Bacteria Classification

• Bacteria, belonging to Domain Bacteria, include 5,007 identified species.

Phenotypic Categories of Bacteria

• Gram-negative bacteria stain pink and possess a cell wall.
• Gram-positive bacteria stain purple and possess a cell wall.
• Some bacteria lack a cell wall, are pleomorphic, and can exist in a variety of shapes (e.g., Mycoplasma).
• Cell-wall-deficient bacteria are pleomorphic.

Bacterial Characteristics Used for Identification

• Cell Morphology: shapes and arrangements of bacteria
• Staining Reaction: how bacteria react to different stains
• Motility: ability to move
• Colony Morphology: appearance of bacterial colonies
• Atmospheric Requirements: oxygen needs
• Nutritional Requirements: nutrients needed for survival
• Biochemical and Metabolic Activities: processes carried out
• Specific Enzymes: enzymes produced
• Pathogenicity: ability to cause disease
• Genetic Composition: the genetic makeup of the bacteria

Cell Morphology: Shapes

• Cocci are spherical bacteria (singular: coccus).
• Bacillus are rod-shaped bacteria (plural: bacilli).
• Bacteria can also be curved (comma-shaped) or spiral (twisted).

Cell Morphology: Arrangements of Cocci

• Diplococcus: pairs of cocci due to division in one plane; example is Neisseria gonorrhoeae
• Streptococcus: chains of cocci due to division in one plane; example is Streptococcus pyogenes
• Tetrad: squares of four cocci due to division in two planes
• Sarcina: cubes of eight cocci due to division in three planes
• Staphylococcus: random, irregular clusters of cocci due to division in random planes; example is Staphylococcus aureus

Medical Significance of Cocci Arrangements

• Neisseria gonorrhoeae (gram-negative, diplococcus) causes gonorrhea.
• Streptococcus pyogenes (streptococcus) causes strep throat.
• Staphylococcus aureus causes boils.

Cell Morphology: Arrangements of Bacilli

• Bacilli can occur singly.
• Diplobacilli: pairs of bacilli (few occur in this arrangement)
• Streptobacilli: chains of bacilli
• Coccobacilli: oval-shaped bacilli; example is Bortedella pertussis

Medical Significance of Bacilli

• Pseudomonas aeruginosa (bacilli) causes respiratory infections.
• Bortedella pertussis (coccobacilli) causes whooping cough, a respiratory infection.

Cell Morphology: Spiral Bacteria

• Vibrio: comma-shaped bacteria; example is Vibrio cholerae
• Spirillum: thick, rigid spiral bacteria
• Spirochete: thin, flexible spiral bacteria; example is Treponema pallidum

Medical Significance of Spiral Bacteria

• Vibrio cholerae (vibrio) causes cholera, a diarrheal disease.
• Treponema pallidum (spirochete) causes syphilis, a sexually transmitted infection.
• Leptospira interrogans (spirochete) causes leptospirosis.

Staining Reaction

• Staining is a technique used for bacterial classification.

Fixation in Staining

• Fixation is done so that bacteria stays in place on the slide.
• Heat fixation: passing the slide through a Bunsen burner flame
• Methanol fixation: flooding the smear with methanol for 30 seconds

Purpose of Fixation

• Kills the organism.
• Preserves cell morphology.
• Anchors the smear to the slide.

Staining Techniques

• Simple Staining: to determine cell morphology
• Structural Staining: to identify bacterial capsules, spores, and flagella
• Differential Staining: for classification (e.g., Gram staining and acid-fast staining)

Gram Staining

• Developed by Hans Christian Gram.
• Gram-positive bacteria stain purple due to a thick peptidoglycan layer.
• Gram-negative bacteria stain pink due to a thin peptidoglycan layer.
• Primary stain: Crystal Violet
• Mordant: Iodine
• Decolorizer: Ethanol
• Counterstain: Safranin

Acid-fast Staining

• Developed by Paul Ehrlich.
• Used to identify Mycobacteria species (have wax in their cell walls).
• Primary stain: Carbol fuschin (bright red)
• Decolorizer: Acid-alcohol

Medical Significance of Staining

• Clostridium tetani (gram-positive) causes tetanus.
• Penicillin is a common treatment for gram-positive infections.
• Mycobacterium tuberculosis (acid-fast) causes Tuberculosis (TB).
• Mycobacterium leprae (acid-fast) causes leprosy.

Special Stains

• Negative staining: useful for capsules
• Endospore staining: requires heat
• Flagella staining: requires a mordant

Motility

• Bacterial motility refers to the ability of bacteria to move.

