Microbiology: Bacteria, Fungi, and Helminths

• The scientific method describes the process of science, where refinement of hypothesis and experiments can cycle
• Involves making an observation and asking a question

Steps

• Develop a testable explanation, called a hypothesis
• Design experiments to test the hypothesis
• Include a control to help rule out alternative explanations
• Do the experiment, collect, and analyze data
• Draw a conclusion
• Communicate methods, results, and conclusions
• A scientific theory is an explanation supported by a large amount of evidence

Scientific Rules

• Summarize material with a general rule for introductory courses
• Every rule has exceptions
• Understanding the exceptions often strengthens the rule's utility
• Information always flows from DNA → RNA → Protein
• There are only four RNA BASES → A, G, C, & U

Information Stored in Nucleic Acids (DNA or RNA)

• Survival often depends on guessing correctly in a given situation
• Correct guesses lead to survival and reproduction, passing on the memory
• The timescale is hard to imagine as it is a very slow process

Universal Tree of Cellular Life

• Assesses the accumulation of mutations in DNA
• Line lengths correlate with evolutionary time
• Cellular life evolved from a single-celled ancestor
• Earth is approximately 4.6 billion years old
• Life started 3.5–3.8 billion years ago
• Single-celled organisms terraformed the planet by adding oxygen to the atmosphere 2.5 million years ago
• Life has spread and evolved to fit essentially every habitable zone

Ways Microorganisms Impact Humans

• Microbiomes impacts in humans (notably Clostridium difficile)
• Environmental impacts and Ecology
• Commercial uses range from food production and preservation, biodegradation, and production of specialized compounds
• Research tools

Humankind's Long Recognition of Diseases

• Recognizes illnesses and death distinct from physical injury and poisons, including sanitation, without knowing why
• Disease diagnoses were often accurate, but etiology explanations were haphazard
• Good sanitation was understood, with explicit instructions in Deuteronomy 23:12-14
• Fermentation was used to preserve foods, linking preservation to selected caves or vats

Discovery of the Micro Universe

• Microorganisms can cause disease, disease and suffering are not their intent
• Microorganisms have evolved for survival, growth, and reproduction, not to kill
• Understanding their needs allows manipulation for benefits like infection control, food preservation, and stimulating good health
• There are emerging commensal relationships where Microorganisms support humans' growth/reproduction, and humans protect the Microorganisms

Categories of Infectious Diseases

• Some diseases have evolved a balance with hosts and defense systems, allowing organisms to grow, reproduce, and spread
• Other diseases result from Microorganisms evolved in a different environment or organism, causing imbalance, deadly outcomes, and no benefit to Microorganisms

Microorganisms Learning

• If a Microorganism kills too quickly, there is no growth/transmission, resulting in no adaption(Ebola)
• If a Microorganism is quickly killed by the host, there is no growth/transmission, resulting in no adaptation(Tetanus)
• In a Goldilocks environment, Microorganism and host can learn, evolving into a balance

Infectious Disease Concepts

• Most microorganisms are not harmful, some beneficial
• Pathogens cause disease by:
  • Directly damaging body cells and tissues
  • Creating toxins that damage cells and tissues
  • Releasing waste products that damage cells and tissues
  • Stimulating body's defense mechanisms, resulting in collateral damage
• The impact of pathogens can far exceed other causes of death
• Influenza in 1918-1919 killed more Americans than WWI, WWII, and the Korean, Vietnam, and Iraq wars combined
• The COVID-19 pandemic has globally caused death of over 15 million

Microorganisms Non-Infectious Impact

• The great famine in Ireland in the 1800s was largely caused by a microbial disease of potatoes
• A bacterial disease killing olive trees, first seen in southern Italy in 2013, led to the recent worldwide drop in olive oil production
• Wheat blast, a fungal disease, devastated wheat crops in South America and Bangladesh in 2016, resulting in loss of 35,000 acres in Bangladesh
• Frog populations have been decimated worldwide by chytridiomycosis

Specific Successes

• Smallpox eradicated with no reported cases since 1977
• Plague deaths have fallen to less than 100 per year
• Polio is nearly eliminated by vaccination

"Accidental" Pathogens

• Emerging Infections are frequently a Zoonosis, with climate change facilitates spread
• Includes COVID-19 (SARS-CoV-2), mpox (monkeypox), Ebola, Congenital Zika syndrome, Middle East respiratory syndrome (MERS), Influenza, Lyme disease, AIDS, Hantavirus pulmonary syndrome, and Mad cow disease
• Emerging infectious diseases from accidental crossover include E. coli O104:H4, Ebola, and HIV-1
• Climate change exacerbated the rise of Lyme disease, Chagas disease, and Malaria
• Societal factors can exacerbate drug resistance in tuberculosis and staph, facilitate rapid world-wide travel/connections, create unequal access to medical care and treatments, spread misinformation preventing application of medical care and treatments.

"Usual Suspects"

• All living cells are classified into three domains: Bacteria, Archaea, Eukarya
• All three domains include known or suspected pathogens

Binomial System of Nomenclature

• Generally uses two words: Genus (capitalized) and species name (not capitalized)
• Both genus and species names are either italicized or underlined
• Genus may be abbreviated, e.g., E. coli
• 'spp.' can be used for multiple species: Plasmodium spp.

