Microbiology Exam 1

Microorganisms

Organisms that are too small to be seen with the unaided eye. They are capable of growing into visible colonies if placed in the appropriate environment.

Pathogens

Disease-causing microorganisms. Notably, less than 1% of all microbes are pathogenic

Ubiquitous:

A term meaning "found everywhere." Microbes outnumber humans and live in us, on us, and nearly everywhere around us

Ubiquitous example

Microscopic algae/cyanobacteria can live inside the hollow hairs of polar bears, temporarily turning their coats green in the summer without causing them harm.

Microbes exist on the—————metric scales

micrometer ($\mu$m) and nanometer (nm)

For perspective, there can be as many microbial cells associated with

your body as there are human cells in your body

Bacteriology:

The study of bacteria

Mycology

The study of fungi

Protozoology

The study of protozoans

Virology:

The study of viruses

Parasitology

The study of parasites

Phycology / Algology:

The study of algae

Morphology

The study of structural form and features.

Physiology

The study of microbial metabolic and physical function

Taxonomy:

The classification, naming, and identification of microbes

Microbial Genetics / Molecular Biology:

The study of genetic mechanisms

Microbial Ecology

The study of how microbes interact with their environments

Energy & Nutrient Flow:

Microbes drive photosynthesis (acting as primary producers of carbon compounds) and decomposition (breaking down organic waste)

Subsurface Biomass:

An estimated 50% of all organisms on Earth exist beneath the planet's crust.

Nutrient Recycling

Bacteria recycle essential chemical elements like carbon, sulfur, phosphorus, and nitrogen so they can be re-utilized by plants and animals.

Nitrogen Fixation

Bacteria metabolize atmospheric nitrogen gas ($N_2$) into usable plant compounds like nitrates and ammonia

Fermentation

Microbes produce fermented staples such as vinegar, cheese, and bread.

Bread

Saccharomyces cerevisiae (yeast) metabolizes carbohydrates in flour and releases carbon dioxide ($CO_2$), forcing the dough to rise

Cheese

Rennin coagulates milk into curds, which are cut and compressed. Specific strains of bacteria and fungi are inoculated to directly alter flavor, odor, texture, acidity, and color.

Chemical Synthesis

Used to manufacture industrial chemicals like ethanol and acetone

Antibiotics

Natural metabolic products created by certain bacteria and fungi to inhibit or kill competing microbes (e.g., Penicillium mold producing penicillin to inhibit Staphylococcus aureus)

Recombinant DNA Technology:

Inserting foreign human or animal genes into a microbial chromosome to force the microbe to produce a desired protein

Recombinant DNA Technology example

Production of vaccines, enzymes, and insulin

Gene Therapy:

Using a harmless, modified vector (such as an attenuated virus) to replace missing or defective genes inside human patient cells.

Bioremediation:

A process using naturally occurring or genetically engineered microorganisms to degrade, remove, or detoxify environmental pollutants.

Sewage Treatment:

Bacteria break down organic matter in waste systems

Oil Spills

Strains like Pseudomonas sp. and Alcanivorax borkumensis metabolize hydrocarbons from ocean oil spills for energy.

Landfills

Bioremediation breaks down landfill toxins but requires a strictly balanced environment of moisture + oxygen + organic material to succeed

Biopesticides

Bacillus thuringiensis is a bacterium used safely in commercial agricultural dusts. It produces toxic protein crystals next to its endospores. When insects ingest them, the toxins break down their digestive tracts, while remaining completely harmless to humans and plants.

Emerging Infectious Diseases (EIDs):

New or changing diseases increasing in incidence (e.g., Coronaviruses like SARS, MERS, or Ebolavirus).

Reemerging Diseases:

Older diseases that were once under control but are rising in frequency again.

Zoonoses

Infectious diseases indigenous to animals that can naturally transmit to humans.

Gastric Ulcers are driven by infections of the bacterium

Helicobacter

Cervical Cancer is strongly tied to infections of the

Human Papillomavirus (HPV).

Obesity has emerging correlation research linked to certain common

adenoviruses

Ancient Foundations & Early Sanitary Practices

Before the discovery of microorganisms, the relationship between cleanliness, food spoilage, and sickness was poorly understood. Early thinkers, however, began noticing environmental and natural patterns.

Hippocrates (400 BC)

Renowned as the "Father of Western Medicine". He dismissed the prevailing belief that disease was sent by supernatural or angry gods, arguing instead that illnesses had natural causes originating from the environment or patient behaviors.

Thucydides:

An ancient Greek historian who noted during the Athenian plague that individuals who survived the sickness could tend to the ill without contracting it a second time. This is the earliest recorded description of immunity (host resistance).

Marcus Terentius Varro:

An ancient Roman writer who remarkably hypothesized that disease was caused by "certain minute creatures" (animalia minuta) that were too small for the eye to see, which traveled through the air and entered the body via the mouth and nose.

Cloaca Maxima:

The "Greatest Sewer" of ancient Rome. It was an engineering marvel designed to transport urban waste safely away from the city and into the River Tiber, showcasing an early public awareness of the link between sanitation and health.

