers and the environment from exposure to hazardous biological agents.

Biosafety: The practice of managing biological risks to protect health and the environment.

Bio-safety Levels (BSL): Classification system for laboratories based on the level of risk associated with the biological agents handled.

Blood Agar: A rich medium that supports the growth of a wide range of bacteria and is used to assess hemolytic activity.

Boiling: A heat-based method used to kill microorganisms, though not always effective against all types of spores.

Broth: A liquid culture medium used to grow bacteria in a liquid form.

Campylobacter Agar: A selective medium for isolating Campylobacter species, important in foodborne illness.

Casease Test: A test used to determine if a bacterium produces the enzyme casease, which breaks down casein in milk.

Catalase Test: A test used to identify bacteria that produce the enzyme catalase, which breaks down hydrogen peroxide.

Chocolate Agar: A type of enriched agar medium used for growing fastidious bacteria, named for its chocolate-brown color.

Citrate Agar: A medium used to test an organism's ability to utilize citrate as the sole carbon source.

Coagulase Test: A test to identify bacteria that produce the enzyme coagulase, which clots blood plasma.

Cocci: Spherical-shaped bacteria.

Coccobacillus: A bacterial shape that is intermediate between cocci and bacilli.

Colony Counting: The process of counting the number of colonies on an agar plate to estimate the number of viable microorganisms.

Colony Morphology: The characteristics of bacterial colonies, including shape, size, color, and texture, used for identification.

Comedones: Skin lesions caused by clogged hair follicles, commonly associated with acne.

Contact Tracing: The process of identifying and notifying individuals who may have been exposed to an infectious disease.

Cysts: A dormant, resistant form of some microorganisms that can survive in harsh conditions.

Decontamination: The process of removing or neutralizing contaminants to reduce the risk of infection.

Deeps: Tubes of solidified agar used to determine the oxygen requirements of microorganisms.

Desoxycholate Agar: A selective medium for isolating gram-negative bacteria, particularly enteric bacteria.

Differential Media: Media designed to distinguish between different types of bacteria based on specific biochemical characteristics.

Differential Staining: Staining techniques that differentiate between types of cells or cellular components, such as Gram staining.

Differential Tests: Tests used to differentiate bacterial species based on biochemical reactions.

Dilution Series: A series of solutions with decreasing concentrations used to determine the concentration of microorganisms.

Diplo: Referring to bacteria that occur in pairs.

Direct Contact: Transmission of pathogens through physical contact with an infected individual or contaminated surface.

Disinfecting: The process of cleaning to remove or destroy pathogens.

Disinfection: The use of chemical or physical agents to destroy or inhibit the growth of pathogens.

DNase Test: A test used to determine if an organism produces deoxyribonuclease, an enzyme that breaks down DNA.

Edge Margin: The appearance of the edge of a bacterial colony, which can help in identification.

Elevation: The height of a bacterial colony above the surface of the agar, which can be observed during colony morphology studies.

Emergence: The appearance of new infectious diseases or the reappearance of old ones.

Endo Agar: A selective medium used to isolate gram-negative bacteria, particularly coliforms.

Endospore Staining: A staining technique used to visualize bacterial endospores, which are resistant to harsh conditions.

Enriched Media: Media that contain additional nutrients to support the growth of fastidious organisms.

Environmental: Pertaining to the surroundings or conditions in which microorganisms live and grow.

Eosin Methylene Blue Agar: A selective and differential medium used to isolate gram-negative bacteria and differentiate between lactose fermenters and non-fermenters.

Facultative Anaerobes: Microorganisms that can grow in both the presence and absence of oxygen.

Fanny Hesse: A microbiologist known for her contributions to the development of agar as a medium for bacterial culture.

Fecal-Oral Transmission: Transmission of pathogens from feces to the mouth, often through contaminated food or water.

Filtration: A method of separating microorganisms from liquids or gases using a filter.

Flaming: The process of sterilizing equipment by passing it through a flame.

Follicular Hyperkeratinization: An abnormal increase in keratin production in hair follicles, often seen in acne.

Gelatinase Test: A test used to determine if a microorganism produces gelatinase, an enzyme that liquefies gelatin.

Good Documentation Practices (GDP): Procedures for ensuring accurate and reliable documentation in laboratories.

Good Laboratory Practices (GLP): Standards for ensuring the quality and reliability of laboratory practices and data.

Gram Staining: A differential staining method used to classify bacteria into gram-positive and gram-negative based on cell wall properties.

Hektoen Enteric Agar: A selective and differential medium used to isolate and differentiate enteric gram-negative bacteria.

Impact: The effect or influence of an event, action, or pathogen on a population or environment.

Incineration: A method of sterilization that involves burning waste materials to destroy microorganisms.

Indirect Contact: Transmission of pathogens through contaminated intermediate objects or surfaces.

Inoculating Loop: A tool used to transfer microorganisms onto culture media.

Inoculating Needle: A tool used to transfer microorganisms into media, typically used for stab cultures.

Kirby-Bauer: A method for testing the susceptibility of bacteria to antibiotics using agar diffusion.

Lawn Creation (Spread Plating): A technique for evenly spreading bacteria over an agar plate to create a uniform growth lawn.

Lipase Test: A test used to determine if a bacterium produces lipase, an enzyme that breaks down lipids.

Lowenstein-Jensen Medium: An enriched medium used for the cultivation of Mycobacterium species, particularly tuberculosis.

MacConkey Agar: A selective and differential medium used to isolate and differentiate gram-negative bacteria based on lactose fermentation.

Magnification: The process of enlarging the appearance of an object using a microscope.