Scientific Name Conventions

• Name often reflects organism characteristics or honors a scientist
• Members of a species with key minor differences may be indicated with a strain designation (E. coli K12)
• Informal names resembling genus names are not italicized
• Members of the genus Staphylococcus are called staphylococci

Characteristics of the Three Domains:

• Bacteria are prokaryotic, unicellular and have peptidoglycan in the cell wall
• Archaea are prokaryotic, unicellular and do not have peptidoglycan in the cell wall
• Eukarya are eukaryotic and can be unicellular and multicellular

Bacteria

• Bacteria are Single-celled prokaryotes that have a rigid cell wall containing peptidoglycan
• Typically move using one or more flagella and multiply via binary fission
• Obtain energy from varied sources, also, are photosynthetic
• Have a consistent, specific cell shape

Bacterial Shapes:

• Coccus: Spherical cells
• Bacillus: Rod-shaped, cylindrical cells
• Vibrio: Short, curved rods
• Spirillum: Curved rods long enough to form spirals
• Spirochete: Long, spiral-shaped cells with a flexible cell wall
• Pleomorphic: Bacteria that vary in shape/mix multiple shapes

Bacteria Clusters

• Diplococci: cocci that remain as pairs
• Streptococcus: Division in one plane can form long chains of cocci.
• Streptococcus means "twisted chain"
• Sarcina: Cocci that divide in perpendicular planes forming cubical packets
• Staphylococcus: Cocci that divide randomly in several planes forming grape-like clusters
• Staphylococcus means "bunch of grapes"

Archaea

• Archaea are single-celled prokaryotes that have a similar size, shape, and properties to bacteria but differ in chemical composition
• Cell walls in Archaea lack peptidoglycan
• High salt concentration and Temperature extremophiles
• Found in human microbiomes like (intestine, oral cavity)

Eukarya

• Eukarya is defined as either Single-celled or multicellular eukaryotes, including fungi, algae, protozoa, and helminths (worms)
• Algae and protozoa are also referred to as protists

Eukaryotic Organisms

Fungi

• Uses organic material for energy
• Can range from microscopic yeasts to macroscopic molds
• Molds have microscopic filaments called hyphae forming visible mats (mycelium)
• Filamentous molds spread by microscopic spores (conidia), and some form macroscopic reproductive structures (mushrooms)
• Secretes enzymes onto organic materials to absorb the released nutrients
• Can cause opportunistic infections on skin and in lungs

Algae

• Diverse group of photosynthetic eukaryotes, single-celled or multicellular, containing chlorophyll or other pigments in chloroplasts
• Usually live near the surface of water or in moist habitats and have cell walls and flagella distinct from prokaryotes
• Rarely a pathogen, but some species secrete toxins into water (Cyanobacteria are bacteria, NOT algae)

Protozoa

• Diverse group of single-celled eukaryotes
• Ingest organic compounds for energy and most are motile, with no cell walls
• Pathogenic protozoa are often included under the term Parasites

Helminths

• Defined as Parasitic worms that live at the expense of a host
• Adult worms are visible to the naked eye, but diagnostic stages (larvae and ova/eggs) require a microscope
• Includes roundworms, tapeworms, and flukes

Acellular Infectious Agents

• They are not cells as such, they are not on the Universal Tree of Life, as they start perfectly reasonable laws and rules
• They can get twisted beyond recognition for their own benefit, with unknown origin

Viruses

• Consist of DNA or RNA with protein coat and are obligate intracellular agents using host cell machinery

Viroids

• Consist of RNA, no protein coat, and are obligate intracellular agents; use host cell machinery

Prions

• Consist of protein, no DNA or RNA; misfolded versions of normal proteins cause misfolding in others, and have no pathogenic components

Viruses

• Viruses have nucleic acid that is packaged in a protein coat
• Infect living cells, referred to as hosts and are obligate intracellular agents multiplying using host cell machinery and nutrients, remaining inactive outside of host

Viroids

• Consist only of a single short piece of RNA and are obligate intracellular agents that cause plant diseases
• Generally need a buddy for initial plant entry; one known human disease caused by it is Hepatitis D

Prions

• Prions can get misfolded due to normal cellular proteins found in the brain
• Misfolded proteins in contact with normal proteins cause misfolding
• Proteins form fibrils, and as cells die, spaces form, these are the main features of spongiform encephalopathy
• Resistant to usual sterilization procedures

Scientific Method and Information Transfer

• Before 1900s - scientists used the term proteins as the only molecule sufficiently complex molecule to transfer information
• 1930 through 1944, Avery, MacLeod, & McCarty identified DNA was the molecule transmitting genetic information
• Finally in, from 1970 to 1988, Pruisner showed protein could be involved in carrying with infecting.
• The scientific method will always sort it out!

Test your knowledge of microbiology! Questions cover scientific names, bacterial domains, E. coli strains, fungi vs. protozoa, bacterial vs. archaeon, bacterial multiplication, helminths, and genus Staphylococcus.