Microbiology Course Overview
GPT Knowledge File - Institution-Neutral Version
This document is a simplified, institution-neutral course overview for a microbiology course and its laboratory component. It combines the course overview, lecture and lab schedule, grading structure, attendance expectations, and laboratory safety agreement into one AI-readable file.
This file is intended for a course overview GPT. It is not a replacement for the official course syllabus, official Canvas site, official announcements, or instructor directions. If anything in this file differs from the most recent official course communication, students should follow the most recent official course communication.
1. Course Identity
Course Title
Microbiology Course
Course Type
Lecture course with required laboratory component.
Term
Summer 2026
Delivery Modality
Live in-person course, with official course materials and updates provided through Canvas or the official course learning management system.
Meeting Pattern
- Lecture sessions generally meet Mondays and Tuesdays, 1:00 pm to 2:50 pm.
- Laboratory sessions generally meet Wednesdays, 1:00 pm to 3:50 pm.
- Students should always verify the official room/location and any changes through the official course Canvas site or instructor announcements.
Final Exam Period
Final course activities and examinations are scheduled during the week of August 10 to August 14, 2026.
2. Instructor Communication and Office Hours
Students may contact the instructor through the official course communication channels, including Canvas Inbox or the official course email method provided by the instructor.
The instructor will generally try to respond within 24 hours. For non-essential matters, responses may take up to 48 hours. For urgent matters, students should follow the official communication process provided by the course or university.
Office / Online Hours
Official office hours are Tuesdays, 3:00 pm to 4:00 pm, after lecture. Students may also schedule Zoom meetings or other online meetings throughout the week by prior appointment. Students should contact the instructor in advance to arrange an appointment.
Best Time to Contact
Students should try to contact the instructor before 8:00 pm Pacific Time for routine course-related communication.
3. Course Description
Medical microbiology is the study of microorganisms that cause infection and disease in humans, with emphasis on clinically important bacteria, fungi, viruses, and parasites relevant to medical and podiatric practice. The course introduces students to the structure, transmission, virulence, diagnosis, prevention, and treatment-related principles of infectious organisms.
Students will learn to distinguish normal microbial flora, true pathogens, opportunistic pathogens, and non-pathogens, and to connect common microbes with the diseases and clinical patterns they produce.
The laboratory component emphasizes basic microbiological techniques used for the isolation, observation, and identification of common bacteria and fungi encountered in clinical and podiatric settings. Laboratory exercises may include aseptic technique, microscopy, staining, culture methods, interpretation of microbial growth, and antimicrobial susceptibility testing.
4. Course Materials
Required Textbook
Lippincott Illustrated Reviews: Microbiology is the required textbook for this course. The overall learning framework, visual organization, and core microbiology structure of the course are based on this resource. Students are strongly expected to obtain access to the textbook as early as possible.
Students are encouraged to maintain a physical copy of the textbook because repeated review, annotation, visual memory, and long-term retention are valuable for medical training and board preparation. Students may also use legally accessible electronic versions, library-accessible versions, or other authorized digital formats when available.
Additional Required Materials
Additional required course materials may include instructor-provided lecture slides, laboratory instructions, handouts, study guides, review materials, Canvas modules, and other materials posted in Canvas.
Recommended Materials
First Aid for the USMLE Step 1 may be used as a supplemental board-style review resource for microbiology and related high-yield concepts. It is useful for organizing and reviewing high-yield information, but it does not replace instructor-directed course content or the required Lippincott textbook.
Additional instructor-approved resources may be provided in Canvas to support APMLE-relevant, podiatry-relevant, and clinically relevant microbiology learning.
5. Course Learning Outcomes
By the end of the course, students should be able to:
- Describe the structural components of microbes, including bacteria, fungi, and viruses, and relate these components to the pathogenesis of disease.
- Correlate common microbes associated with specific clinical diseases with their source, mode of transmission, virulence factors, and disease risk groups.
- Relate results of common clinical laboratory tests to the diagnosis and management of specific infectious diseases.
- Explain the role of antimicrobial methods, including sterilization, disinfection, antisepsis, antimicrobial drugs, and vaccines, in the treatment and prevention of microbial diseases.
- Consult the scientific literature to verify, expand, and maintain the currency of professional knowledge.
- Perform and interpret common clinical laboratory microbiological methods, including aseptic technique, Gram stain, isolation of pure cultures, and antibiotic sensitivity testing.
