Microbial Taxonomy and Classification

Microbiology in Perspective

• The course is taught by Dr. Juan Rivera-Correa
• Office hours are Tuesdays from 12-2 pm in A-302-E
• Contact Dr. Rivera-Correa at [email protected]
• The section number for this course is BIO 3302-D068 (22767)
• The class is taught on Tuesdays from 2:15 PM - 3:55 PM in Room A-709

Learning Outcomes - Section 1.1

• List the types of microorganisms that colonize humans
• Describe the impact that microbes have on the earth
• Explain the theory of evolution
• Explain the ways humans have manipulated organism for their own uses
• Summarize the burden of human disease caused by microbes
• Differentiate among bacteria, archaea, and eukaryotic microorganisms
• Identify two acellular infectious agents of concern to microbiology
• Compare and contrast the size of different microbes

Daily Group Questions - Lecture 1

• There are 8 types of microbes
• Microbes are essential; they can be used for food production, bioremediation, and can be used in medicine
• The 4 macromolecules include:
  • Carbohydrates (monosaccharides)
  • Lipids (fatty acids + glycerol)
  • Proteins (amino acids)
  • Nucleic acids (nucleotides)
• Taxonomy is the science that classifies organisms
• Woese Fox System classifies microbes by comparing small subunit ribosomal RNA (ssu rRNA) sequences

Participation Format

• Each student is to be assigned to a group of 3-4 students
• Participation is mandatory and questions will be assigned accordingly
• Group members are to discuss the questions among themselves and choose one representative to answers
• Each group is to be assigned 1 vocabulary word and they must define it by the end of the lab/lecture

Essential Concepts of Biology

• There are 12 levels of organization in biology ranging from atom to the biosphere
• From the smallest to largest units of life: atoms, molecules, organelles, cells, tissue, organ, organ system organism, population, community, ecosystem, biosphere
• Basic unit of life: cell
• There are 8 characteristics of life including:
  • Cellular organization, reproduction, metabolism, homeostasis heredity, response to stimuli, growth and development, adaptation through evolution

Definitions of Microbes

• Microbiology - a specialized area of biology that deals with living things ordinarily too small to be seen without magnification
• Microbes include:
  • Bacteria
  • Archaea
  • Protozoa
  • Fungi
  • Helminths
  • Algae
  • Viruses
  • Prions
• Prokaryotes don't have a nucleus, they have nucleoids.
• Eukaryotes have a membrane-bound nucleus.
• Acellular organisms are biological entities, but are not technically "alive"

Relative Size

• Relative sizes of microbes range from 10 nm (prion) 10,000 nm (eukaryote)
• Microbes reproduce rapidly, but can not be seen directly
• Microbes can be grown quickly in large populations in the laboratory, and are viewed through microscopes or analyzed through indirect measures

Question 1: What is not considered a microbe?

• The correct answer is Plant, all other options are considered microbes

Microbes on Earth

• Single-celled organisms appeared on this planet about 3.8 billion years ago
• Cell types arose from a single (extinct) common ancestor:
  • Eukaryotes: "true nucleus”
  • Bacteria: single-celled, no true nucleus
  • Archaea: single-celled, no true nucleus, distinct from bacteria
  • Prokaryotes: bacteria and archaea "pre-nucleus"
  • Akaryotes: "no nucleus” (alternate term used for prokaryotes)

Domains

• There are 3 domains: Bacteria, Archaea, Eukarya
• Bacteria and archaea are predominantly single-celled
• Eukaryotes:
  • May be single celled
  • Highly complex, multicellular
  • Are of larger size compared to other biological units

Prokaryotes vs Eukaryotes

• Cellular Organization: prokaryotes vs eukaryotes Eukaryotes:
  • Organelles: small, double-membrane-bound structures that perform specific functions. Examples include the nucleus, mitochondria, and chloroplasts.
  • Some are microorganisms; some are macroscopic
  • Ten times smaller than eukaryotes, but the opposite with all are microorganisms Bacteria and Archaea (prokaryotes)
  • Lack organelles
  • All are microorganisms

Fundamental characteristics of cells

• Bacteria and protozoa: are single-celled life forms
• Animals and plants: comprise trillions of cells
• Characteristics:
  • Spherical, polygonal, cuboidal, or cylindrical
  • Contain a protoplasm encased in a cell membrane
  • Have chromosomes containing DNA
  • Ribosomes for protein synthesis
  • Exceedingly complex in function

