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Humans and the Microbial World: Chapter 1

• This chapter covers the history of microbiology, scientific methods, the human perspective, and members of the microbial world.

Microorganisms

• Microorganisms examples include Prokaryotes and Eukaryotes
• Microorganisms may be both good and bad

A Glimpse of History

• Antony van Leeuwenhoek made a simple magnifying glass (1674).
• He studied lake water and observed 'animalcules'.
• Robert Hooke is also credited with the discovery of microbes.
• Hooke described 'microscopical mushroom' (common bread mold) in 1665.

Key Areas of Study

• 1.1 The dispute over spontaneous generation
• 1.2 Human perspective of Microbiology, benefits to humans in health, environment, industry, and research.
• 1.3 Members of the Microbial world, including cellular and acellular agents.

1.1 Learning Outcomes

• Key experiments of scientists who disproved spontaneous generation
• How the challenge to spontaneous generation led to the Golden Age of Microbiology
• Describe the scientific method, using Pasteur's swan-necked flask experiment.

1.1 Spontaneous Generation

• Spontaneous generation is the belief that life arises spontaneously from non-living material.
• Over 200 years of experiments were needed to provide evidence that microorganisms do not arise by spontaneous generation.

1.1 The Dispute Over Spontaneous Generation

• Francesco Redi showed that worms on rotting meat came from eggs of flies landing on the meat in 1668.
• Redi placed meat in two jars, covered one jar with gauze, and the gauze prevented flies from depositing eggs, which resulted in no worms.
• John Needham demonstrated that boiled broths still produced microorganisms in 1749.
• Father Spallanzani contradicted Needham's results in 1776.
• He boiled broths longer and sealed flasks by melting necks, then the broths remained sterile unless the neck cracked.
• The controversy remained because some argued heating destroyed "vital force" necessary for spontaneous generation.

Work of Louis Pasteur

• Demonstrated that air is filled with microorganisms.
• Filtered air through a cotton plug and observed trapped microorganisms
• Many looked identical to those found in broths.
• The plug in sterilized broth gave rise to microorganisms.

Dispute over Pasteur's results

• Pasteur's results were not fully reproducible.
• English physicist John Tyndall explained the conflicting data and showed Pasteur correct.
• Sterilizing broths required different times and some sterilized in 5 minutes, while others were not sterilized after 5 hours.
• Broths, made from hay, contained heat-resistant microbes.
• Labs that could not reproduce Pasteur's results used broths made from hay.
• German botanist Ferdinand Cohn discovered endospores in the same year, 1876.
• Heat-resistant form of bacteria
• Extreme heat resistance of endospores explains differences between Pasteur's results and those of other investigators.
• Pasteur used broths made with sugar or yeast extract
• It is important that you reproduce all conditions as closely as possible when conducting research

The Golden Age of Microbiology

• Key events were the American Revolution in 1775-1783 and the American Civil War in 1861-1865.
• The Worldwide influenza epidemic occurred in 1918.
• World War I was from 1914-1918.
• World War II was from 1939-1945.

Scientists to Remember

• 1674-Antony van Leeuwenhoek: first microscope
• 1796-Edward Jenner: first vaccine against smallpox
• 1847-Semmelweis: handwashing reduces childbed fever-postpartum infections
• 1857-Pasteur: fermentation by yeast
• 1867-Lister: first use of an antiseptic
• 1876-81-Koch: bacteria cause infections-medical microbiology, pure culture technology
• 1892-Iwanowsky: first description of a virus
• 1928-Flemming: first antibiotic-Penicillin

Scientific Method

• Observation -> Question -> Hypothesis -> Experiment -> Conclusion -> Result

Scientific Methods - Approaches

• Qualitative methods look at overall problems, not just numerical evidence
• Qualitative methods look for categories like events, descriptions, and comments.
• Qualitative methods are an inductive process and develop theories from the data gathered
• Quantitative methods focuses on data that can be measured numerically and generalizes data across subjects.
• Quantitative methods collect number-based data and it is analyzed in statistics
• Quantitative methods use a deductive process that is descriptive or comparative.

1.2 Microbiology, a Human Perspective - Learning Outcome

• The importance of microorganisms in human health and the surrounding environment.
• Commercial benefits of microorganisms.
• Why microorganisms are useful research tools.
• The role of microbes in disease, including past triumphs and remaining challenges.

