1 The Microbial World and You: Foundations of Microbiology

Chp 1. The Microbial World and You

Roles and Applications of Microbes

Microorganisms are essential to life on Earth, playing critical roles in ecological, industrial, and health-related processes. They are found in diverse environments and contribute to the cycling of nutrients, food production, and biotechnology.

• Ecological Roles: Marine and freshwater microbes form the base of aquatic food chains, while soil microbes recycle chemical elements and fix nitrogen.

• Photosynthesis: Certain microbes generate food and oxygen, supporting life on Earth.

• Commercial Applications: Microbes are used in the synthesis of drugs and in the food industry to produce cheese, yogurt, and bread.

The Human Microbiome

The human microbiome (or microbiota) consists of all the microbes that live stably in or on the human body. These microbes are crucial for maintaining health by aiding digestion, preventing pathogenic microbe growth, and training the immune system.

• An adult human contains about 30 trillion body cells and harbors about 40 trillion bacterial cells.

• Microbiota can be normal (permanent residents) or transient (temporary residents).

• Factors such as temperature, pH, and chemical presence influence microbial colonization.

• The Human Microbiome Project (2007) aimed to characterize typical microbiota and their relationship to health and disease.

Naming and Classifying Microbes

Binomial Nomenclature

Nomenclature is the system of naming organisms, established by Carolus Linnaeus in 1735. Scientific names are Latinized and consist of two parts: the genus (capitalized) and the species epithet (not capitalized). For example, Yersinia pestis is the bacterium that causes bubonic plague.

• Names may describe the organism, honor a researcher, or indicate habitat.

Microorganism	Source of Genus Name	Source of Species Name
Salmonella enterica	Honors Daniel Salmon	Found in intestines (entero-)
Saccharomyces cerevisiae	Fungus that uses sugar (saccharo-)	Makes beer (cerevisiae)
Trypanosoma cruzi	Corkscrew-shaped (trypano-)	Honors Oswaldo Cruz
Tobacco mosaic virus	First plant virus found	Describes symptoms/type

Types of Microorganisms

Overview of Microbial Diversity

Understanding the different types of microorganisms is essential in healthcare and environmental science. The main groups include bacteria, archaea, fungi, protozoa, algae, viruses, and multicellular animal parasites.

• Bacteria

• Archaea

• Fungi

• Protozoa

• Algae

• Viruses

• Multicellular animal parasites

Prokaryotes vs. Eukaryotes

Microorganisms are classified based on cellular organization into prokaryotes and eukaryotes.

• Prokaryotes: Lack a nucleus and membrane-bound organelles; include bacteria and archaea.

• Eukaryotes: Have a nucleus and organelles; include fungi, protozoa, algae, and multicellular parasites.

Bacteria

Bacteria are unicellular prokaryotes with diverse shapes and metabolic capabilities. Their cell walls contain peptidoglycan, and they reproduce by binary fission. Many bacteria are motile via flagella.

• Nutrition: Use organic chemicals, inorganic substances, or photosynthesis.

• Shapes: Cocci (spherical), bacilli (rod-shaped), spirilla (spiral).

Archaea

Archaea are prokaryotic cells that often inhabit extreme environments. Their cell walls lack peptidoglycan. Major groups include methanogens, extreme halophiles, and extreme thermophiles. Archaea are not known to cause human diseases.

Fungi

Fungi are eukaryotic organisms that can be unicellular (yeasts) or multicellular (molds, mushrooms). Their cell walls are primarily composed of chitin. Fungi obtain nutrients by absorbing organic material from their environment.

Protozoa

Protozoa are unicellular eukaryotes that move by pseudopods, flagella, or cilia. They may live freely or as parasites, and can reproduce sexually or asexually. Some protozoa are photosynthetic.

Algae

Algae are photosynthetic eukaryotes, mostly unicellular, with cell walls made of cellulose. They are abundant in aquatic environments and produce oxygen and carbohydrates through photosynthesis.

