The Microbial World and You

Microbes in Our Lives: Germs vs Microbes

Microorganisms, commonly referred to as microbes, are minute living things that are typically too small to be seen with the unaided eye. The term germ originates from the Latin word germen, meaning to sprout or germinate, and was first used in the nineteenth century to describe rapidly growing cells that cause disease. Microbes include bacteria, fungi, protozoa, microscopic algae, and viruses.

• Pathogenic microbes: Only a few microbes cause disease.

• Decomposition: Microbes decompose organic waste, recycling nutrients.

• Photosynthesis: Microbes generate oxygen, supporting life on Earth.

• Industrial applications: Microbes produce chemicals (ethanol, acetone, vitamins), fermented foods (vinegar, cheese, bread), and products for manufacturing and medicine (cellulose, insulin).

Importance of Microorganisms

Understanding microorganisms is essential for human welfare and environmental health.

• Prevention of food spoilage

• Prevention and control of disease

• Understanding disease transmission to prevent epidemics

The Microbiome

Definition and Role

The microbiome (or microbiota) refers to the group of microbes that live stably on or in the human body. An adult human is composed of approximately 30 trillion body cells and harbors another 40 trillion bacterial cells.

• Helps maintain good health

• Prevents growth of pathogenic microbes

• May help train the immune system to discriminate threats

Normal Microbiota

Normal microbiota is the collection of acquired microorganisms on or in a healthy human being. These microbes:

• Begin to be acquired as newborns

• May colonize the body indefinitely or transiently (transient microbiota)

• Colonization occurs only at body sites that provide nutrients and suitable environments

Major Microbiome Research Initiatives

• The Human Microbiome Project (started in 2007): Determines the makeup of typical microbiota in various body areas and explores relationships between microbiome changes and human diseases.

• The National Microbiome Initiative (NMI) (started in 2016): Explores the role of microbes in different ecosystems.

Naming and Classifying Microorganisms

Scientific Nomenclature

Carolus Linnaeus established the system of scientific nomenclature in 1735. Each organism has two names: the genus and the specific epithet.

• Names are italicized or underlined

• Genus is capitalized; specific epithet is lowercase

• Names are Latinized and used worldwide

• May be descriptive or honor a scientist

Nomenclature Examples

• Escherichia coli (E. coli): Honors Theodor Escherich; describes habitat (colon)

• Staphylococcus aureus (S. aureus): Describes clustered (staphylo-) spherical (coccus) cells and gold-colored (aureus) colonies

Classification of Microorganisms

Three-Domain System

Developed by Carl Woese in 1978, microorganisms are classified into three domains based on cellular organization:

1. Bacteria

2. Archaea

3. Eukarya (includes protists, fungi, plants, animals)

Types of Microorganisms

• Bacteria

• Archaea

• Fungi

• Protozoa

• Algae

• Viruses

• Multicellular Animal Parasites

Major Groups of Microorganisms

Bacteria

Bacteria are single-celled prokaryotes with peptidoglycan cell walls. They divide by binary fission and derive nutrition from organic or inorganic chemicals or photosynthesis. Some bacteria are motile via flagella.

Bacterial Shapes and Arrangements

Archaea

Archaea are prokaryotes that lack peptidoglycan cell walls and may lack cell walls entirely. They often live in extreme environments and include methanogens, extreme halophiles, and extreme thermophiles. Archaea are generally not known to cause disease in humans.

Fungi

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

Protozoa

Protozoa are eukaryotes that absorb or ingest organic chemicals. They may be motile via pseudopods, cilia, or flagella. Protozoa can be free-living or parasitic, some are photosynthetic, and they reproduce sexually or asexually.

Algae

Algae are eukaryotes with cellulose cell walls, found in freshwater, saltwater, and soil. They use photosynthesis for energy, producing oxygen and carbohydrates. Both sexual and asexual reproduction are possible.

Viruses

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

Multicellular Animal Parasites

These are eukaryotic multicellular animals, not strictly microorganisms. Parasitic flatworms and roundworms (helminths) have some microscopic stages in their life cycles.

A Brief History of Microbiology

The First Observations

• 1665: Robert Hooke reported that living things are composed of cells, marking the beginning of cell theory.

• 1623-1673: Anton van Leeuwenhoek observed the first microbes (“animalcules”) using magnifying lenses.

The Debate over Spontaneous Generation

Spontaneous generation was the belief that life could arise from nonliving matter. This was challenged through several experiments:

The Theory of Biogenesis

• Biogenesis: Living cells arise only from preexisting cells (Rudolf Virchow, 1858)

• Louis Pasteur (1861) disproved spontaneous generation, showing that microorganisms are present in the air and originate from other microorganisms

• Development of aseptic technique to prevent contamination in laboratory and medical procedures

The Golden Ages of Microbiology

The First Golden Age

• Pasteur demonstrated microbes are responsible for fermentation: microbial conversion of sugar to alcohol in the absence of air

• Pasteurization: Application of high heat for a short time to kill harmful bacteria in beverages

• Germ Theory of Disease: Microorganisms cause disease (Bassi, Pasteur, Semmelweis, Lister, Koch)

• Koch’s postulates: Experimental steps to prove a specific microbe causes a specific disease

• Jenner’s vaccination: Cowpox virus used to confer immunity to smallpox

The Second Golden Age

• Chemotherapy: Treatment of disease with chemicals

• Synthetic drugs: Developed to treat infectious diseases (e.g., salvarsan for syphilis, sulfonamides)

• Antibiotics: Chemicals produced by bacteria and fungi that inhibit or kill other microbes (e.g., penicillin discovered by Fleming)

The Third Golden Age

• Research into overcoming antimicrobial resistance

• Genetic modification of microbes for production of hormones and medical substances

Branches of Microbiology

• 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

• Microbial genetics: Study of how microbes inherit traits

• Molecular biology: Study of how DNA directs protein synthesis

• Genomics: Study of an organism’s genes; provides tools for classifying microorganisms

• Recombinant DNA: DNA made from two different sources; enables production of proteins and medical substances

Microbes and Human Welfare

Recycling Vital Elements

• Microbial ecology: Study of the relationship between microorganisms and their environment

• Bacteria convert carbon, oxygen, nitrogen, sulfur, and phosphorus into forms usable by plants and animals

Sewage Treatment

• Sewage is mostly water with a small amount of suspended solids

• Microbes convert organic materials in wastewater into by-products such as carbon dioxide

Bioremediation

• Bacteria degrade organic matter in sewage

• Bacteria degrade or detoxify pollutants such as oil and mercury

Insect Pest Control by Microorganisms

• Microbes pathogenic to insects are alternatives to chemical pesticides

• Bacillus thuringiensis produces protein crystals toxic to insects; toxin gene inserted into plants for resistance

Biotechnology and Recombinant DNA Technology

• Use of microbes for practical applications (food, chemicals)

• Recombinant DNA technology enables production of proteins, vaccines, and enzymes

• Gene therapy and genetically modified bacteria for crop protection and medical applications

Microbes and Human Disease

Normal Microbiota and Resistance

• Normal microbiota prevent growth of pathogens and produce growth factors (e.g., vitamins B and K)

• Resistance: Ability of the body to ward off disease; factors include skin, stomach acid, and immune system

Emerging Infectious Diseases (EIDs)

• New diseases and diseases increasing in incidence (e.g., Zika virus disease)

• Pathogens may overcome host resistance and cause epidemics

• Antimicrobial resistance (e.g., MRSA, VRSA) is a growing concern