The Human Microbiome

• Human body carries enormous population of microorganisms called the normal microbiota
• Plays essential role in human health
• It can prevent disease by competing with disease-causing microbes
• It is useful for aiding in digestion
• It promotes the development of the immune system
• May decrease allergies, asthma
• May affect brain chemistry and body weight
• The Human Microbiome Project was started in 2007

Microorganisms in the Environment

• Recycling of nutrients
• Oxygen production through photosynthesis
• Nitrogen fixation
• Decomposers of material that break down Cellulose in the environment and in the digestive tracts of ruminants
• National Microbiome Initiative (NMI) started in 2016
• It expands the scope of microbiome research

Commercial Benefits of Microorganisms

• Food production by fermentation- beers, yogurts, cheeses, buttermilk, baking bread (using yeast)
• Biodegradation can degrade environmental pollutants and lessen damages from oil spills
• Bacteria synthesizes commercially valuable products, such as antibiotics to treat diseases. - Ethanol (biofuel), Hydrogen gas, oils (biofuels)
• Bacteria synthesizes amino acids (dietary supplements) and insect toxins (insecticides)
• Cellulose (headphones), Hydroxybutyric acid (disposable diapers and plastics)
• Biotechnology
• Useful use of microbiological and biochemical techniques to solve practical problems
• Genetic engineering enables the production of medications with microorganisms, including insulin for treatment of diabetes
• Production of plants with desirable qualities

Microbes as Research Tools

• Model organisms have same fundamental metabolic and genetic properties as higher life forms
• All cells composed of same chemical elements
• Synthesize cell structures by similar mechanisms
• Duplicate DNA
• Degrade foods via same metabolic pathways
• "What is true of elephants is also true of bacteria, and bacteria are much easier to study" (Jacques Monod)
• Microbes grow very quickly on inexpensive growth media

Microbes and Disease

• Most microorganisms are beneficial or not harmful
• Some are pathogens that can cause disease
• Diseases can result in Damage to body tissues
• Damage can be the Result of a pathogen's growth and products OR the Result of body's defense mechanisms
• Influenza killed more Americans in 1918-1919 than WWI, WWII, Korean, Vietnam, and Iraq wars combined
• The COVID-19 pandemic resulted in over 1,000,000 deaths worldwide, including over 200,000 Americans.

Nonhuman Epidemics

• Epidemics are not limited to human populations.
• The great Irish famine in the 1800s was due to microbial disease of potatoes.
• 2013: a bacterial disease was found in Southern Italy that kills olive trees, spread to Spain and France, contributing to worldwide drop in olive oil production
• A fungal disease called “wheat blast" devastated wheat crops in South America
• It spread to Bangladesh in 2016 and resulted in the loss of over 35,000 acres of crops.
• Frog populations around the world were decimated by a fungal disease called chytridiomycosis.

Microbes and Disease - Figure 1.4

• Modern sanitation, vaccination, and antibiotic treatments have reduced of incidence of infectious diseases

Past Triumphs

• Smallpox has been eradicated
• It once killed one-third of victims and left others blind or scarred
• It devastated unexposed populations, like native inhabitants of the Americas
• There have been no reported cases have since 1977, but laboratory stocks of the virus still remain
• Black death/Plague is now less than 100 deaths per year

How the Plague was controlled

• Killed one-third of population of Europe (approximately 25 million people) between 1347 to 1351
• Control of rodent populations and human respiratory secretions prevents spread
• Antibiotics provide treatment
• Polio is nearly eliminated by vaccination

Emerging Infectious Disease

• An Emerging Infectious Disease (EID) has become is one that has become more common in last several decades.
• Newly recognized diseases: Covid-19 - caused by a virus called SARS-CoV-2
• Ebola virus disease
• Congenital Zika syndrome
• Middle East respiratory syndrome (MERS)
• Influenza (certain types)
• Lyme disease
• AIDS
• Hantavirus pulmonary syndrome
• Mad cow disease (bovine spongiform encephalopathy)

Emerging Infectious Disease

• Common diseases that that have become even more common include malaria and tuberculosis
• Disease agents now evolve and Infect new hosts (HIV-1), COVID-19 arose from a strain infecting bats, cause different damage (E. coli O104:H4), and become resistant to antibiotics (tuberculosis, malaria)

Changes in society

• Mobile populations can carry pathogens around globe
• Diseases like malaria and cholera have largely been eliminated from developed countries, but still exist in many areas of the world
• Expansion off cities into rural areas allows closer contact with organisms that people have not encountered previously

Emerging Infectious Disease

• Decades of vaccination have controlled many common diseases in developed countries
• Lack of first-hand knowledge of the dangers of diseases can lead people to fear vaccines more than the diseases they prevent
• Due to low vaccination rates, diseases like measles, mumps, and whooping cough- nearly eliminated from developed countries- could become common again.

