Lecture 12 Notes - BIOL211: Fundamentals of Microbiology

Course Introduction

  • BIOL211: Fundamentals of Microbiology

  • Date: October 20, 2025

  • Lecture 12

  • Join Poll Everywhere:

    • Username: biol211

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Instructor Background

  • Professor: Sumedha

  • Academic Qualifications:

    • B.S. in Microbiology at UC Berkeley

      • Focus: Cyanobacteria

    • Research Scientist at the University of Washington

      • Focus: Pseudomonas aeruginosa

    • Ph.D. and Postdoctoral Research at UC San Diego

      • Focus: Group B Streptococcus (GBS) and Mycobacterium tuberculosis

Research Focus

  • Use of Zebrafish Larvae as a Model Organism

    • Investigating how GBS and Tuberculosis (TB) can enter the brain

Personal Aspects

  • Outside interests:

    • Baseball fan (Chicago White Sox)

    • Loves to travel (visited 33 countries)

    • Pets: two rescue corgis named Peach and Pippin

    • Recently became a parent to a son born early in August

Student Guidance

  • Reminder to students:

    • You are more than your grades; one bad grade does not define you.

Interactive Component

  • "Which Peach are you today?"

    • Options: A, B, C, D, E, F

Lecture Agenda

  • Today's Focus:

    • Importance of the course

    • Microbial metabolites with commercial potential

    • Screening and improving microbes for production

    • Growing microbes for commercial production

    • Examples of important microbial metabolites

Importance of the Course

  • Goals for Students:

    • Gain essential knowledge in microbiology

    • Understand microbiology's relevance for nursing majors and the medical field

    • Importance of understanding infectious diseases (e.g., COVID-19)

    • Develop critical thinking and scientific skills

    • Prepare for future academic and career paths

Office Hours

  • Office Hours:

    • Mondays, 3:30 PM - 4:30 PM, LSS 270 (before class)

    • Encouragement for students to visit with inquiries

    • If sick, do not attend; opt for Zoom meetings instead

Communication

  • Email Protocol:

    • Email: sravishankar@sdsu.edu

    • Expected response time: within 24 hours

    • Importance of proofreading and respectful communication

Letters of Recommendation

  • Professor willing to provide LORs, with the condition of prior interaction

  • Encouragement to engage during office hours for potential LORs

Attendance Policy

  • If sick, students are encouraged to stay home

  • Ability to miss classes without penalty (more lectures than points needed)

  • Contact professor for point make-up arrangements if necessary

Study Recommendations

  • To succeed in the course:

    • Attend lectures

    • Watch recordings for missed lectures

    • Take comprehensive notes during class

    • Read the textbook for deeper understanding

    • Ask questions whenever needed

Commercial Potential of Microbial Metabolites

  • Reference: Textbook Chapter 17

Contributions of Microbes to Humanity

  • Definition of Industrial Microbiology:

    • The discipline that uses microbes to produce commercial products on a large scale

  • Major Applications include:

    • Food Production: Fermentation techniques for cheese, beer, wine, etc.

    • Drug Production: Antibiotics and other pharmaceuticals generated from microbes

    • Biofuels:

    • Role of algae as significant biofuel sources

Microbial Metabolites

  • Definition of Metabolites:

    • Compounds produced by microbes during their metabolic processes, either as intermediate by-products or final products

  • Example:

    • Antibiotics that serve evolutionary functions by inhibiting competitor microbes

Microbial Interactions in Ecosystems

  • Metabolites are used by microbes to engage with their community.

  • In soil environments:

    • Interactions can be:

    • Harmful, where one microbe may kill another

    • Beneficial, where microbes cooperate

    • Neutral, having no significant effect on each other

Identifying Microbial Metabolites

  • Process of selecting microbial metabolites for commercial application:

    • Primarily conducted through bioprospecting in natural environments, especially soils rich in microbial competition

    • Other potential sources include oceans, plants, and animals

Screening for Metabolites

  • Bioprospecting:

    • The investigative process of searching for biological metabolites with commercial applications from natural environments

    • Acknowledgment of prevailing challenges in culturing many microbes, traditionally labeled as unculturable

Steps for Metabolite Production

  • Four primary steps to transition from microbial metabolite identification to commercial production:

    1. Identifying the metabolite and the relevant strain of interest

    2. Strain Improvement: Enhance the chosen microbe's yield of the metabolite

    3. Safety Assessment: Ensure the microbe meets safety criteria for commercial use

    4. Scale-Up: Transition from laboratory production to manufacturing settings

Strain Improvement Techniques

  • Concept:

    • Microbes naturally may not produce metabolites in large volumes, as it's energetically costly.