6. Teaching Methods and Learning Experiences
This course uses in-person lectures, laboratory exercises, clinical correlations, case-based discussion, posted lecture materials, and Canvas-supported course materials.
Lecture sessions introduce core microbiology concepts, clinically important organisms, mechanisms of disease, diagnostic principles, antimicrobial and prevention concepts, and board-relevant patterns.
Laboratory sessions support hands-on and applied learning through microbiological techniques, organism observation, staining, culture-based exercises, interpretation of laboratory findings, and clinical identification skills.
Students are expected to engage with lecture content, laboratory activities, Canvas materials, assigned resources, and review materials throughout the course.
7. Methods of Student Assessment
Student performance may be assessed through lecture-based quizzes, lab-based assignments, the final lecture examination, the final laboratory examination, the Grand Microbiology Rounds seminar/presentation, and other course assignments as posted in Canvas.
Lecture-based quizzes will generally be administered after lecture sessions and will emphasize clinically relevant and board-aligned multiple-choice questions, clinical application, and microbiology concepts relevant to medical and podiatric practice.
Lab-based assignments will generally be completed during or after laboratory sessions and may include handwritten or submitted work demonstrating engagement with laboratory material, organism identification, board-relevant points, and instructor-directed learning tasks. Lab-based assignments may be graded primarily on completion, submission, and reasonable evidence of active work, as specified in Canvas.
Students are responsible for all assigned lecture content, laboratory content, Canvas materials, instructor-directed course materials, and posted instructions for course assignments and presentations.
8. Grading
Assignment Weights
| Assignment Group | Weight |
|---|---|
| Lecture-based quizzes | 40% |
| Lab-based assignments | 20% |
| Grand Microbiology Rounds seminar/presentation | 10% |
| Final lecture examination | 20% |
| Final laboratory examination | 10% |
| Total | 100% |
Grading Scale
| Course Percentage | Letter Grade |
|---|---|
| 89.9% - 100% | A |
| 79.9% - 89.9% | B |
| 69.9% - 79.9% | C |
| Below 69.9% | F |
9. Course Policies
Late or Missed Assignments
Late or missed assignments, quizzes, laboratory assessments, examinations, or presentations will be handled according to the university's official excused absence and course procedures. Students should contact the appropriate administrative office or official course contact and notify the instructor as soon as possible if they anticipate missing a required course activity.
The instructor understands that emergencies, illness, or critical situations may occur and will make reasonable accommodations when appropriate. However, students remain responsible for covering missed course content and completing or submitting required assignments, quizzes, laboratory work, examinations, or presentations as directed. Completion and submission of required work may be tracked through Canvas or other course records.
Attendance
Attendance is mandatory for scheduled lectures, laboratories, examinations, and required course activities unless excused through the appropriate official university procedures.
Participation
Participation is mandatory. Students are expected to participate professionally in lectures, laboratories, discussions, presentations, and other required course activities.
Official Policies
Students are responsible for following all applicable university policies, course policies, student conduct expectations, academic integrity rules, safety requirements, and official instructor directions. Students should refer to the official university handbook, Canvas course, and instructor communications for the authoritative version of all institutional policies.
10. Important Week 1 Schedule Note
The first scheduled lecture, originally planned for Monday, June 22, 2026, has been specially rescheduled because of a conflicting university event.
Special Rescheduled Session 1
- Date and time: Thursday, June 25, 2026, 10:00 am to 11:50 am.
- This reschedule applies only to the first lecture session.
- For this one session only, synchronous/in-person attendance is not mandatory.
- The lecture will be recorded live and posted online.
- Students who would like to attend live during the recording are welcome to do so at the assigned recording location.
- Students who do not attend live must watch the posted Panopto recording.
- Completion of the recording is mandatory and will be tracked through Panopto viewing/completion data.
- All other lectures and labs require attendance unless a student has a documented issue or special circumstance and communicates with the instructor.
- Because of this special reschedule, Session 2 will occur before Session 1 on the calendar during Week 1 only.