Cell functions and Characteristics

• Eukaryotic cells:
  • Animals, plants, fungi, protozoa
  • Contain organelles that are encased by membranes and perform specific functions
• Bacteria and Archaea (Prokaryotic):
  • Have no nucleus or other organelles
  • Complex fine structure
  • Can engage in same activities as eukaryotic cells

Viruses and Prions

• Viruses:
  • Not independently living cellular organisms
  • Exist at the level of complexity somewhere between large molecules and cells
  • Composed of a small amount of hereditary material (DNA or RNA) surrounded by a protein coat and sometimes a membrane
• Prions:
  • Simpler than viruses
  • Have no nucleic acid, contain only protein, act like infectious microorganisms

Types of Microorganism

• There are 8 types of microorganism:
  • Bacteria, Archaea, Protozoa, Fungi, Helminths, Algae, Viruses, and Prions

Question 5: Place them from largest to smallest

• Helminth- protozoan-bacterium-virus-prion

Evolutionary Time Line

• Single-celled organisms appeared on this planet about 3.8 billion years ago

Location of Microbes

• Microbes are Ubiquitous

• Microbes are ubiquitous and are found:

  • Deep in the earth's crust
  • In polar ice caps and oceans
  • Inside the bodies of plants and animals
  • In the earth's landscape

• Essential to life

Theories of Evolution and Science

• Theory of evolution:
  • The accumulation of changes that occur in organisms as they adapt to their environments
  • Documented every day in all corners of the planet
  • Testable by science
• Theories in science:
  • Have undergone years and years of testing and have not been disproved
  • A well-studied and well-established natural phenomenon
  • Not just a random guess
• Theory: explains WHY natural phenomena occur
• Law: summarizes a set of observations about natural phenomena

Concept Check 2: The following statement is false

• The theory of evolution is not widely accepted among scientists because it still remains unproven

Concept Check 3: The following statement is false

• Microbes are found everywhere on the planet except in the deeper layers of the earth's crust, which are largely considered to be sterile

Roles of Microbes: Photosynthesis

• Photosynthesis:
  • Light-fueled conversion of carbon dioxide to organic material
  • Accompanied by the formation of oxygen
• Anoxygenic photosynthesis:
  • Occurred in bacteria before plants evolved
  • Did not produce oxygen
  • More efficient in extracting energy from sunlight
• Oxygenic photosynthesis:
  • Evolved from anoxygenic photosynthesis
  • Photosynthetic microorganisms are responsible for 70% of the earth's photosynthesis

How Microbes Shape Earth

• Microorganisms are the main forces that drive the structure and content of the soil, water, and atmosphere:
  • Microbes produce CO2, NO, and CH3 that insulate the earth's atmosphere
  • Bacteria are the most abundant cellular organisms in the oceans
  • Viruses are the most abundant inhabitants of the oceans
  • Bacteria and fungi live in close associations with plants and assist them in obtaining nutrients and water and may protect them against disease

Old Uses of Microbes

• Microbes have historically been used to produce bread, alcohol, and cheese
• Microbes have also been used in the treatment of wounds, for mining ore and Cleaning -up human-created contamination

Genetic Identification of Human Microbes

• Even though the exact microbes found in and on people are highly diverse, the overall set of metabolic capabilities the bacterial communities possess is remarkably similar among people
• The amount of bacterial cells in the human body are in the trillions and vastly outnumber the amount of human cells by 10-1
• Much less than 1% of bacteria species are actually pathogenic human pathogens

Genetic Engineering

• Genetic engineering: Manipulates the genetics of microbes, plants, and animals for the purpose of creating new products and genetically modified organisms (GMOs)
• Recombinant DNA technology: Makes it possible to transfer genetic material from one organism to another and deliberately alter DNA
• Bioremediation: Uses microbes already present or introduced intentionally to restore stability or clean up toxic pollutants

Pathogens

• Pathogens (<1%): microbes that cause disease:
  • Over 2,000 different microbes cause disease
  • Ten billion infections occur across the world every year
  • Infectious diseases are important common causes of death worldwide

Top 4 Infections

• TB was the world's second deadliest disease, with 1.13 million deaths worldwide in 2022
• Malaria caused 0.62 million deaths in 2021
• HIV/AIDS caused 0.63 million deaths in 2022
• Covid-19 was responsible for 1.24 million deaths in 2022
• The top 4 infections in the world:
  1. Tuberculosis* \
  2. COVID-19
  3. HIV/AIDS
  4. Malaria
• Resurged to the top in 2024

