Taxonomy

Taxonomy of Living Things

• Domain: Eukaryota
• Kingdom: Animalia
• Phylum: Chordata
• Class: Mammalia
• Order: Primates
• Family: Hominidae
• Genus: Homo
• Species: sapiens

History of Taxonomic Concepts

• Linnaeus, 1735

  • Proposed a two Kingdom classification: Animalia and Vegetabilia.

• Haeckel, 1866

  • Introduced a three Kingdom system.

• Chatton, 1937

  • Proposed the concept of two Empires: Protista, Plantae and Animalia; Prokaryota and Eukaryota.

• Copeland, 1956

  • Established a four Kingdom classification: Monera (prokaryotes), Protista, Plantae and Animalia.

• Whittaker, 1969

  • Expanded to five Kingdoms: Monera, Fungi, Protista, Plantae and Animalia.

• Woese et al, 1977

  • Introduced the six Kingdom system: Eubacteria, Archaea, Protista, Fungi, Plantae, and Animalia.

• Woese and Fox, 1999

  • Suggested a three Domain system: Eubacteria, Archaea, and Eukaryotes.

Nomenclature

• Binomial Nomenclature: Assigning two names to a particular species, first proposed by Carolus Linnaeus, known as the Father of Taxonomy.
  • Every species scientific name comprises two parts:
  • Genus (generic name)
  • Species (specific epithet)
  • Example: Homo sapiens

Rules of Binomial Nomenclature

• The genus name begins with a capital letter.
• The species name begins with a lowercase letter.
• When handwritten, both names should be underlined separately.
• When printed, scientific names should be in Italics.

Overview of Nomenclature

• The system for scientifically naming organisms is known as nomenclature, a part of classification.
• Nomenclature was introduced by Carolus Linnaeus in his book Systema Naturae.
• Scientific naming results from the classification process, placing an organism within a taxonomy.
• The name combines Genus and Species allowing consistency across the globe.
• The names are primarily derived from the Latin language.

Importance of Taxonomy in Medicine

• Taxonomy is crucial for identifying, classifying, and studying pathogens, diseases, and treatments in medicine. The key roles include:
  1. Identification of Pathogens
  2. Diagnosis of Diseases
  3. Treatment Development
  4. Epidemiology and Disease Tracking
  5. Antibiotic Resistance
  6. Vaccine Development
  7. Medical Research and Drug Discovery
  8. Human Microbiome Research
  9. Understanding Genetic Relationships
  10. Prevention and Public Health

Examples of Classification

1. Mango (Mangifera indica)

   • Kingdom: Plantae
   • Division: Angiosperm
   • Class: Dicotyledonous
   • Order: Sapindales
   • Family: Anacardiaceae
   • Genus: Mangifera
   • Species: indica
   • Scientific name when typed: Mangifera indica; when handwritten: Mangifera indica.

2. Lion (Panthera leo)

   • Kingdom: Animalia
   • Phylum: Chordata
   • Class: Mammalia
   • Order: Carnivora
   • Family: Felidae
   • Genus: Panthera
   • Species: leo
   • Scientific name when typed: Panthera leo; when handwritten: Panthera leo.

Phylogenetic Tree (Domain)

• Domains:
  • Bacteria
  • Archaea
  • Eukaryota
  • Spirochetes
  • Chloroflexi
  • Entamoebae
  • Slime molds
  • Animals
  • Fungi
  • Plants
  • Various bacterial phyla such as Proteobacteria, Cyanobacteria, Planctomyces, Bacteroides, Cytophaga, Thermotoga, Aquifex, Methanococcus, Thermococcus, Thermoproteus, Pyrodicticum.

Archaebacteria

• Characteristics:
  • Resemble the first life forms on Earth, considered primitive.
  • Capable of surviving in extreme conditions, categorized as extremophiles.
  • Thermophiles: thrive in extreme temperatures.
  • Halophiles: thrive in extremely salty environments.
  • Acidophiles: thrive in very acidic conditions.
  • Alkaliphiles: thrive in very basic conditions.
  • Methanogens: produce methane gas.

Eubacteria

• Characteristics:
  • Largest group of Monerans.
  • Majority of bacteria.
  • Most are decomposers, heterotrophs, or saprophytes.
  • Some can photosynthesize like cyanobacteria, or chemosynthesize.

Classification of Bacteria

• Bacteria can be classified based on:
  • Morphology
  • Gram staining
  • Oxygen requirements
  • Mode of nutrition
  • Genetic relationships

Based on Morphology

• Four main shapes:
  • Cocci (spherical-shaped): e.g., Streptococcus, Staphylococcus
  • Bacilli (rod-shaped): e.g., Escherichia coli, Bacillus subtilis
  • Spirilla (spiral-shaped): e.g., Spirillum volutans
  • Vibrios (comma-shaped): e.g., Vibrio cholerae

Based on Gram Staining

• Gram-positive Bacteria: Thick peptidoglycan layer, stains purple; e.g., Staphylococcus aureus, Bacillus subtilis.
• Gram-negative Bacteria: Thin peptidoglycan layer, stains pink; e.g., Escherichia coli, Pseudomonas aeruginosa.

