Introduction to Microbiology: The Microbial World and You

Microbes in Our Lives

What are Microorganisms?

Microorganisms, or microbes, are tiny living organisms that are usually too small to be seen with the naked eye. They play essential roles in ecosystems and human health.

• Bacteria

• Fungi

• Protozoa

• Microscopic algae

• Viruses

Roles of Microorganisms in the Environment

• Decomposers: Break down dead organic matter, recycling nutrients.

• Photosynthesis: Some microbes (e.g., algae, cyanobacteria) convert sunlight into chemical energy, producing oxygen and carbohydrates.

• Microbiome: Communities of microbes living in and on organisms, including humans, contributing to health and disease resistance.

• Pathogens: Only a small fraction of microbes cause disease.

• Aquatic food webs: Microbes form the base of many aquatic ecosystems.

Applied Roles of Microorganisms

• Chemical producers: Synthesize substances like ethanol, acetone, and vitamins.

• Food fermentation: Used in making vinegar, cheese, bread, and other foods.

• Biofactories: Engineered to produce enzymes (e.g., cellulase) and pharmaceuticals (e.g., insulin).

• Pest control: Certain microbes are used as biological control agents against pests.

The Microbiome

Definition and Importance

The microbiome refers to the collection of microbes that live stably on or in the human body. These microbes are essential for maintaining health, preventing the growth of pathogens, and training the immune system.

• ~30 trillion body cells in an adult human

• Harbors another ~40 trillion bacterial cells

• Normal microbiota may be acquired before birth and can colonize the body indefinitely or transiently

Major studies: The Human Microbiome Project (2007–2016), The National Microbiome Initiative (2016–present)

Naming Microorganisms

Binomial Nomenclature

Developed by Carolus Linnaeus (1735), binomial nomenclature assigns each organism two names: the genus and the specific epithet (species). Names are italicized or underlined, with the genus capitalized and the species lowercase.

• Example: Escherichia coli honors Theodor Escherich and refers to the colon (coli).

• Example: Staphylococcus aureus describes clustered (staphylo-) spherical (coccus) cells with gold-colored (aureus) colonies.

Table: Examples of Scientific Names

Name	Pronunciation	Source of Genus Name	Sense of Specific Epithet
Salmonella enterica	sal-mo-NEL-la en-TER-i-ka	Honors Daniel Salmon	Found in the intestines (enteric)
Streptococcus pyogenes	strep-to-KOK-us pi-OJ-e-neez	Chains (strepto-) of spherical cells (coccus)	Forms pus (pyo-)
Penicillium chrysogenum	pen-i-SILL-ee-um kris-OJ-e-num	Fungus (penicillus = paintbrush)	Produces a yellow (chryso-) pigment
Trypanosoma cruzi	trip-an-o-SO-ma KROO-ze	Cruzi honors Oswaldo Cruz	None

Types of Microorganisms

• Bacteria: Prokaryotic, single-celled, peptidoglycan cell walls, reproduce by binary fission, may have flagella, derive nutrition from various sources.

• Archaea: Prokaryotic, lack peptidoglycan, often extremophiles (methanogens, halophiles, thermophiles), not known to be pathogenic.

• Fungi: Eukaryotic, chitin cell walls, absorb organic chemicals, include unicellular yeasts and multicellular molds/mushrooms (mycelia & hyphae).

• Protozoa: Eukaryotic, absorb/ingest organic chemicals, motile via pseudopods, cilia, or flagella, free-living or parasitic, some photosynthetic, reproduce sexually/asexually.

• Algae: Eukaryotic, cellulose cell walls, photosynthetic, found in various aquatic/soil environments, produce oxygen and carbohydrates, sexual/asexual reproduction.

• Viruses: Acellular, DNA or RNA core, protein coat (sometimes lipid envelope), replicate only inside host cells, inert outside hosts.

• Multicellular Animal Parasites: Eukaryotic, multicellular, include helminths (flatworms, roundworms), some have microscopic stages.

Classification of Microorganisms

Developed by Carl Woese in 1978, classification is based on cellular organization into three domains:

• Bacteria

• Archaea

• Eukarya (includes protists, fungi, plants, animals)

The First Observations

• Robert Hooke (1665): Observed "cells" in cork, beginning of cell theory.

• Anton van Leeuwenhoek (1623–1673): First to observe microbes ("animalcules") using a simple microscope.

Spontaneous Generation versus Biogenesis

• Spontaneous generation: Hypothesis that life arises from nonliving matter, requiring a "vital force."

• Biogenesis: Hypothesis that living cells arise only from preexisting living cells.

Key Experiments in the Debate

Scientist	Experiment	Conditions	Results
Francesco Redi (1668)	Decaying meat in jars	Jars covered with net, opened, sealed	Maggots appeared only in open jars
John Needham (1745)	Boiled broth in covered flask	Heated, then covered (not sealed)	Microbes appeared
Lazzaro Spallanzani (1765)	Boiled broth in sealed flask	Sealed, then heated	No microbes appeared
Louis Pasteur (1861)	Swan-neck flask experiment	Heated, not sealed vs. heated, sealed	Microbes grew only in open flasks

The First Golden Age of Microbiology (1857–1914)

This era saw major discoveries linking microbes to disease, immunity, and chemical activities, as well as advances in microscopy, culturing, vaccines, aseptic techniques, and chemotherapeutic drugs.

• Pasteur: Disproved spontaneous generation, developed pasteurization, studied fermentation.

• Koch: Identified causative agents of disease, formulated Koch's postulates.

• Jenner: Developed vaccination for smallpox.

• Semmelweis & Lister: Introduced handwashing and antiseptic surgery.

Germ Theory of Disease

The theory that microorganisms cause disease. Key contributors:

• Bassi & Pasteur: Linked microbes to silkworm diseases.

• Semmelweis: Advocated handwashing to prevent puerperal fever.

• Joseph Lister: Used phenol to sanitize surgical wounds.

• Robert Koch: Discovered anthrax bacterium, developed Koch's postulates.

Vaccination and Immunity

• Edward Jenner (1796): Used cowpox virus to immunize against smallpox.

• Vaccination comes from Latin vacca (cow).

• Immunity: Protection against disease.

Second and Third Golden Ages of Microbiology

• Chemotherapy: Use of chemicals to treat disease (e.g., quinine for malaria, salvarsan for syphilis, sulfonamides, penicillin).

• Antibiotics: Penicillin discovered by Fleming (1928).

• Molecular discoveries: Genes encode enzymes (Beadle & Tatum, 1941), DNA as hereditary material (Avery et al., 1944), DNA structure (Watson & Crick, 1953), mRNA in protein synthesis (Jacob & Monod, 1961).

Branches of Microbiology

• Bacteriology: Study of bacteria

• Mycology: Study of fungi

• Parasitology: Study of protozoa and parasitic worms

• Immunology: Study of immunity (including vaccines and interferons)

• Virology: Study of viruses