Emerging Diseases

• Emerging and reemerging diseases:
  • AIDS, Hepatitis C, Zika virus, West Nile virus ,Tuberculosis ,Malaria
• Associations between noninfectious diseases and microbes:
  • Gastric ulcers are caused by Helicobacter pylori.
  • Multiple sclerosis, OCD, coronary artery disease, and obesity have been linked to chronic infections with microbes

Antibiotic Drug Resistance

• Increasing number of patients with weakened defenses:
• Subject to infections by common microbes that are not pathogenic to healthy people
• Increase in microbes that are resistant to drugs

Timeline

• 1928, Date of AntiBiotic Discovery, 1940- Date of resistance identified
• 1948, Date of Antibiotic Discovery, 1953- Date of resistance identified
• 1985, Date of Antibiotic Discovery, 1985- Date of resistance identified
• 1985 as well a, Date of Antibiotic Discovery, 1993- Date of resistance identified
• There has not been new class of antibiotics in 30 Years since the last one was introduce
• Antibiotic resistance is on track to be one of the lead causes of death by 2050

Theories in History

• Spontaneous generation:
  • The belief that invisible vital forces present in matter led to the creation of life
• Abiogenesis:
  • Even after the discovery of microbes, the belief in abiogenesis, which embraced spontaneous generation, was still embraced by some scientists
• Biogenesis:
  • Other scientists advocated biogenesis, saying that living things arise only from others of their same kind

Pasteur

• Pasteur's Swan-Neck Flask Experiments were used disproved spontaneous generation:
  • Filled flasks with broth and shaped the openings into long, swan-necked tubes
  • Heated the flasks to sterilize the broth
  • Flasks that were exposed to dust from the air showed microbial growth
  • Flasks exposed to air but not to dust showed no microbial growth
• Louis Pasteur studied the roles of microorganisms in the fermentation of beer and wine

Medical Microbiology

• Robert Hooke is credited with describing cellular structures
• Antonie van Leeuwenhoek built the first microscope!
• Ferdinand Cohn discovered and described heat-resistant endospores
• Oliver Wendell Holmes and Ignaz Semmelweis described the importance of hand washing to prevent spread of disease in the hospital setting
• Joseph Lister is credited with first using aseptic techniques in surgery
• Louis Pasteur invented pasteurization; conducted the first studies linking human disease to infection
• Robert Koch created Koch's postulates and showed that anthrax was caused by Bacillus anthracis in 1875

Concept Check 6

• The scientist who built the first simple microscope was Antonie van Leeuwenhoek

Contributions by LatinX scientist to microbiology:

• Carlos Chagas, discovered Chaga's disease in 1909
• Maria Elena Bottazzi is the Honduran scientist co-nominated for the Nobel Peace Price for the creation of the cheaper COVID-19 vaccine Corbevax
• Kizzmekia S Corbett: led to the the team that developed the Moderna COVID-19 mRNA vaccine

Reminders

• Quiz 1 and homework is due the following week

Types of Biochemicals

• The macromolecules include:
• Carbohydrates
• Lipids
• Proteins
• Nucleic acids

Macromolecule

• Molecules in a cell and life can be categorized in these 4 macromolecules including carbohydrates, lipids, proteins and nucleic acids

Carbohydrates

• Carbohydrates are a combination of carbon and water. They have the general formula of (CH2O)n. The chains of carbohydrates usually end with a suffix.
• Types of carbohydrates:
  • Hexose: 6-carbon sugar
  • Pentose: 5-carbon sugar
  • Glucose: the most common and universally important hexose
  • Fructose: named for fruit
  • Xylose: from the Greek word for "wood”
  • Lactose: important component of milk
  • Maltose: malt sugar
  • Sucrose: table sugar or cane sugar
• Polysaccharides: Contribute to structural support and protection and act as a nutrient

Lipids

• Lipids are molecules composed of fatty acids and glycerol
• Triglycerides: important storage lipid Composed of a single molecule of glycerol bound to three fatty acids. These molecules consist of saturated or unsaturated molecules that store energy
• Lipids have several functions, including:
  • Are important storage lipid
  • Storage of energy
  • Composed of a single molecule of glycerol bound to three fatty acids
• -Fatty acids can be saturated or unsaturated-Stored in long-term concentrated form as droplets or globules-Yield twice as much energy per gram as other storage molecules (carbohydrates)
• Cholesterol reinforces the cell membrane in animal cells and cell-wall deficient bacteria,