Flagella Arrangements

• Monotrichous: single flagellum at one end
• Lophotrichous: tuft of flagella at one end
• Amphitrichous: flagella (one or more) at both ends
• Peritrichous: flagella all over the cell body

Axial Filaments

• Also known as endoflagella, located inside the cell in spirochetes
• Cause movement through rotation or a spiral motion

Gliding Motility

• Bacteria glide with the assistance of a slime layer.

Colony Morphology

• A colony is a group or pile of bacteria, potentially containing millions.

Solid Media

• Typically uses agar in a Petri dish for bacterial growth

Liquid Media

• Sterile liquid media has total absence of bacteria.
• Slight turbidity indicates some bacterial growth.
• Significant turbidity indicates considerable bacterial growth.
• Turbid liquid with sediments indicates substantial bacterial growth.

Atmospheric Requirements

• Atmospheric requirements refer to whether bacteria needs oxygen or not.

Obligate Aerobes

• Require oxygen to survive, needing 20-21% oxygen
• Grow at the top of a test tube in liquid culture

Facultative Anaerobes

• Can grow with or without oxygen

Obligate Anaerobes

• Do not need oxygen to survive; can only grow in an anaerobic environment
• Grow at the bottom of a test tube in liquid culture

Aerotolerant Anaerobes

• Do not require oxygen but grow better in its absence

Microaerophiles

• Need only 5% oxygen
• Grow in the middle of a test tube

Capnophiles

• Grow better in the presence of increased CO2

Pathogenicity

• Pathogenicity refers to the ability of a microorganism to cause infection.
• Bacteria with capsules can cause more severe infections.
• Pili (fimbriae) on bacteria make surfaces harder to clean (bleach is an effective cleaning agent).
• Bacteria can produce endotoxins (gram-negative) and exotoxins (gram-positive).

Genetic Composition

• Bacterial cells lack a nuclear membrane and have a nucleoid instead.

Unique Bacteria: Obligate Intracellular Parasites

• Must live within another cell
• Example: Rickettsia spp.

Unique Bacteria: Human Pathogens

• Bartonella causes trench fever.
• B. henselae causes cat-scratch disease.

Unique Bacteria: Chlamydia

• Unique as energy parasites (need energy from others to survive)
• C. trachomatis causes sexually transmitted infections (STDs) and urethritis.
• C. pneumoniae and C. psittaci cause psittacosis.

Unique Bacteria: Mycoplasma

• Unique because they are wall-less and pleomorphic (can change shape).
• Resistant to antibiotics.
• M. pneumoniae causes pneumonia.

Sizes of Bacteria

• Thiomargarita namibiensis: largest bacteria (750 micrometers), aquatic and non-pathogenic
• Epulopiscium fishelsonii: second largest bacteria (80 by 600 micrometers)
• Nanobacteria: less than 1 micrometer, found in soil, ocean water, dental plaque, and meteorites

Photosynthetic Bacteria

• Oxygenic: perform oxygenic photosynthesis
• Non-oxygenic: perform non-oxygenic photosynthesis
• Cyanobacteria: oxygenic bacteria

Domain Archaea

• Discovered in 1977, includes 217 species.
• More closely related to eukaryotes than bacteria.
• Possesses different types of RNA.
• Cell walls lack peptidoglycan.
• Many live in extreme environments.

Types of Archaea: Thermophiles

• Heat-loving, found near hydrothermal vents and hot springs.
• Many are chemosynthetic, using sulfur.

Types of Archaea: Halophiles

• Thrive in high salinity environments (some can tolerate 9% salt, like the Dead Sea).

Types of Archaea: Psychrophiles

• Cold-loving, found in arctic and antarctic oceans (can live even down to -10°C).

Types of Archaea: Methanogens

• Produce methane.
• Found in treatment plants and intestinal tracts of ruminants.
• Ancient methanogens are the source of natural gas.

Eukaryotic Microbes: Kingdom Protista

Algae

• Photosynthetic organisms with pellicle (thickened cell membrane), stigma (light-sensing organelle), and flagella.
• Range in size from unicellular and microscopic to large and multicellular.
• Found in freshwater, saltwater, wet soil, or rocks.
• Most are photoautotrophs.

Phylum Bacillariophyta

• E.g., diatoms.
• Microscopic, unicellular organisms.
• Live in freshwater and saltwater.
• Cell walls contain silicon dioxide (diatomaceous earth).
• Geometric in appearance.

Phylum Dinoflagellata

• Dinoflagellates or fire algae.
• Unicellular, flagellated, often photosynthetic.
• Medical Significance: release neurotoxins causing paralytic shellfish poisoning or "red tide."

Phylum Chlorophyta

• Green algae.
• Cellulose cell walls, found in freshwater.
• Characteristics:
  • Spirogyra: filamentous
  • Chlamydomonas: biflagellated
  • Volvox: biflagellated, forms a sphere
  • Desmids: banana-shaped
• Medical Significance:
  • Chlamydomonas is unrelated to the bacteria Chlamydia, which causes a sexually transmitted infection.

