Chapter 1: The Microbial World and You – Structured Study Notes

The Microbial World and You

Introduction to Microbiology

Microbiology is the study of microorganisms, which are organisms too small to be seen with the unaided eye. These include bacteria, fungi, protozoa, microscopic algae, and viruses. Microbes play essential roles in ecosystems, industry, and human health.

• Microorganisms: Tiny living organisms, often unicellular, that require magnification to be observed.

• Microbes: Encompass bacteria, fungi, protozoa, algae, and viruses.

• Pathogenic microbes: Cause diseases in humans, animals, or plants.

• Beneficial microbes: Decompose organic waste, generate oxygen, produce chemicals (e.g., ethanol, acetone), and are used in food production (e.g., cheese, bread).

Normal Intestinal Bacteria and Microbiota

The human body hosts trillions of microbial cells, collectively known as the microbiome. These microbes are found on the skin, in the gut, and other body sites, contributing to health and disease resistance.

• Normal microbiota: Microbes regularly found in and on the human body; prevent growth of pathogens and produce essential vitamins (e.g., B, K).

• Transient microbiota: Microbes that colonize the body temporarily.

• Resistance: The body's ability to ward off disease, aided by skin, stomach acid, and antimicrobial chemicals.

Microbes in Our Lives

Understanding microorganisms enables humans to prevent food spoilage, control disease, and manage epidemics. Microbes are integral to biotechnology, environmental recycling, and industrial processes.

• Food spoilage prevention: Knowledge of microbes helps preserve food.

• Disease prevention: Understanding transmission and causes of disease.

• Industrial applications: Microbes produce chemicals, enzymes, and are used in manufacturing.

Naming and Classifying Microorganisms

Scientific Nomenclature

Microorganisms are named using a binomial system: the genus and specific epithet. Names are italicized or underlined, with the genus capitalized and the specific epithet lowercase.

• Genus: First part of the scientific name, always capitalized.

• Specific epithet: Second part, always lowercase.

• Example: Escherichia coli (abbreviated as E. coli), Staphylococcus aureus (S. aureus).

Taxonomic Hierarchy

Organisms are classified in a hierarchical system: Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species. This system reflects evolutionary relationships and similarities among organisms.

• Domains: Bacteria, Archaea, Eukarya.

• Taxonomy: The science of classification.

• Systematics/Phylogeny: Study of evolutionary history.

The Three Domains of Life

The three-domain system, developed by Woese in 1978, is based on rRNA nucleotide sequences. It divides life into Bacteria, Archaea, and Eukarya.

• Bacteria: Prokaryotic, peptidoglycan cell walls, diverse metabolism.

• Archaea: Prokaryotic, lack peptidoglycan, often extremophiles.

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

Types of Microorganisms

Bacteria

Bacteria are prokaryotes with peptidoglycan cell walls. They reproduce by binary fission and may be motile via flagella. Nutrition is derived from organic/inorganic chemicals or photosynthesis.

• Prokaryotes: Cells lacking a nucleus.

• Binary fission: Asexual reproduction method.

• Flagella: Motility appendages.

Archaea

Archaea are prokaryotes that lack peptidoglycan in their cell walls and often live in extreme environments. They include methanogens, extreme halophiles, and extreme thermophiles.

• Extremophiles: Organisms thriving in extreme conditions.

• Methanogens: Produce methane.

• Halophiles: Thrive in high salt concentrations.

• Thermophiles: Thrive in high temperatures.

Fungi

Fungi are eukaryotes with chitin cell walls. They absorb organic chemicals for energy. Yeasts are unicellular, while molds and mushrooms are multicellular. Molds consist of mycelia made of hyphae.

• Chitin: Structural polysaccharide in fungal cell walls.

• Mycelia: Masses of hyphae.

• Hyphae: Filamentous structures.

Protozoa

Protozoa are eukaryotes that absorb or ingest organic chemicals. They may be motile via pseudopods, cilia, or flagella. Some are free-living, others parasitic, and some are photosynthetic.

• Pseudopods: Temporary projections for movement.

• Cilia: Short, hair-like structures for movement.

• Flagella: Long, whip-like structures for movement.

Algae

Algae are eukaryotes with cellulose cell walls. They use photosynthesis for energy, producing oxygen and carbohydrates. Algae are found in freshwater, saltwater, and soil, and reproduce sexually or asexually.

• Cellulose: Structural polysaccharide in cell walls.

• Photosynthesis: Conversion of light energy to chemical energy.

Viruses

Viruses are acellular entities consisting of a DNA or RNA core surrounded by a protein coat, sometimes enclosed in a lipid envelope. They replicate only inside living host cells and are inert outside hosts.

• Acellular: Not composed of cells.

• Obligate parasites: Require a host for replication.

Multicellular Animal Parasites

These are eukaryotic multicellular organisms, such as helminths (parasitic flatworms and roundworms), with some microscopic stages in their life cycles.

• Helminths: Parasitic worms.

• Microscopic stages: Eggs or larvae visible only under a microscope.

A Brief History of Microbiology

Early Microscopic Observations

Robert Hooke and Anton van Leeuwenhoek were pioneers in microscopy. Hooke described cells, while Leeuwenhoek observed "animalcules" (microbes) with magnifying lenses.