Proteins

• Proteins: Shapers of Life
  • Predominant organic molecules in cells
  • Made of 20 different amino acids

Protein Structures

• Primary (1°) structure: type, number, and order of amino acids in the chain
  • Primary structure gives protein diversity
• Secondary (2°) structure:
  • Arises when various functional groups (called R groups) interact by forming hydrogen bonds: Alpha helix Beta pleated sheet
• Tertiary (3°) structure:
  • Created by additional bonds between functional groups:
  • Amino acids containing cysteine form disulfide bonds Quaternary (4°) structure:
  • When more than one polypeptide forms a large, multiunit protein
  • Each protein develops a unique shape, and its surface displays a distinct pattern of pockets and bulges
  • Proteins can only interact with molecules that fit its particular surface features, like a lock and key
• Native state: The functional three-dimensional form of a protein
• Denatured: Disruption of the native state of a protein through the application of various agents:
  • Heat, Acid, Alcohol, Some disinfectants

DNA vs RNA

• DNA: contains a special coded genetic program with detailed and specific instructions for each organism's heredity

Nucleic Acid Types

• RNA: “helper” molecules responsible for carrying out DNA's instructions and translating the DNA program into proteins that can perform life functions
• mRNA: copy of a gene that provides the information for the order and type of amino acids in a protein
• tRNA: carrier that delivers the correct amino acids for protein assembly
• rRNA: major component of ribosomes
• Fourth type of RNA acts to regulate the genes and gene expression

Structures

• DNA Structures -Composed of -Alternating deoxyribose -phosphates RNA
• Monomer -Both ->A nucleotide is the monomer of both DNA and RNA. ->Nucleotides are composedof aphosphate, apentose sugar, and a nitrogen base (A, T, C, G, or U).
• Composed DNA molecules: -alternating deoxyribose (D) -phosphates (P). Nitrogen bases (A, T, C, G):-Nitrogen bases are attached to the deoxyribose.
• DNA almost always exists as two strands twisted together- the bases are paired across the centre.
• RNA molecules are composed of alternating ribose
• DNA is formed to two nucleic strands connected via hydrogen bonding
  • Adenine pairs with thymine (or uracil in RNA)
  • Guanine pairs with cytosine (G-C) • RNA: Organizers of Protein Synthesis – Long chains of nucleotides, usually in a single strand:

1. mRNA: type of a gene that provides the information for the order and type of amino acids in a protein
2. tRNA: that carries the correct amino acids for protein assembly
3. rRNA: the major component of ribosomes

Taxonomic Terminology

• Taxonomy- science of classifying living things- Carl Von Linne (1701 to 1778)
• Nomenclature- scientific names to various taxonomies
• Classification- arrangement to hierarchy
• The process used in discovering and recording organisms, they can be recognized and named and then classified taxonomy: • Naming
• Binomial system of nomenclature:
  • Scientific name as a combination of the genus and species names -When abbreviated, first initial is presented followed by the full name written Binomial nomenclature: -Domain -Kingdom -Phylum -Class --Order -Family -Genus -Species”

Woese-Fox system:

• “Based on conserved small subunit ribosomal RNA sequences (ssu 16S rRNA)

• Analysis sequences revealed that a separate group for the archaeabacteria called Archaea The analysis indicated domains being based from the domain:

• Phylogeny:the taxonomy represent’s the natural relatedness that exists between various groups of beings-

3 Domains:

• “Eukarya “ “bacteria “ Archaea They are linked by the hereditary information of living beings gradually changing through time””Changes caused Structural and functional - that were shown to go through many generations selective for those changes that favor survival and reproduction", what are the -natural “selection EX. antibiotic resistance, virus variants • Classification" -Domain is to be known as eukarya- with the rest to be “homo sapiens, -Bacteria are the same from the bacteria cell as much as they are to the “homosapien “ -Woese-Fox system, taxonomy has the domains as bacteria, archaea, and eukarya

Explore microbial taxonomy, including hierarchical arrangement, binomial nomenclature, and scientific naming conventions. Learn about taxonomic ranks, ribosomal RNA sequence comparison, and classification steps for bacteria.