Malonate Test: A test used to determine if a bacterium can use malonate as the sole carbon source.

Mannitol Salt Agar: A selective and differential medium used to isolate Staphylococcus species based on their ability to ferment mannitol.

Media: Substances used to grow microorganisms in a laboratory setting.

Mesophiles: Microorganisms that thrive at moderate temperatures, typically between 20°C and 45°C.

Methyl Red: A test used to detect mixed acid fermentation in bacteria.

Micrograph: An image taken through a microscope, showing details not visible to the naked eye.

Microscopes: Instruments used to view objects that are too small to be seen with the naked eye.

Modes of Transmission: The various ways in which pathogens spread from one host to another.

Nitrate Reduction Broth: A medium used to test a microorganism's ability to reduce nitrate to nitrite or other nitrogenous compounds.

Nodules: Solid, raised lesions found in the skin or under the skin, often associated with certain infections or conditions.

Nutrient Agar: A general-purpose medium used to grow a wide range of non-fibrous bacteria.

Nutrient Broth: A liquid medium used for growing bacteria in a liquid form.

Oxidase Test: A test used to determine if a bacterium produces the enzyme cytochrome c oxidase.

Papules: Small, raised skin lesions that can be inflamed or infected.

Pasteurization: A heat treatment process that kills pathogens in food and beverages without significantly affecting taste or quality.

Personal Protective Equipment (PPE): Clothing and equipment worn to protect individuals from exposure to hazardous materials.

Phenol Red Broth: A medium used to test carbohydrate fermentation and gas production in bacteria.

Phenylethyl Alcohol Agar: A selective medium used to isolate gram-positive bacteria.

Pigmentation: The color of bacterial colonies or cells, which can aid in identification.

Pipette: A laboratory tool used to transfer precise volumes of liquids.

Plates: Petri dishes containing agar used to culture and isolate microorganisms.

Post-Inflammatory Hyperpigmentation: Darkening of the skin that occurs after an inflammatory skin condition has healed.

Preservation: Methods used to prevent the growth of microorganisms and maintain the integrity of samples.

Prevalence: The proportion of a population that has a particular condition or disease at a specific time.

Psychrophiles: Microorganisms that thrive at very low temperatures, typically below 15°C.

Pustules: Small, inflamed lesions containing pus, often seen in acne.

Quadrant Streaking: A technique used to isolate individual bacterial colonies on an agar plate.

Resolution: The ability of a microscope to distinguish between two points that are close together.

Retinoids: A class of compounds related to vitamin A, used in the treatment of acne and other skin conditions.

Sabouraud Dextrose Agar: A medium used to grow fungi, particularly yeasts and molds.

Salicylic Acid: An active ingredient in many acne treatments, known for its ability to exfoliate and unclog pores.

Sanitization: The process of reducing the number of microorganisms to a safe level.

Scarring: The formation of fibrous tissue following injury or inflammation of the skin.

Sebaceous Glands: Glands in the skin that produce sebum, an oily substance that helps lubricate and protect the skin.

Sebum: An oily substance produced by sebaceous glands that helps to lubricate and protect the skin.

Selective Media: Media designed to inhibit the growth of some microorganisms while allowing others to grow.

Sexually Transmitted Infections (STIs): Infections transmitted through sexual contact.

Slants: Tubes of agar that are solidified at an angle, providing a larger surface area for bacterial growth.

Specialized Media: Media formulated to support the growth of specific types of microorganisms.

Spirillum: A genus of spiral-shaped bacteria.

Spirochete: A type of spiral-shaped bacteria with a unique motility pattern.

Spreaders: Tools or techniques used to evenly distribute microorganisms over an agar plate.

Staphylo: Referring to bacteria that occur in clusters, such as Staphylococcus species.

Starch Agar: A medium used to test the ability of microorganisms to hydrolyze starch.

Sterilants: Chemicals used to completely destroy all forms of microbial life, including spores.

Sterilization: The process of eliminating all forms of microbial life from an object or surface.

Streaking: A technique used to isolate individual bacterial colonies on an agar plate.

Strepto: Referring to bacteria that occur in chains, such as Streptococcus species.

Sulfide Indole Motility Agar (SIM): A medium used to test for sulfide production, indole formation, and motility in bacteria.

Susceptibility Testing: Tests used to determine the effectiveness of antibiotics or other antimicrobial agents against microorganisms.

Swab: A tool used to collect samples from surfaces or individuals for microbiological analysis.

Tetrads: Groups of four bacteria arranged in a square pattern.

Thayer-Martin Agar: A selective medium used to isolate Neisseria gonorrhoeae.

Thermophiles: Microorganisms that thrive at high temperatures, typically above 45°C.

Thioglycollate Broth: A medium used to determine the oxygen requirements of microorganisms.

Triple Sugar Iron Agar (TSI): A differential medium used to test for glucose, lactose, and sucrose fermentation as well as hydrogen sulfide production.

Tryptic Soy Agar: A general-purpose medium used for the growth of a wide variety of bacteria.

Urease Test: A test used to determine if a bacterium produces urease, an enzyme that hydrolyzes urea to ammonia.

Vector-borne Transmission: Transmission of pathogens through vectors such as insects.

Vertical Transmission: Transmission of pathogens from parent to offspring during pregnancy, childbirth, or breastfeeding.

Vibrio: A genus of comma-shaped bacteria, some of which are pathogenic.

Voges-Proskauer: A test used to detect acetoin production in bacterial fermentation.

Xylose Lysine Desoxycholate Agar: A selective and differential medium used to isolate gram-negative enteric bacteria.

This manual references and supports the OpenStax Microbiology textbook, along with other sources from the public domain.