    • Improvement Techniques include:

    1. Mutation:

    • Mutate various strains of the microbe to find variants that produce more metabolites

    • Example of Ashbya gossypii: Achieved 20,000x increased riboflavin production

    1. Growth Condition Optimization:

    • Adjusting variables such as temperature, pH, and oxygen to stimulate metabolite production

    • Differentiating between primary (more growth = more metabolite) and secondary metabolites (produced during stationary phase)

    1. Gene Cloning:

    • For microbes that cannot be cultured, analyze gene sequences linked to metabolite production and clone into a well-studied organism like E. coli

Additional Microbial Requirements for Commercial Use

  • Criteria for microbes suitable for commercial applications:

    1. Cultivation Ability: Microbes should be easily grown in large fermentation settings

    2. Cost-Effective Media Usage: Microbes should thrive in inexpensive growth media

    3. Safety Concerns: Must not include pathogens, and selected lab strains should be benign and not competitive against natural strains

Transitioning from Lab to Factory Production

  • Steps to scale production:

    • Start with laboratory flask trials, develop to fermenters (5 gallons), followed by pilot plants (500-1000 gallons), and eventually large-scale industrial fermenters

    • Key objectives are to test optimization conditions and assert the feasibility of commercial production

Summary of Metabolite Production Steps

  • Consolidated overview of steps reiterated for clarity:

    1. Identify the target metabolite and strain

    2. Enhance the strain to improve metabolite yield

    3. Validate safety for commercial use

    4. Scale production effectively

Commercial Applications of Microbial Metabolites

  • Examples discussed from Textbook Chapter 17:

Antibiotics

  • Naturally produced by microbes to eliminate competitors

    • Predominantly sourced from Streptomyces and fungi (e.g., penicillin)

    • Drug must meet the following criteria to be commercially viable:

    • Capable of large scale production

    • Effective in vivo efficacy

    • Safety validated through clinical trials

Steroid Hormones

  • Produced via bioconversion:

    • Definition: A process involving minor chemical modifications of products using microbial enzymes

    • Transforming sterols into steroid hormones as a cost-effective strategy

Bioremediation

  • Definition: Utilization of living organisms for the removal or degradation of environmental contaminants

    • Specific microbes have the enzymes to target particular contaminants for a clean-up process

Biofuels

  • Considering finite petroleum resources, microbes present renewable alternatives:

    • Production methods through microbial digestion and fermentation for hydrocarbons

Biofuel Production Types:

  1. Ethanol: Derived from cellulose digestion by microbes leading to fermentation

  2. Methane: Generated by methanogenic microbes that can be converted to hydrocarbons

  3. Hydrogen:

    • Clean energy with oxidized hydrogen producing only water as waste

    • Sourced from certain photosynthetic microbes during fermentation

  4. Algae Biofuels:

    • Rapid growth and minimal water needs, subject to optimization for diverse fuel types

Poll Questions

  • Poll Question 1: What constitutes metabolites?

    • A) Substrate converted by microbes

    • B) Intermediate products

    • C) Final products

    • D) A or C

    • E) B or C

  • Poll Question 2: Do natural environmental microbes provide commercial-sized volumes of metabolites? True or False

  • Poll Question 3: Factors preventing antibiotic commercial production:

    • A) Large-scale production capability

    • B) Effective against multiple bacterial species

    • C) Harmful to eukaryotes

    • D) Efficacy in vivo

    • E) Efficacy in vitro

Conclusion

  • Industrial microbiology plays a crucial role in generating commercial products through microbial metabolites

  • Microbial sources are screened through bioprospecting, aiming for effective utilization for drugs, biofuels, and more

  • Strain improvement remains a pivotal method for enhancing metabolite production and viability for commercial endeavors

Final Remarks

  • Instructor thanks students for their engagement with an invitation for questions or clarifications at the end of the lecture.