11. Lecture Schedule
| Week | Date | Session | Lecture Title | Main Content |
|---|---|---|---|---|
| Week 1 | Tue, June 23 | Session 2 | Diagnostics & Microbial Control | Specimens, microscopy, Gram stain and acid-fast stain logic, media/culture, hemolysis, susceptibility testing, MIC/MBC, sterilization, disinfection, antisepsis, microbial control methods. |
| Week 1 | Thu, June 25, 10:00-11:50 AM | Session 1 - Special Rescheduled Session | Foundations | Normal flora, microbiome, colonization vs. infection, contamination vs. disease, acute/chronic/latent infection vocabulary, transmission, reservoirs, vectors, basic pathogenesis, podiatric wound/diabetic-foot infection reasoning. |
| Week 2 | Mon, June 29 | Session 3 | Basic Bacteriology | Prokaryotic structure, Gram-positive/Gram-negative/acid-fast walls, peptidoglycan, capsules, pili, flagella, biofilm, growth, metabolism, spores, bacterial genetics, toxins, virulence. |
| Week 2 | Tue, June 30 | Session 4 | Antimicrobial Foundations | Empiric vs. targeted therapy, bactericidal vs. bacteriostatic drugs, antibacterial classes, mechanisms of action, resistance mechanisms, stewardship, source control, podiatric wound/osteomyelitis antibiotic logic. |
| Week 3 | Mon, July 6 | Session 5 | Gram-Positive Cocci | Staphylococcus, Streptococcus, Enterococcus, catalase/coagulase/hemolysis logic, MRSA, cellulitis, abscess, necrotizing fasciitis, osteomyelitis, septic arthritis, toxic shock, post-strep complications. |
| Week 3 | Tue, July 7 | Session 6 | Gram-Positive Rods & Anaerobes | Bacillus, Clostridium/Clostridioides, Corynebacterium, Listeria, Actinomyces, spores, toxin-mediated disease, tetanus, gas gangrene, C. difficile, anaerobic wound infection, debridement/source control. |
| Week 4 | Mon, July 13 | Session 7 | Gram-Negative Organisms | Neisseria, Haemophilus, Enterobacteriaceae, E. coli, Klebsiella, Proteus, Salmonella, Shigella, Yersinia, Pseudomonas, Vibrio, endotoxin, sepsis, wound/GU/GI/respiratory relevance. |
| Week 4 | Tue, July 14 | Session 8 | Atypical, Chronic & Intracellular Organisms | Mycoplasma, Chlamydia, Rickettsia, Coxiella, Ehrlichia, Anaplasma, spirochetes, mycobacteria, Nocardia, Actinomyces, chronic cutaneous lesions, intracellular survival, granuloma/TB logic. |
| Week 5 | Mon, July 20 | Session 9 | Podiatry Core I: Skin & Soft Tissue | Lesion vocabulary, cellulitis vs. erysipelas vs. abscess, necrotizing infection, puncture wounds, bite wounds, bacterial skin pathogens, viral skin pathogens, dermatophytes, superficial fungi, cutaneous parasites. |
| Week 5 | Tue, July 21 | Session 10 | Podiatry Core II: Diabetic Foot, Bone & Joint | Diabetic foot infection, colonization vs. infection, osteomyelitis, septic arthritis, polymicrobial infection, anaerobes, biofilm, deep culture/bone culture, podiatric mycology, antifungal logic. |
| Week 6 | Mon, July 27 | Session 11 | Virology I: Structure & DNA Viruses | Viral structure, envelope vs. non-envelope, viral replication, latency/reactivation, DNA viruses, herpesviruses, HPV, HBV, parvovirus, poxviruses, antiviral target logic, vaccine-platform recognition. |
| Week 6 | Tue, July 28 | Session 12 | Virology II + Fungal & Parasite Foundations | RNA viruses, influenza, HIV, hepatitis viruses, SARS-CoV-2 recognition, prions, fungal cell biology, KOH prep, dermatophytes, systemic fungi, parasite life stages, protozoa, helminths, antiparasitic logic. |
| Week 7 | Mon, August 3 | Session 13 | Systems I: Gastrointestinal + Genitourinary/STI | Diarrhea mechanisms, GI bacteria/viruses/parasites, food poisoning timing, hepatitis A-E, oral infections, UTIs, STI organisms, syphilis serology, gonorrhea, chlamydia, HSV, HPV, Trichomonas, Candida. |
| Week 7 | Tue, August 4 | Session 14 | Systems II + Final Clinical Integration | Respiratory infections, CNS infections, meningitis/encephalitis, cardiac infections, endocarditis/myocarditis, sepsis, DIC, zoonotic infections, opportunistic infections, bite wounds, final board-style clinical integration. |
| Finals Week | Mon, August 10 | Review / Presentation Preparation | Final Review & Grand Seminar Preparation | Review of major course themes, board-style integration, organism ID, diagnostic reasoning, culture/stain/media interpretation, antimicrobial logic, podiatric applications, and preparation for the Grand Microbiology Seminar presentations. |
