Six Kingdoms and Biological Classification System

• Living organisms are divided into six major groups based on characteristics in the six-kingdom system
• The system was developed to improve reflect evolutionary relationships and biological diversity

Six Kingdoms

• Animalia: Multicellular, heterotrophic animals
• Plantae: Multicellular, autotrophic plants
• Fungi: Mostly multicellular, decomposers, and heterotrophic
• Protista: Mostly unicellular, a diverse group
• Eubacteria: Unicellular prokaryotes, found everywhere
• Archaeabacteria: Unicellular prokaryotes, often in extreme environments
• Organisms are grouped based on structural, genetic, and functional characteristics

Biological Classification System

• The major levels are Kingdom, Phylum, Class, Order, Family, Genus, and Species
• This system groups organisms from broad categories to more specific ones
• Kingdom is the highest and most general classification
• Organisms are grouped based on fundamental characteristics
• Animalia (animals), planate (plants), fungi are some kingdom examples
• Phylum is a division within a kingdom
• Same phylum organisms share major structural similarities
• Chordata (vertebrates) and Arthropoda (insects, spiders, crustaceans) are phylum examples
• Class is a further subdivision of phylum
• Class organisms share more specific features
• Mammalia (mammals) and Insecta (insects) are class examples
• Order is a groups within a class
• Order organisms share particular triats
• Carnivora (carnivorous mammals) and Primates (humans, apes, monkeys) are order examples
• Family is a division within an order
• Organisms in a family are closely related and share even more specific traits
• Canidae (the dog family) and Felidae (the cat family) are family examples
• Genus are closely related species that share common features
• The genus name is always capitalized and italicized
• Canis (the genus for dogs, wolves, and foxes) and Felis (the genus for small cats) are Genus examples
• Species is the most specific classification
• A species consists of individuals that can interbreed and produce fertile offspring
• The species name is always italicized and lowercase
• Canis lupus (the species for wolves) and Felis catus (the species for domestic cats) are species examples

Taxonomic Hierarchy Summary (broad to specific)

• Kingdom (e.g., Animalia)
• Phylum (e.g., Chordata)
• Class (e.g., Mammalia)
• Order (e.g., Carnivora)
• Family (e.g., Canidae)
• Genus (e.g., Canis)
• Species (e.g., Canis lupus)
• Only learning genus and species of bacteria

Taxonomy/Classification of Bacteria

• Utilizes a hierarchical system to classify bacteria based on shared characteristics
• Bacteria classification is similar to other organisms, but includes categories specific to microbial characteristics

Bacteria Domain Classification

• Eubacteria: Broadest category of prokaryotic organisms with peptidoglycan cell walls
• Archaea: Prokaryotes differing biochemically from bacteria, especially in cell membranes and RNA
• Eukarya: Includes all eukaryotic organism like plants, animals, and fungi

Bacteria Kingdom classification

• Bacteria: The kingdom of true bacteria which are further divided based on shape, metabolic properties, and genetic factors

Bacteria Phylum Classification

• Bacteria divided into phyla, such as Proteobacteria, Firmicutes, and Actinobacteria, based on genetic similarities and distinct physiological characteristics

Class, Order, Family (Bacteria)

• Further divisions are within each phylum broken down into classes, orders, and families
• Phylum Proteobacteria includes classes like Alpha, Beta, Gamma, Delta, and Epsilon
• Class Gamma-proteobacteria has families like Enterobacteriaceae (includes Escherichia and Salmonella)

Bacteria Genus Classification

• Genus is a group of species that share a common ancestor and are closely related
• Genus Staphylococcus includes species like Staphylococcus aureus

Bacteria Species Classification

• Species is the most specific level that refers to bacteria that are closely related and capable of interbreeding or sharing very similar genetic characteristics

Additional Criteria for Bacterial Classification

• Phenotypic and genotypic characteristics are two main ways to classify and identify bacteria and other microorganisms
• Observable traits (phenotype) and genetic information (genotype) help scientists distinguish and classify organisms

Phenotypic Characteristics (Physical Characteristics)

• These relate to an organism's observable traits

Colony Morphology (Phenotypic)

• Appearance of bacterial colonies grown on a solid medium
• Includes shape (round, irregular, filamentous), size, color, texture (smooth, rough, shiny), elevation (flat, raised, convex), edge (entire, irregular, lobate)
• Colony morphology can help differentiate species, but is not always definitive

Gram Staining (Phenotypic)

• A lab method to classify bacteria into gram-positive and gram-negative groups
• Gram-positive has thick peptidoglycan layers that stain purple
• Gram-negative has thinner peptidoglycan layers and an outer membrane, staining pink
• Gram staining identifies bacterial species and guides treatment decisions like antibiotic choice

Biochemical Testing (Phenotypic)

• Tests that identify bacteria based on metabolic and chemical activities
• Includes sugar fermentation, production of gases, enzyme activities
• The tests help distinguish between species based on ability to metabolize different substrates

Genotypic Characteristics (Genetic Characteristics)

• These characteristics examine the genetic makeup of an organism through DNA or RNA sequences

Nucleotide Sequence (Genotypic)

• The order of nucleotides (A, T, C, G) in a DNA molecule
• involves sequencing the DNA to identify species and determine evolutionary relationships
• Genetic sequencing allows for accurate identification and classification of bacteria and is useful for detecting new organisms

rRNA Genes(Genotypic)