Viruses

Viruses are acellular entities, visible only with electron microscopes. They consist of a nucleic acid core (DNA or RNA) surrounded by a protein coat (capsid), and sometimes a lipid envelope. Viruses replicate only inside host cells.

Multicellular Animal Parasites

These include parasitic worms (helminths) such as flatworms and roundworms. Although not strictly microorganisms, some life stages are microscopic and of medical importance.

Classification of Microorganisms

The Three Domains of Life

In 1978, Carl Woese proposed a classification system based on cellular organization, dividing life into three domains: Bacteria, Archaea, and Eukarya.

Foundations of Microbiology

Hooke and The Cell Theory

Robert Hooke's observation of cells in cork (1665) led to the development of the Cell Theory, which states that all living things are composed of cells.

Leeuwenhoek and The Animalcules

Anton van Leeuwenhoek was the first to observe live microorganisms, which he called "animalcules," using handcrafted microscopes.

Spontaneous Generation vs. Biogenesis

Spontaneous generation was the belief that life could arise from nonliving matter. Experiments by Redi, Needham, Spallanzani, and Pasteur ultimately disproved this, leading to the acceptance of biogenesis—the idea that living cells arise only from preexisting cells.

Aseptic Techniques

Pasteur's work demonstrated that microbial contamination could be prevented by heat and exclusion of airborne microbes, forming the basis of aseptic techniques in laboratories and medicine.

The Golden Ages of Microbiology

The First Golden Age (1857–1914)

This period saw major discoveries in microbial metabolism, microscopy, culturing, vaccines, and surgical techniques. The germ theory of disease emerged, linking microbes to disease.

Fermentation and Pasteurization

Pasteur discovered that yeasts ferment sugars to alcohol, while bacteria can spoil alcohol by converting it to vinegar. Pasteurization involves heating to kill spoilage microbes.

The Germ Theory of Disease

The realization that microbes cause fermentation led to the hypothesis that they might also cause disease. Joseph Lister applied this theory to surgery, reducing infections by using phenol as a disinfectant.

Koch’s Postulates

Robert Koch established a series of experimental steps (Koch’s postulates) to directly link specific microbes to specific diseases, using Bacillus anthracis as a model.

Vaccination and Immunity

Edward Jenner developed the first vaccine (against smallpox) using material from cowpox lesions. Pasteur later coined the term "vaccine" and demonstrated that avirulent microbes could induce immunity.

The Second Golden Age: Chemotherapy and Antibiotics

After linking microbes to disease, scientists searched for chemicals to destroy pathogens without harming the host. Paul Ehrlich developed the first synthetic drug (salvarsan) for syphilis, and Alexander Fleming discovered penicillin, the first antibiotic.

Modern Microbiology and Molecular Genetics

New Scientific Disciplines

• Bacteriology: Study of bacteria

• Mycology: Study of fungi

• Parasitology: Study of protozoa and parasitic worms

• Immunology: Study of immunity

• Virology: Study of viruses

Molecular Genetics and Genomics

Key discoveries include the identification of DNA as hereditary material, the structure of DNA, and the genetic code. Molecular biology studies how genetic information is carried and expressed, while genomics analyzes all genes in an organism.

Recombinant DNA Technology

Recombinant DNA (rDNA) technology allows genes from one organism to be inserted into another, enabling the production of medically important proteins and genetically modified organisms.

Microbes and Human Welfare

Beneficial Roles of Microbes

• Recycle vital elements (carbon, nitrogen)

• Bioremediation: Remove toxins from the environment

• Biological control: Use of microbes to control pests

• Biotechnology: Industrial and medical applications, including gene therapy

Microbes and Human Disease

Infectious Diseases and Immunity

The balance between host defenses and microbial pathogenicity determines health or disease. Resistance is provided by physical barriers, immune responses, and antimicrobial chemicals.

• Emerging Infectious Diseases (EIDs): New or changing diseases increasing in incidence, such as Zika virus disease and Middle East Respiratory Syndrome (MERS).