Chapter 1: The Microbial World & You – Foundations of Microbiology

Definition and Diversity of Microbes

What is a Microbe?

Microbes, or microorganisms, are microscopic living organisms that exist as single cells or cell clusters. They are found in nearly every environment on Earth and play essential roles in ecological and human processes.

• Microbe: Any organism too small to be seen with the naked eye, including bacteria, archaea, fungi, protozoa, algae, and viruses.

• Not all microbes are cellular: Viruses are acellular entities requiring host cells for replication.

• Contradictions: Some microscopic animals (e.g., mites) are not considered microbes; some large unicellular organisms (e.g., certain algae) blur the definition.

• Examples: Staphylococcus aureus (bacterium), Escherichia coli (bacterium), Plasmodium (protozoan), influenza virus.

Additional info: Microbes can be prokaryotic (bacteria, archaea) or eukaryotic (fungi, protozoa, algae).

Types of Microorganisms

• Bacteria: Prokaryotic, single-celled, diverse metabolisms, cell wall usually present.

• Archaea: Prokaryotic, often extremophiles (e.g., thermophiles, halophiles), cell wall composition differs from bacteria.

• Fungi: Eukaryotic, includes yeasts (unicellular) and molds (multicellular), cell wall contains chitin.

• Protozoa: Eukaryotic, mostly unicellular, motile, lack cell wall.

• Algae: Eukaryotic, photosynthetic, can be unicellular or multicellular.

• Viruses: Acellular, consist of nucleic acid (DNA or RNA) and protein coat, require host for replication.

Microbial Taxonomy and Classification

Three Domains of Life

Microbial taxonomy organizes life into three domains based on genetic and structural differences.

• Bacteria: Prokaryotic, single circular chromosome, diverse metabolic types.

• Archaea: Prokaryotic, distinct from bacteria in genetics and biochemistry, often extremophiles.

• Eukarya: Eukaryotic, includes fungi, protozoa, algae, plants, and animals.

Representative Types: Thermus aquaticus (bacterium), Sulfolobus (archaeon), Saccharomyces cerevisiae (fungus).

Taxonomic Methods

• Genotypic: DNA/RNA sequencing, especially 16S rRNA for prokaryotes.

• Phenotypic: Morphology, metabolic capabilities, chemical analysis.

Discovery and Historical Perspectives

Microscopy and Early Observations

The development of microscopy was crucial for the discovery of microbes.

• Robert Hooke (1665): First microscope (20–50x), observed cells in cork and molds.

• Antonie van Leeuwenhoek (1670s): First to observe single-celled microbes (“animalcules”) with a 300x microscope.

Spontaneous Generation vs. Biogenesis

Debate over the origin of life led to key experiments.

• Spontaneous Generation: Belief that life arises from non-living matter.

• Biogenesis: Life arises only from pre-existing life.

• Louis Pasteur: Swan-neck flask experiments disproved spontaneous generation for microbes.

Fermentation and Germ Theory

Pasteur’s Contributions

Pasteur demonstrated that microbes cause fermentation and disease.

• Fermentation: Yeast convert sugars to alcohol anaerobically; bacterial contamination leads to acetic acid production.

• Germ Theory: Microorganisms are the cause of many diseases.

• Pasteurization: Gentle heating to reduce microbial numbers in food.

Koch’s Postulates

Koch established criteria to link specific microbes to specific diseases.

1. The microorganism must be found in all cases of the disease.

2. It must be isolated and grown in pure culture.

3. The cultured microbe must cause disease when introduced into a healthy host.

4. It must be re-isolated from the experimentally infected host.

Immunization, Antiseptics, and Antibiotics

Vaccination and Immunity

Vaccination uses weakened or inactivated pathogens to stimulate immunity.

• Edward Jenner: Used cowpox to vaccinate against smallpox.

• Pasteur: Developed attenuated vaccines for fowl cholera and rabies.

• Immunity: The body’s ability to resist infection via antibodies and immune cells.

Antiseptics, Disinfectants, and Antibiotics

• Antiseptics: Chemicals used to prevent infection by killing or inhibiting microbes on living tissue.

• Disinfectants: Chemicals used to destroy microbes on non-living surfaces.

• Antibiotics: Naturally produced compounds that inhibit or kill bacteria (e.g., penicillin discovered by Fleming).

• Synthetic drugs: Chemically synthesized agents (e.g., Ehrlich’s treatment for syphilis).

Microbial Genomics and Metagenomics

Genomics

Genomics studies the complete genetic material of microbes, revealing their capabilities and interactions.

• Genome size: Prokaryotes: 500 kb to 5 million bp.

• Core genes: Shared by all members of a species.

Metagenomics

Metagenomics analyzes genetic material recovered directly from environmental samples, allowing study of unculturable microbes.

• Extract all DNA from a sample.

• Fragment and clone DNA into vectors.

• Sequence and analyze to identify microbial diversity and function.

Ecological Roles and Benefits of Microbes

Microbial Ecology

Microbes are essential for ecosystem functioning, nutrient cycling, and bioremediation.

• Winogradsky: Discovered chemoautotrophs using enrichment cultures.

• Chemoautotrophs: Use inorganic minerals (NH4+, H2S, Fe2+) for energy.

• Nutrient cycling: Bacteria and archaea convert nitrogen, sulfur, phosphorus, and carbon between organic and inorganic forms.

• Bioremediation: Use of microbes to treat pollutants and recycle water.

Microbes and Human Health

Human Microbiome

The human microbiome consists of all microbes living in and on the human body, most of which are harmless or beneficial.

• Normal microbiota: Stable, beneficial microbial communities.

• Transient microbiota: Temporary microbial residents.

• Symbiosis: Commensalism and mutualism are common relationships.

Pathogenicity and Disease

• Pathogen: Microbe capable of causing disease.

• Opportunistic pathogen: Causes disease in compromised hosts.

• Biofilms: Surface-attached microbial communities, often resistant to antibiotics.

• Emerging Infectious Diseases (EIDs): New or increasing diseases, often zoonotic (e.g., Ebola, COVID-19).

Table: Comparison of Microbial Groups

Group	Cell Type	Cell Wall	Reproduction	Example
Bacteria	Prokaryotic	Peptidoglycan	Asexual (binary fission)	Escherichia coli
Archaea	Prokaryotic	Varied (no peptidoglycan)	Asexual	Halobacterium
Fungi	Eukaryotic	Chitin	Asexual/Sexual	Saccharomyces cerevisiae
Protozoa	Eukaryotic	None	Asexual/Sexual	Plasmodium
Algae	Eukaryotic	Cellulose	Asexual/Sexual	Chlamydomonas
Viruses	Acellular	None	Requires host	Influenza virus

Summary of Key Concepts

• Definition and diversity of microbes, including contradictions.

• Taxonomy: Three domains (Bacteria, Archaea, Eukarya).

• Discovery of microbes: Hooke, Leeuwenhoek, Pasteur.

• Spontaneous generation vs. biogenesis.

• Medical microbiology: Koch’s postulates, germ theory, pure culture.

• Immunization: Jenner, Pasteur; antibiotics: Fleming; antisepsis/disinfection: Lister, Semmelweis.

• Microbial ecology: Winogradsky, bioremediation, biotechnology.

• Microbial genomes and metagenomes.

• Human microbiome, biofilms, emerging infectious diseases.