• Cell theory: All living things are composed of cells.

• Animalcules: Early term for microorganisms.

The Golden Age of Microbiology

Louis Pasteur demonstrated that microbes cause fermentation and spoilage. Pasteurization was developed to kill harmful bacteria in beverages. Robert Koch established Koch's postulates, linking specific microbes to specific diseases.

• Fermentation: Microbial conversion of sugar to alcohol.

• Pasteurization: Application of heat to kill bacteria.

• Koch's postulates: Experimental steps to prove a microbe causes a disease.

The Germ Theory of Disease and Immunity

Robert Koch and Edward Jenner contributed to understanding disease causation and immunity. Jenner's work led to vaccination, providing protection against smallpox.

• Immunity: Protection against disease.

• Vaccination: Introduction of a harmless microbe to induce immunity.

Modern Chemotherapy

Chemotherapy is the treatment of disease with chemicals. Antibiotics are produced by microbes to inhibit or kill other microbes. Key discoveries include penicillin and synthetic drugs.

• Antibiotics: Microbial products that inhibit other microbes.

• Penicillin: First antibiotic discovered by Alexander Fleming.

Modern Developments in Microbiology

Microbial Genetics and Molecular Biology

Microbial genetics studies inheritance in microbes. Molecular biology explores how DNA directs protein synthesis. Genomics analyzes an organism's genes, aiding classification. Recombinant DNA technology combines DNA from different sources.

• Microbial genetics: Inheritance of traits in microbes.

• Molecular biology: DNA's role in protein synthesis.

• Genomics: Study of all genes in an organism.

• Recombinant DNA: DNA from two sources.

Microbes and Human Welfare

Microbes recycle vital elements, treat sewage, and clean up pollutants (bioremediation). They are used in insect pest control and biotechnology, including recombinant DNA technology for producing proteins and vaccines.

• Bioremediation: Use of microbes to degrade pollutants.

• Biotechnology: Practical use of microbes in industry.

• Gene therapy: Replacement of defective genes in humans.

Microbes and Human Disease

Biofilms

Biofilms are masses of microbes attached to surfaces, such as rocks, pipes, teeth, and medical implants. They can cause infections and are often resistant to antibiotics.

• Biofilm: Community of microbes growing on a surface.

• Antibiotic resistance: Biofilms are difficult to treat.

Emerging Infectious Diseases

Emerging infectious diseases (EIDs) are new or increasing in incidence. Examples include Zika virus, MERS, H1N1 influenza, avian influenza, MRSA, and Ebola hemorrhagic fever.

• Emerging infectious diseases: Newly identified or increasing diseases.

• Factors: Pathogen invasion, resistance, environmental changes.

Summary Table: Characteristics of Archaea, Bacteria, and Eukarya

Characteristic	Archaea	Bacteria	Eukarya
Cell Type	Prokaryotic	Prokaryotic	Eukaryotic
Cell Wall	Varies; no peptidoglycan	Peptidoglycan	Varies; no peptidoglycan
Membrane Lipids	Branched carbon chains	Straight carbon chains	Straight carbon chains
First Amino Acid in Protein Synthesis	Methionine	Formylmethionine	Methionine
Antibiotic Sensitivity	No	Yes	No
rRNA Loop	Lacking	Present	Lacking
Common Arm of tRNA	Lacking	Present	Lacking

Summary Table: Prokaryotic Cells and Eukaryotic Organelles Compared

Characteristic	Prokaryotic Cell	Eukaryotic Cell	Eukaryotic Organelles
DNA	One circular; some two circular; some linear	Linear	Circular
Histones	In archaea	Yes	No
First Amino Acid in Protein Synthesis	Formylmethionine (bacteria), Methionine (archaea)	Methionine	Formylmethionine
Ribosomes	70S	80S	70S
Growth	Binary fission	Mitosis	Binary fission

Summary Table: Making Scientific Names Familiar

Microbial Name	Pronunciation	Source of Genus Name	Source of Specific Epithet
Salmonella enterica	sal'mo-NEL-la en-TER-i-ka	Honors Daniel Salmon	Found in intestines
Streptococcus pyogenes	strep-to-KOK-us pyo-O-jen-es	Appearance of cells in chains	Forms pus
Saccharomyces cerevisiae	sack-a-ro-MY-sees ser-e-VIS-e-a	Fungus that uses sugar	Makes beer
Penicillium chrysogenum	pen-i-SILL-i-um kris-OJ-e-num	Tuftlike or paintbrush appearance	Produces a yellow pigment
Trypanosoma cruzi	tri-pan-o-SO-ma KROO-ze	Corkscrew shape	Honors Oswaldo Cruz

Summary Table: Taxonomic Hierarchy Example

Domain	Kingdom	Phylum	Class	Order	Family	Genus	Species
Eukarya	Fungi	Ascomycota	Hemiascomycetes	Saccharomycetales	Saccharomycetaceae	Saccharomyces	S. cerevisiae
Archaea	None assigned	Euryarchaeota	Methanococci	Methanococcales	Methanococcaceae	Methanococcus	M. okinawensis
Bacteria	None assigned	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Escherichia	E. coli