Bubonic Plague (Black Death):

A catastrophic pandemic during the mid-1300s that decimated over one-third of the European population (approx. 25 million deaths).

Bubonic Plague (Black Death) Causative Agent

Yersinia pestis (a gram-negative, rod-shaped bacterium).

Bubonic Plague (Black Death) Vector

Fleas that lived on infected rodents (rats) acted as the primary transmission vector to humans.

Bubonic Plague (Black Death) Buboes

Severely swollen, painful lymph nodes that manifest in the armpits or groin.

Bubonic Plague (Black Death) Intravascular Coagulation

Blood clotting that happens inside the blood vessels, blocking blood flow.

Bubonic Plague (Black Death) Subcutaneous Hemorrhaging:

Bleeding occurring underneath the skin layers

Bubonic Plague (Black Death) Necrosis / Gangrene:

Rapid cell and tissue death resulting from blood loss, turning limbs black (hence the term "Black Death"). Victims typically died within 2 to 4 days of showing clinical signs.

1918 Spanish Flu:

A highly lethal pandemic caused by an H1N1 influenza virus strain, resulting in 30 to 40 million global deaths. It was characterized by extreme lung hemorrhaging, essentially causing victims to drown in their own fluids within a matter of hours.

The Birth of Microscopy & Cell Theory

The invention of high-quality magnification tools allowed scientists to transition from theoretical guessing to direct observation.

Robert Hooke (1665):

Used a crude compound microscope to inspect thin slices of cork (plant matter). He observed regular box-like compartments and coined the term "cells" because they resembled the small rooms (cella) inhabited by monks. His work laid the groundwork for Cell Theory (the tenet that all living organisms are composed of structural and functional units called cells).

Antonie van Leeuwenhoek (1676):

A Dutch linen merchant who ground extraordinarily precise, single-lens microscopes capable of up to 300X magnification. He was the first human to observe living, moving microorganisms in rainwater and teeth scrapings.

father of bacteriology

Animalcules:

The historic name Leeuwenhoek gave to the active microscopic organisms he saw swimming under his lens. Because he was protective of his lens-making secrets, he is called the "Father of Bacteriology", though his secrecy inadvertently stalled microbiology's progress for decades.

Ferdinand Cohn (19th Century):

A German botanist who made early contributions to the classification of bacteria and became the first to discover and describe highly resistant bacterial structures called endospores.

Spontaneous Generation (Abiogenesis):

The obsolete concept that living organisms can routinely arise from non-living or decaying organic matter if a mystical "vital force" is present.

Biogenesis:

The scientific law stating that living matter and cells can only arise from preexisting living matter and matching cells.

Francesco Redi (1668):

Attempted to disprove abiogenesis using jars of meat. Uncovered jars developed maggots; sealed jars developed no maggots; jars covered with fine mesh netting developed maggots only on top of the netting (where flies laid eggs). This proved macro-organisms do not spontaneously generate.

Louis Jablot (1680s):

Divided boiled nutrient broth into an open container and a sealed container. The open container grew microbes, while the sealed container remained sterile, supporting biogenesis.

John Needham (1740s):

Briefly boiled nutrient broth and then sealed the containers. Heavy microbial growth appeared anyway. He claimed this proved spontaneous generation, failing to realize his insufficient boiling time left heat-resistant microbes alive.

Lazzaro Spallanzani (1765):

Repeated Needham's work but boiled the nutrient mixtures for a full hour after sealing the glass flasks. The fluids stayed entirely sterile. Proponents of abiogenesis argued he simply destroyed the "vital force" in the air.

Schroder and Von Dusch (~1840):

Passed ambient air through a cotton fiber filter into a flask containing boiled broth. The broth stayed clear, demonstrating that filtering out physical dust particles prevents contamination without treating the air with harsh heat or chemicals.

Louis Pasteur (1861):

Permanently resolved the debate using a specialized Swan-Neck Flask (an S-shaped neck). He boiled broth inside it; the unique S-curve allowed fresh air to freely cycle through but trapped floating environmental dust and microbes in its lower bend. The liquid remained completely sterile for months, proving that airborne microbes—not a vital force—cause contamination.

Industrial & Medical Milestones

Once scientists accepted that microbes exist in ambient environments, they began applying this knowledge to control food spoilage and prevent disease transmission.

Fermentation:

metabolic process where yeasts convert sugars into alcohol in an anaerobic (oxygen-free) environment. Pasteur discovered that wine spoilage (souring) occurs when contaminating bacteria (Lactobacillus) turn that alcohol into sour lactic acid.

Pasteurization:

• A thermal disinfection process invented by Pasteur to eliminate spoilage microbes without ruining flavor or boiling off alcohol. It involves heating a liquid quickly to $162degrees celsius for 15 seconds.

Germ Theory of Disease:

The fundamental principle that specific microscopic pathogens (bacteria, viruses, fungi) are the true cause of specific infectious illnesses.

