Taxonomy and Phylogeny

• Microorganisms (microbes) are small organisms found nearly everywhere on Earth in huge quantities.
• Most microbes are too small to be seen with the human eye, but are mostly harmless or even helpful to humans.
• Microbes play key roles in ecosystems, forming food webs and being used in biofuels, medicine, and food.

Ancestral Knowledge of Microbes

• Before the microscope, the existence of many microbes could not be proven.
• Humans have understood and utilized microbial life since prehistoric times for food and disease prevention/treatment.

Fermented Foods and Beverages

• Fermented foods and beverages like beer, wine, bread, and yogurt have been enjoyed worldwide for recorded history.
• Neolithic China made fermented beverages from rice, honey, and fruit as early as 7000 BC.
• Microbial fermentation uses bacteria, mold, or yeast to convert sugars into alcohol, gases, and organic acids.

Iceman Treatment

• Prehistoric people attempted to treat illnesses and infections.
• Ötzi the Iceman, a 5300-year-old mummy from the Ötzal Alps, was found in 1991.
• Researchers found Ötzi was infected with Trichuris trichiura eggs (abdominal pain/anemia) and Borrelia burgdorferi (Lyme disease).
• Ötzi may have tried to treat infections with Piptoporus betulinus fungus (laxative/antibiotic properties).
• Ötzi's tattoos, made by cutting incisions, filling them with herbs, and burning the herbs, may have been another attempt to treat his health ailments.

Early disease theories

• Ancient civilizations knew diseases could be transmitted by unseen things
• The Bible describes quarantining people with leprosy, showing an understanding of communicable diseases
• Ancient Greeks linked disease to "miasmatic odors" (bad air) and developed hygiene practices.
• Romans had a miasma hypothesis, so built infrastructure like aqueducts and the Cloaca Maxima sewer to protect against waterborne illnesses.
• Doctors and philosophers understood invisible forces (microbes) could cause infection and disease.

Historical Figures

• Hippocrates (460-370 BC), the "father of Western medicine," dismissed supernatural causes of disease.
• Hippocrates thought diseases had natural causes within patients or their environments.
• Thucydides (460-395 BC), the "father of scientific history," advocated for cause-and-effect reasoning based on evidence.
• Thucydides observed that Athenian plague survivors did not get reinfected, suggesting an early understanding of immunity.
• Marcus Terentius Varro (116–27 BC) proposed unseen things (microorganisms) could cause disease in his 36 BC publication, Res Rusticae.

Microbiology Birth

• The microscope's invention confirmed "minute creatures" existence.
• Antonie van Leeuwenhoek (1632-1723), a Dutch cloth merchant, made a lens powerful enough to see microbes.
• In 1675, Leeuwenhoek saw single-celled organisms ("animalcules" / "wee little beasties"), now known as bacteria and protists.
• Louis Pasteur and Robert Koch advanced the field during the "Golden Age of Microbiology."
• Pasteur showed individual microbial strains have unique properties and that microorganisms cause fermentation.
• Pasteur invented pasteurization (spoilage prevention) and vaccines to treat animal and human diseases like rabies.
• Robert Koch connected a single, isolated microbe to a known human disease.
• Koch discovered the bacteria causing anthrax (Bacillus anthracis), cholera (Vibrio cholera), and tuberculosis (Mycobacterium tuberculosis).
• Knowledge of human cells and many tools for studying cells/genetics come from work with microbes.

Microbiological Tools

• Microscopes magnify microorganisms, cells/tissues, and specimens too small to see.
• Stains and dyes add color to microbes for better viewing; some work on living microbes, others on fixed specimens.
• Growth media grow microorganisms in the lab and supply nutrients like water, salts, carbon/nitrogen sources for reproduction.
• Petri dishes are flat-lidded dishes (10-11 cm diameter, 1-1.5 cm high) used to hold growth media.
• Test tubes are cylindrical tubes used to grow microbes in broth, semisolid, or solid media.
• Bunsen burners (or microincinerators) sterilize equipment with a flame.
• Inoculation loops streak microorganisms on agar or transfer them from one test tube to another after sterilization.

Systematics

Taxonomy

• Taxonomy classifies, describes, identifies, and names living organisms.
• Classification organizes organisms into groups based on shared characteristics.
• Carolus Linnaeus (1701–1778) was an early taxonomist who published Systema Naturae.
• Linnaeus used a standard format to categorize/name organisms for consistent scientific terminology.
• Linnaeus divided the natural world into animal, plant, and mineral kingdoms. He grouped organisms hierarchically by similarites into kingdom, class, order, family, genus, species.