• Genes that code for ribosomal RNA in the ribosome
• 16S rRNA gene is is commonly used for bacterial identification because it is highly conserved across different species
• rRNA genes analysis provides clear evolutionary relationship and is used for taxonomic classification

G+C Content (Genotypic)

• The percentage of guanine (G) and cytosine (C) bases in a DNA molecule
• Classification is aided as different species have different G+C content, which affects stability and structure
• Organisms with similar G+C content are closely related, which can help bacterial identification and taxonomy
• Phenotypic characteristics focus on observable traits like colony morphology and metabolic behavior
• Genotypic characteristics focus on genetic information like DNA sequence and G+C content
• Both accurate identification and classification of bacteria

Hierarchical Classification Summary

• Domain
• Kingdom
• Phylum
• Class
• Order
• Family
• Genus
• Species
• Bacteria is categorized by examining shape, metabolic needs, and genetic makeup, which reflects evolutionary relationships

Gram-Negative Bacteria

• Spiral Shape (Vibriod)
  • Treponema pallidum: Spiral shape, causes syphilis and has gram negative staining
  • Borrelia Burgdorferi: Spiral shape, causes Lyme disease with bullseye rash and has gram negative staining
  • Helicobacter Pylori: Spiral shape, causes peptic ulcers with pain in stomach, gram negative staining
  • Campylobacter jejuni: Spiral shape, causes enteritis or food poisoning, gram negatuve staining
  • Vibrio cholerae: Spiral shape, causes cholera with rice water stools, gram negative staining
  • Vibrio vulnificus: Spiral shape, causes severe food poisoning or wound infection, gram negative staining

Bacteria Rod Shape

• Pseudomonas aeruginosa: Rod shapred, causes burn, wound infections, and pneumonia with green appearance and multidrug resistant with gram negative staining
  • Legionella pneumophila: Rod shaped, causes Legionnaires' disease (grows in standing water), pneumonia-like symptoms, gram negative staining
  • Bordotella pertussis: Rod shaped, causes whooping cough, gram negative staining -Escherichia coli: Rod shaped, causes enteritis, UTIs, hemolytic uremic syndrome, gram negative staining
• Shigella dysenteriae: Rod shaped, causes profuse watery diarrhea, transmitted by poor water quality, gram negative staining
• Salmonella: Rod shaped, causes enteritis (food poisoning), gram negative staining
• Klebsiella pneumoniae: Rod shaped, causes pneumonia, wound infection, UTI and is becoming antibiotic resistant, has gram negative staining
  • Proteus: Rod shaped, causes UTI, gram negative staining -Yersinia pestis: Rod shaped, causes bubonic plague, carried in fleas gram negative staining

Bacteria - Diplococci

-Neisseria meningitidis: Diplococci shaped, causes meningococcal meningitis with Petechial rash, neck rigidity, fever, gram negative staining -Neisseria: Diplococci shaped, causes Gonorrhoeae, painful urination, abdominal tenderness, cervical exudate, gram negative staining

Bacteria - Random Shape

-Haemophilus influenzae: Causes bacterial meningitis, otitis media, gram negative staining -Rickettsias and chlamydias: Grouped, Obligate intracellular parasites causes rocky mountain spotted fever and Petechial rash caused by ticks

• Chlamydia trichimonis: causes Chlamydia (NGU), most common bacterial STD, same symptoms as Gonorrhea, can lead to PID and infertility

Bacteria - Cell Wall-Less

• Mycoplasma pneumoniae: no cell wall, causes atypical pneumonia with fried egg appearance

Gram-Positive Bacteria

• Cocci Shape -Staphylococcus aureus: Cocci shaped (clusters), causes wound infections, MRSA, boils, impetigo, gram positive staining -Streptococcus pyogenes: Cocci shaped, causes strep throat, rheumatic heart disease, glomerulonephritis and necrotizing fasciitis, B-hemolytic on blood agar, gram positive staining -Strep agalactiae: Cocci shaped, causes newborn meningitis, gram positive staining -Streptococcus pneumoniae: Cocci shaped, comes with or without a capsule, causes Pneumococcal pneumonia, capsule provides protective barrier for strength, and gram positive staining

Bacteria - Spore Formers

-Bacillus anthracis: Spore-formers shaped, causes anthrax cutaneous, inhaled, and ingested spores, gram positive staining -Clostridium tetani: Spore-formers shaped, causes tetany and lock jaw anaerobic, gram positive staining -Clostridium botulinum: Spore-formers shaped, causes botulism poisoning anaerobic, gram positive staining -Clostridium perfringens: Spore-formers shaped, causes gangrene and food poisoning, gram positive staining

• Clostridium difficile: Spore-formers shaped, causes C Diff diarrhea or pseudomembranous colitis anaerobic, gram positive staining

Bacteria - Pleomorphic Shape

-Corynebacterium diptheriae: Pleomorphic shaped, causes heart and kidney failure anaerobic, pseudomembrane in throat, gram positive staining

Bacteria - Acid-Fast Rods

• Mycobacterium tuberculosis: Acid-fast rods shaped, causes TB (active or latent), latent TB can activate anytime, gram positive staining