Dr. Oliver Wendell Holmes:

An American physician who made the epidemiological observation that mothers giving birth at home suffered far fewer postpartum infections than mothers delivering in public hospital wards.

Dr. Ignaz Semmelweis

Correlated high rates of puerperal sepsis (childbed fever) in maternity wards with medical students coming straight from performing autopsies to delivering babies without cleaning up. He instituted a mandatory handwashing rule using a chlorinated lime solution, causing maternal death rates to drop from over 20% to under 1%.

Joseph Lister

The "Father of Antiseptic Surgery". Inspired by Pasteur's findings, he introduced aseptic techniques to operating rooms. He used phenol (carbolic acid) to disinfect surgical wounds, skin, hands, and surgical instruments, drastically minimizing post-operative wound infections.

Florence Nightingale (1855)

A foundational pioneer of modern nursing and a wartime statistician. During the Crimean War, she meticulously gathered data proving that unsanitary military hospital conditions led to more soldier deaths than battlefield wounds. By enforcing rigid cleaning protocols, fresh air, and structural sanitation, she revolutionized public health.

Koch's Postulates:

A systematic series of 4 experimental guidelines published in 1876 used to definitively prove a causal relationship between an individual pathogen and a specific disease. Koch used these steps to identify the causes of anthrax (Bacillus anthracis), tuberculosis, and cholera.

4 Koch's Postulates:

• The pathogen must be found in all cases of the disease and be absent from healthy individuals.

• The pathogen must be isolated from the sick host and grown in a pure culture.

• The isolated pathogen must cause the same illness when injected into a healthy, susceptible host.

• The same pathogen must be recovered and re-isolated from the newly infected host.

Joseph Priestly (British)

▪ Discovers oxygen in 1774

▪ Now necessary to have air in all experiments!

Pure Culture:

• A laboratory culture containing only a single species or strain of microorganism, completely free from outside contaminants

Agar:

A solidifying agent derived from red sea algae, suggested to Koch by Fannie Hess. Unlike gelatin, agar stays completely solid at human body incubation temperatures (~37°C), melts near boiling point, and cannot be digested or liquefied by most bacteria.

Richard Petri (1887)

Invented the Petri dish, a shallow glass or plastic container with a loose-fitting nested lid. It shields agar growth media from falling dust while allowing oxygen to circulate, accelerating the isolation of pure bacterial strains.

Immunology:

The scientific study of how host organisms protect themselves against infectious agents and foreign substances.

Edward Jenner (1798):

Created the world's first formal vaccination procedure. He observed that milkmaids who contracted mild cowpox (vaccinia virus) were protected from deadly smallpox (variola virus). He inoculated a young boy with cowpox blisters, demonstrating the boy had gained complete protection when later exposed to smallpox.

Smallpox Eradication (1979):

• Smallpox was a highly infectious disease with a 40% mortality rate that could survive for years in dried scabs. Following extensive global vaccination campaigns, the World Health Organization (WHO) declared smallpox completely eradicated in 1979—marking the first time humanity completely wiped out an infectious disease.

Walter Reed (1900):

An American army physician who proved that yellow fever is transmitted by mosquitoes, marking the discovery of insect vectors carrying viral diseases.

Chemotherapy

The treatment of disease using chemical substances that travel internally to destroy pathogens without killing host tissue.

Paul Ehrlich (1908):

A pioneer of modern chemotherapy who searched for a "magic bullet"—a chemical compound that could target and destroy specific microbes without harming the patient. He developed the first effective synthetic treatment for syphilis.

Alexander Fleming (1929):

Accidentally discovered the first natural antibiotic. He observed that a contaminating green mold colony (Penicillium notatum) growing on an open Petri dish produced an antibacterial substance that cleared a ring of nearby Staphylococcus aureus bacteria. This substance was isolated as penicillin and mass-produced in the 1940s.

Needed to isolate pure cultures→need individual colonies

broth→Problem: no isolaton

Sliced potatoes

can get isolated, individual colonies

▪ Problem: not everything grows on it

gelatin

good for isolation of colonies

▪ Problems: many bacteria digest it

His postulates were significant because:

established the

criteria whereby the scientific community could determine the etio logical agent of a disease and thus work on controlling the disease

Smallpox spread by inhalation of

droplets and scabs carrying virus

scabs stay infectious for 2 years

Bacillus anthracis

anthrax

endospore-forming bacteria

phenol=

carbonic acid

Dr.Ignaz Semmelweis (Austria)

1818-1865

▪ (~1848) 20X mortality rate of mothers from puerperal sepsis(Streptococcus infection) in hospital ward compared to midwives

▪ Instituted handwashing with chlorinated lime solution

▪ Reduced mortality rate to <1%

Pasteur- made vaccines against

rabies, anthrax, & chicken cholera

Pasteurization

(not sterilization!) is the application of a high heat for a short time (162 F/15 sec) – kills spoilage bacteria but not yeast or resistant bacteria

sour wine produces

lactobacillus (bacteria)

lactic acid

good wine

yeast

produces alcohol

Theodore Schwann (1836) German

▪ Air passed through flame-heated tube before entering flask