| Finals Week | Tue, August 11 | Grand Seminar | Grand Microbiology Seminar / Student Presentations | Student Grand Microbiology Seminar presentations. Students will integrate microbiology, clinical reasoning, podiatric relevance, diagnostic clues, organism identification, antimicrobial logic, and disease presentation. |
| Finals Week | Wed, August 12 | Final Exam | Combined Lecture + Lab Final Exam | Combined cumulative lecture/lab final held in the microbiology lab. Focus: organism ID, diagnostic reasoning, culture/stain/media interpretation, antimicrobial logic, podiatric application, systemic danger signs, and lab interpretation. |
12. Laboratory Schedule
| Week | Date | Lab Title | Exercises / Main Activities |
|---|---|---|---|
| Week 1 | Wed, June 24 | Lab 1 - Core Microbiology Skills | Ex 1 complete + Ex 2.1 + Ex 3.1. Notebook/microscope orientation, oil immersion, Gram stain, streak plate setup, and air-plate exposure. |
| Week 2 | Wed, July 1 | Lab 2 - Colony Morphology & Human Normal Flora | Ex 2.2 + Ex 3.2 + Ex 5.1. Read streak plates, compare BHI/SAB colony morphology, Gram stain selected colonies, restreak, and begin throat/nose/skin normal-flora cultures. |
| Week 3 | Wed, July 8 | Lab 3 - Normal Flora & Infection Control | Ex 3.3 + Ex 5.2 + Ex 6.1. Read air-microbe pure cultures, observe BA/MSA plates, compare hemolysis/mannitol fermentation, restreak selected colonies, and begin handwashing/antisepsis experiment. |
| Week 4 | Wed, July 15 | Lab 4 - Bacterial Identification Pipeline | Ex 5.3 + Ex 6.2 + Ex 7.1. Gram stain isolate, run catalase/physiologic ID tests, bank BHI slant, read handwashing plates, and begin Gram-negative rod identification. |
| Week 5 | Wed, July 22 | Lab 5 - Identification & Podiatric Mycology | Ex 5.4 + Ex 7.2 + Ex 8.1. Finalize normal-flora ID, read Gram-negative rod results, perform KOH/lactophenol cotton blue fungal work, and inoculate DTM. |
| Week 6 | Wed, July 29 | Lab 6 - Treatment & Wound Microbiology | Ex 8.2 + Ex 9.1 + Ex 10.1. Primary DTM read, antimicrobial susceptibility testing setup, MIC/Kirby-Bauer setup, and anaerobe culture setup. |
| Week 7 | Wed, August 5 | Lab 7 - Final Diagnostic Integration | Ex 8 final + Ex 9.2 + Ex 10.2. Confirmatory DTM observation, MIC/Kirby-Bauer readout, anaerobe interpretation, and diagnostic integration report. |
| Finals Week | Wed, August 12 | Combined Lecture + Lab Final Exam | Combined cumulative lecture/lab final in the microbiology lab. No new cultures are started. |
13. Finals Week Summary
| Date | Activity |
|---|---|
| Mon, August 10 | Final review and Grand Seminar preparation |
| Tue, August 11 | Grand Microbiology Seminar / student presentations |
| Wed, August 12 | Combined lecture and lab final exam in the microbiology lab |
14. Attendance and Completion Policy for the Schedule
Attendance is required for all regular lecture and lab sessions.
The only exception is the specially rescheduled first lecture on Thursday, June 25, 2026, 10:00 am to 11:50 am. For that session only, live attendance is optional, but completion is still required. Students who do not attend live must watch the Panopto recording, and completion will be tracked through Panopto.
Students with special circumstances should contact the instructor as early as possible so appropriate accommodations or arrangements can be discussed.
15. Microbiology Laboratory Student Policy Agreement
Purpose
This section summarizes the laboratory safety and conduct expectations for students participating in the microbiology laboratory. Students must read each item carefully. By completing the acknowledgement section, students confirm that they understand and agree to follow the laboratory policies that apply to the microbiology laboratory.
Students should type their responses directly into the acknowledgement fields if the document is used for submission. The completed acknowledgement should be submitted as directed in Canvas or by the instructor.
Student Acknowledgement Checklist
All students and personnel working in the BSL-2 teaching laboratory must review the items below. This checklist must be completed and submitted to the instructor of record on or before the first day of laboratory class unless the instructor provides a different deadline.