Phylum Phaeophyta

• Brown algae (giant kelp).
• Cell walls: cellulose + alginic acid.
• Multicellular.
• Harvested for alginin (absorbs water quickly).
• Medical Significance:
  • Alginin is used medically as a detoxifier (absorbs poisonous metals from the blood).

Phylum Rhodophyta

• Red algae.
• Cellulose cell walls, multicellular.
• Harvested for agar and carrageenan.
• Medical Significance:
  • Agar is essential in making a culture medium.

Phylum Euglenophyta

• Euglena.
• Have stigma and pellicle.
• Algal feature: photosynthetic.
• Protozoal feature: cytostome (primitive mouth).
• Medical Significance:
  • Prototecha causes protothecosis, resulting in crusty, warty-looking lesions.

Protozoa

• Animal-like, unicellular, and motile.
• No cell walls; pellicle serves as protection.
• Possess a contractile vacuole.
• Feeding state: trophozoite.
• Dormant stage: cyst.
• Asexual reproduction: fission, budding, schizogony.
• Sexual reproduction: conjugation.
  • Conjugation: injecting DNA into another cell.
  • Schizogony: multiple fission (e.g., in malaria, Erythrocytic Schizogony).

Protozoa: Ciliates

• Move by cilia.
• Medical Significance:
  • Balantidium coli is a human parasite.

Protozoa: Flagellates

• Multiple flagella
• Medical Significance:
  • Giardia lambia causes giardiasis, a diarrheal disease.
  • Trichomonas vaginalis is a STD.

Protozoa: Amoebae

• Move using pseudopods (false feet).
• Phagocytosis (cell-eating).
• Medical Significance:
  • Entamoeba causes dysentery and extraintestinal abscesses.
  • Acanthamoeba causes eye infections.

Protozoa: Sporozoa

• Non-motile.
• Medical Significance:
  • Plasmodium causes malaria.

Kingdom Fungi

• Aerobic or facultatively anaerobic.
• Found almost everywhere.
• Some are saprophytic (lives off dead matter).
• Others are parasitic (lives in a host organism).
• Most are decomposers.
• Some are beneficial (cyclosporine & penicillin).
• Mycology: study of fungi.

Fungi Characteristics

• Cell walls contain chitin.
• Can be unicellular (e.g., yeast).
• Can grow as filaments called hyphae (molds), which form a mass called mycelia.
• Septate hyphae: have divisions.
• Aseptate hyphae: no divisions.

Decomposers vs Saprophytes

• Decomposers break down materials.
• Saprophytes absorb nutrients from dead and decaying organic matter.
• All saprophytes are decomposers, but not all decomposers are saprophytes.

Reproduction of Fungi: Sexual Spores

• Formed by fusion of two gametes (ascospores, basidiospores, zygospores).

Reproduction of Fungi: Asexual Spores

• Not formed by fusion (conidia).

Fungi: Medical Significance

• Candida albicans is a resident microflora in the mouth and vagina.
• May cause oral candidiasis (thrush).

Fungi: Major Types

• Yeast
• Mold
• Flesh Fungi

Yeast

• Blastoconidia: individual yeast cell.
• Reproduction:
  • Fission
  • Budding (creation of daughter cell)
  • Pseudohypha: string of elongated buds.
• Chlamydospores

Mold

• Consists of hyphae.
• Some molds are used for antibiotics like penicillium.

Flesh Fungi

• Can be mushrooms, toadstools, puffballs, or bracket fungi.

Fungal Infections (Mycoses)

Superficial Mycoses

• Occur on the outermost layer of skin.
• Tinea infections (ringworms):
  • Tinea pedis (athlete’s foot)
  • Tinea capitis (on the head)
  • Tinea corporis (on the body)
  • Tinea cruris (in the groin area)
  • Tinea unguium (on nails)

Cutaneous Mycoses

• Occur on the living layer of the skin.
• Stomatitis (oral thrush)

Opportunistic Mycoses

• Caused by normal microbiota.

Subcutaneous Mycoses

• Beneath the skin.

Systemic Mycoses

• Deep within the body, usually involving the lymphatic system and blood.

Dimorphic Fungi

• Can exist as yeast or mold depending on temperature.
  • Yeast form at 37°C.
  • Mold form at 25°C.
• Mycetomas

Lichens

• Combination of algae and fungi in a symbiotic relationship.
• Alga provides food (carbohydrates).
• Fungus provides habitat.

Slime Molds

• Have both fungal and protozoal characteristics.
• Start out life as independent amoebae.