Chronic Diseases

• May be caused by microorganisms:
• Stomach ulcers- traditionally caused by stress- are often caused by the Helicobacter pylori bacteria.
• Cervical cancer is caused by human papilloma virus (HPV).

1.3-Members of the Microbial World

• Compare and contrast characteristics of members of the Bacteria, Archaea, and Eukarya.
• Explain the features of an organism's scientific name.
• Compare and contrast the algae, fungi, and protozoa.
• Compare and contrast viruses, viroids, and prions.

Members of the Microbial world: Domains

• The 3 domains of the Microbial world are Bacteria, Archaea and Eukarya

Members of the Microbial World - Table 1.1

• Bacteria contain prokaryotic cells and are unicellular
• Bacteria cell walls have Peptidoglycan
• Their Typical size range is 0.3 to 2 micrometers
• Their Ribosomal RNA sequences are unique to the group
• Archaea contain prokaryotic cells and are unicellular
• Archaea lack Peptidoglycan
• Their Typical size range is 0.3 to 2 micrometers
• Their Ribosomal RNA sequences are unique to the group
• Eukarya contain eukaryotic cells and include unicellular and multicellular organisms
• Their Ribosomal RNA sequences are unique to the group
• Their typical size range is 5 to 50 micrometers
• They have membrane-bound organelles

Scientific Names

• Binomial System of Nomenclature: two words: Genus (capitalized), Specific epithet, or species name (not capitalized)
• The Genus and species are italicized or underlined and The Genus may be abbreviated (E. coli)
• Name reflect characteristic of organism or honor a scientist

Names

• Escherichia honors Theodor Escherich.
• coli indicates the colon, where the bacteria live.
• Members of a species with important minor differences may be indicated with a strain designation (E. coli K12)
• Informal names that resemble genus names are not italicized. Members of the genus Staphylococcus are often called staphylococci.

Sizes in the Microbial World

• Most eukaryotic cells, Most bacteria, Smallest bacteria, Viruses, Proteins, Small molecules
• The basic unit of length is the meter (m): nanometer (nm) = 10-9 meter = 0.000000001 meter, micrometer (μm) = 10-6 meter = 0.000001 meter, millimeter (mm) = 10-3 meter = 0.001 meter
• 1angstrom =10-10 meter, 1micron= 10-6meter

Bacteria

• Single-celled prokaryotes
• Most have specific shapes (cylindrical, spherical, spiral)
• Rigid cell wall contains peptidoglycan (unique to bacteria)
• Many move using flagella
• Multiply via binary fission
• Obtain energy from a wide variety of sources; some are photosynthetic
• Bacteria come in a variety of shapes, but cells of a given species are usually only one shape.

Archaea

• Single-celled prokaryotes similar in size, shape, and properties to bacteria
• Major differences from Bacteria in chemical composition
• Cell walls lack peptidoglycan
• Ribosomal RNA sequences different
• Many are extremophiles
• High salt concentration, temperature
• They are common in moderate environments

Eukarya

• They use organic material for energy. Size range from microscopic (yeasts) to macroscopic (molds; mushrooms are the reproductive structures of some fungi.
• Algae use sunlight for energy and range from microscopic (single-celled algae) to macroscopic (multicellular algae)
• Protozoa uses organic material for energy; single-celled microscopic organisms
• Helminths use organic material for energy. Adult worms are typically macroscopic and often quite large, but their eggs and larval forms are microscopic.

Acellular Infectious Agents

• Viruses consist of DNA or RNA, are surrounded by/covered by a protein coat and Obligate intracellular agents that use the machinery and nutrients of host cells to replicate.
• Viroids consist only of RNA and are Obligate intracellular agents that use the machinery and nutrients of host cells to replicate.
• Prions consist only of proteins, are Misfolded versions of normal cellular proteins and cause the normal versions to misfold

Chapter Summary

• The History of microbiology and major discoveries,
• Discussions on the dispute over spontaneous generation,
• Credit to scientists,
• Scientific methods, using Qualitative and quantitative research
• The human perspective of microbes to humans in health, study, and the environment.
• Prokaryotes, eukaryotes and acellular agents