Based on Oxygen Requirements

• Aerobic Bacteria: Require oxygen; e.g., Mycobacterium tuberculosis.
• Anaerobic Bacteria: Do not require oxygen; e.g., Clostridium botulinum.
• Facultative Anaerobes: Can survive with or without oxygen; e.g., Escherichia coli.
• Microaerophiles: Require low amounts of oxygen; e.g., Helicobacter pylori.

Based on Nutrition

• Autotrophic Bacteria: Produce their own food.
  • Photoautotrophs: Use light energy; e.g., Cyanobacteria.
  • Chemoautotrophs: Use chemical energy; e.g., Nitrosomonas.
• Heterotrophic Bacteria: Depend on organic matter.
  • Saprophytic: Feed on dead matter; e.g., Pseudomonas.
  • Parasitic: Live inside a host; e.g., Rickettsia.

Differences in Domain Classification

Five Kingdom Classification

1. Monera - Kingdom of Prokaryotes
2. Protista - Kingdom of Unicellular Eukaryotes
3. Fungi - Kingdom of Multicellular Decomposers
4. Plantae - Kingdom of Multicellular Producers
5. Animalia - Kingdom of Multicellular Consumers

Characteristics of Monerans

• Unicellular and Prokaryotic.
• Lacks true nucleus and membrane-bound organelles.
• Mainly comprises Bacteria.
• Some possess a cell wall (bacteria and BGA), others do not (mycoplasma).
• Nutrition modes: Autotrophic (make their own food) or Heterotrophic (depend on other organisms).
• Two Main Groups:
  1. Eubacteria (true bacteria): Includes common bacteria and cyanobacteria.
  2. Archaebacteria (ancient bacteria): Examples include E. coli, Anabaena.

Characteristics of Protista

• Unicellular and Eukaryotic.
• Presence of a true nucleus.
• Mostly Protozoa.
• Microscopic organisms.
• Structures like cilia, flagella, and pseudopodia facilitate locomotion and food capture.
• Examples: Diatoms, Amoeba, Paramecium, algae, Euglena.

Characteristics of Fungi

• Heterotrophic and Eukaryotic.
• Mainly multicellular with the exception of yeast (unicellular fungi).
• Presence of a true nucleus.
• Cell wall composed of chitin.
• Nutrition primarily through saprophytism (living on dead and decaying matter).
• Examples: Yeast, Penicillium, Aspergillus.

Characteristics of Animalia

• Eukaryotic and Multicellular.
• Heterotrophs with heterotrophic nutrition.
• No cell wall and absence of chlorophyll.
• Generally possess locomotory organs and are motile.
• Well-developed sensory and neuromuscular systems.
• Classified into 10 divisions:
  • Echinodermata
  • Chordata (animals with backbone)
  • Other phyla include: Porifera, Mollusca, Coelentrata, Arthropoda, Annelida, Platyhelminthes, Nematoda.

Phylogenetic Orders in Animal Kingdom

• Phylum Porifera: Diploblastic, non-motile, with a canal system. Examples include sponges like Spongilla, Sycon, and Euplectela.
• Phylum Cnidaria: Aquatic, tentacled organisms with a gastrovascular cavity. Examples include jellyfish and sea anemones.
• Phylum Platyhelminthes (Flatworms): Flattened dorsoventrally, bilaterally symmetrical, triploblastic, without a true coelom. Free-living examples include planarians; parasitic examples are liver flukes and tapeworms.
• Phylum Nematoda (Roundworms): Cylindrical shape, bilateral symmetry, triploblastic with a pseudocoelom. Parasitic examples leading to diseases included are filarial worms (Wuchereria) causing elephantiasis and Ascaris causing ascariasis.
• Phylum Annelida: Bilaterally symmetrical, true coelom present. Examples include earthworms (land), Nereis (freshwater), and leeches (marine).
• Phylum Arthropoda: Largest phylum; segmented with jointed appendages. Examples include prawns, crabs, scorpions, insects.
• Phylum Chordata: Features a true vertebral column; classes include Pisces (fish), Amphibia (frogs), Reptilia (snakes), Aves (birds), and Mammalia (cats, dogs).

Classes of Vertebrates

1. Pisces (Fish): Aquatic, covered in scales, with gills for oxygen absorption, cold-blooded, two-chambered heart.
2. Amphibia: Capable of living in both water and land; three-chambered heart.
3. Reptilia: Cold-blooded, respiratory through lungs, eggs with tough coverings.
4. Aves: Birds, warm-blooded, four-chambered hearts, feathers, and modified limbs for flight.
5. Mammalia: Warm-blooded with mammary glands, hair, four-chambered hearts. Includes most animals like humans, lions, cows, etc.