16. Access and General Laboratory Restrictions
Access to the laboratory is limited at the discretion of the laboratory coordinator, principal investigator on a research project being conducted in the laboratory, or instructor of record for a course in which biological agents are being used.
The following are prohibited at all times in the laboratory, regardless of whether biological agents are being used:
- Eating or consuming liquids of any kind.
- Smoking.
- Handling or applying contact lenses.
- Applying cosmetics, lip balm, lipstick, or similar products.
- Storing food or liquids intended for human use.
- Mouth pipetting for any reason.
- Street jackets, hats, scarves, gloves, backpacks, shoulder bags, briefcases, and similar personal items may not be brought into the laboratory at any time. These items must be stored in lockers or another designated area outside the laboratory. Computers, notebooks, and limited stationery supplies are allowed. The purpose of this regulation is to prevent contamination of personal items from laboratory benches that may not have been properly decontaminated.
17. Additional Restrictions When Biological Agents Are in Use
The following items are prohibited at all times when biological agents are in use. Biological agents include live microorganisms, live human and/or animal tissue cultures, toxins known to affect humans, human genes, bodily fluids, and unfixed or fixed human tissues.
- All items listed in the general laboratory restrictions above.
- Open-toe shoes, sandals of any kind, flip-flops, or similar footwear.
- Long, unsecured hair. Long hair must be placed in a bun, folded, or netted so that it does not hang loose.
18. Required Practices When Biological Agents Are in Use
The following are required when biological agents are in use. For courses in which no biological agents are used, these items are at the discretion of the instructor of record:
- Gowns, aprons, laboratory coats, or other protective coverings are required. These items may be disposable or non-disposable. Non-disposable items must be placed into a labeled hamper and sent to a laundry facility. Disposable and non-disposable lab coats, gowns, or aprons may not be worn outside the laboratory or taken out of the laboratory for any reason at any time.
- Safety eyeglasses must be worn at all times while in the laboratory.
- Disposable nitrile gloves must be worn at all times while in the laboratory. Gloves are single-use and must be disposed of in the red biohazard-labeled containers.
- Hands must be washed after removing gloves and again before leaving the laboratory.
- All sharps must be placed in red sharps containers labeled with the Biohazard symbol and located on the benches in the laboratory.
- When handling biological agents in a way that may generate aerosols, the work must be done in the laboratory laminar flow hood or biosafety cabinet.
- All students and personnel must know the location of the eyewash station and safety shower.
- Spills and accidents involving biological agents must be reported immediately to the laboratory supervisor, instructor of record, or principal investigator. An incident report must be completed by one of the individuals to whom the accident is reported and submitted to the appropriate university safety or biosafety committee if required.
- All workbench surfaces must be cleaned with 10% v/v bleach in tap or DI water at the end of the class period or following any accident or spill.
- All biological agents, including serums, urines, cultures, tissues, and similar materials, must be placed into leak-proof bags when being transported within or outside of the laboratory. These bags are then placed into labeled floor buckets for disposal if required and are removed for incineration by a contract company.
- All laboratory entrance and exit doors must be locked at all times when biological agents are present. Entrance by students and/or faculty will be only through the approved university identification or access method.
19. Typed Student Acknowledgement
Students should complete the fields below by typing directly into the right-hand column. A typed full name and initials serve as the student acknowledgement for this submitted document.
| Field | Student Response |
|---|---|
| Agreement response | Type YES to agree or NO if you do not agree |
| Student initials | Type initials here |
| Full legal name | Type full name here |
| Course / section | Microbiology course |
| Lab location | Assigned teaching laboratory |
| Date submitted | Type date here |
| Instructor | Type instructor name if requested |
Acknowledgement Statement
I hereby acknowledge that I have read and understand the laboratory guidelines above and will adhere to them as applicable. I understand that failure to follow laboratory safety policies may result in removal from the laboratory and/or additional action according to course and university policy.
20. Suggested Student Questions for the Course Overview GPT
Students may ask this GPT questions such as:
- What is this course about?
- How is the course graded?
- What are the major assignment categories and weights?
- When is the next lecture or lab?
- What topics are covered in a specific lecture?
- What is happening during finals week?
- When is the Grand Microbiology Seminar?
- What is the final exam format based on the course overview?
- What are the general attendance expectations?
- What should I know before attending laboratory?
- What items are prohibited in the lab?
- What protective practices are required when biological agents are in use?
- What should I do if I miss a lecture, lab, quiz, assignment, exam, or presentation?
- Where should I look if the GPT answer conflicts with Canvas or an instructor announcement?