Phylogenies

• In the 1800s, taxonomies began to account for evolutionary relationships (phylogenies).
• Phylogenetic trees show the relatedness of organisms on a diagram and indicate their lineages.
• Early phylogenetic trees inferred relatedness from visible similarities that are now more complex
• Ernst Haeckel (1866) proposed Protista for unicellular organisms and Monera for those lacking nuclei (like bacteria).
• Robert Whittaker (1969) added Fungi to the tree of life.
• Whittaker's tree categorized levels above kingdom (empire/superkingdom) to distinguish eukaryotes (membrane-bound nuclei) from prokaryotes (no nuclei).
• Empire Prokaryota contained Kingdom Monera.
• Empire Eukaryota contained Fungi, Protista, Plantae, and Animalia kingdoms.
• Whittaker's five-kingdom tree was the standard phylogeny for many years.

Genetics Role

• Genetic methods provide a standardized way to compare living organisms rather than relying on subjective observations
• Modern taxonomy compares nucleic acids (DNA/RNA) or proteins; more similar molecules indicate closer relatedness.
• Carl Woese and George Fox created a genetics-based tree of life based on rRNA gene sequences.
• rRNA analysis suggests archaea, bacteria, and eukaryotes evolved from a common ancestor cell.
• Horizontal gene transfer complicates classification
• Bacteria and Archaea are prokaryotes (no nucleus), while Eukarya are eukaryotes (have a nucleus).
• Viruses do not fit into the three domains of life.

Naming Microbes

• Linnaeus used binomial nomenclature, a two-word naming system of genus and species.
• Example: modern humans are Homo sapiens (italicized), with Homo capitalized genus and sapiens non-capitalized specific epithet
• Bergey's Manuals are used to identify and classify microorganisms and are the standard references for prokaryotes.

Microorganism Types

Bacteria

• Bacteria are found in almost every habitat on earth, including in/on humans
• Most bacteria are harmless or helpful, but some are pathogens that cause disease
• Bacteria are prokaryotic because their DNA is not in a nucleus.
• Most bacteria have peptidoglycan in their cell walls.
• Bacteria shapes: spherical (coccus), rod-shaped (bacillus), or curved (spirillum, spirochete, or vibrio).
• Bacterial metabolic capabilities vary, allowing growth in many environments with different nutrients: photosynthetic (energy from sunlight, fixes carbon dioxide) or nonphotosynthetic (energy from organic/inorganic compounds).

Archaea

• Archaea are unicellular prokaryotes and archaea and bacteria have different evolutionary histories
• Archaeal cell walls lack peptidoglycan but often have pseudopeptidoglycan
• Archaea are found in nearly every habitat on earth, including extreme environments.
• Some archaea live in the human body, but none are pathogenic.

Eukaryotes

• Domain Eukarya contains all eukaryotes (protists, fungi, plants, and animals).
• Eukaryotes' cells contain a nucleus.

Protists

• Informal grouping of eukaryotes that aren't plants, animals, or fungi.
• Algae are protists can be uni- or multicellular and can vary widely in size, apperance, and habitat.
• They have cell walls made of cellulose.
• Algae are photosynthetic, extracting energy from the sun and releasing oxygen and carbohydrates into the environment.
• Many consumer products contain ingredients from algae, such as carrageenan/alginic acid and can also be used for biofuels
• Protozoa are the backbone of food webs, because they make the nutrients for other organisms. Protozoa are diverse.
• Protozoa move with cilia, flagella, or pseudopods ("false feet").
• Some protozoa are photosynthetic and others feed on organic material. Some are free-living, whereas others are parasitic.
• Most protozoa are harmless, but some are pathogens that cause animal or human disease

Fungi

• Fungi are eukaryotic and fungi such as mushrooms, resemble plants, but are actually quite different.
• Fungi aren't photosynthetic, also cell walls are usually made out of chitin rather than cellulose
• Unicellular fungi (yeasts) are included within microbiology.
• There are more than 1000 known species of yeasts found in many environments.
• Some yeasts have beneficial uses, such as fermentation; but yeasts can also cause food to spoil and some cause disease.
• Multicellular molds are filaments that form colonies are found in various environments and play a role in decomposition.
• Some molds cause allergies or produce mycotoxins.
• Molds have been used to make pharmaceuticals, including penicillin (antibiotic) and cyclosporine (organ rejection prevention)

Helminths

• Helminths are multicellular parasitic worms considered in microbiology because diseases caused by helminths eggs/larvae are microscopic.
• Example: guinea worm (Dracunculus medinensis) causes dizziness, vomiting, diarrhea, and painful ulcers when the worm exits skin.
• Infection occurs via water fleas with guinea-worm larvae, but disease has been largely eradicated via coordinated efforts and improvements in sanitation

Viruses

• Viruses are acellular microorganisms (not composed of cells).
• A virus consists of proteins and either DNA or RNA (but never both).
• Viruses are inert outside a host, but can incorporate themselves into the host cell, to co-opt functions.

Microbiology as a field of study

• Microbiology is a broad term that encompasses the study of all different types of microorganisms, so microbiologists tend to specialize in one of several subfields, such as bacteriology, mycology, protozoology, parasitology, virology, immunology, clinical microbiology, environmental microbiology, applied microbiology, or food microbiology.