BACTE

• Microbiology


  The study of all living organisms that are too small to be viewed by the unaided eye (bacteria, viruses, fungi, prions, archaea, protozoa and algae)
• Branches of Microbiology


  • Bacteriology (bacteria)
  • Mycology (molds and yeasts)
  • Virology (viruses)
  • Parasitology (parasites and protozoa)
  • Immunology (immune system)
  • Phycology (algae)
• Microbes/Microorganisms


  Microscopic form of life; disease-causing agents
• Normal Flora/Normal Microbiota


  Microbes/microorganisms which inhabit the human body normally and do not cause disease and harm the host
• Pathogens


  Microbes/microorganisms which inhabit the human body and cause disease
• Two general classifications of microorganisms

  • Acellular (not true cells; obligate intracellular microorganisms; host-dependent (ex. Viruses))
  • Cellular (true cells; microorganisms consisting of cells)
• Cellular microorganisms


  • Kingdom Prokaryote (unicellular that do not have nucleus or any membrane-bound organelles)
  • Kingdom Eukaryote (cells that contain nucleus and organelles enclosed by plasma membrane)
• Prokaryotes


  • Eubacteria (true bacteria; medically important)
  • Archaebacteria (primitive (oldest) single celled bacteria; can withstand heat and extreme temperature; anaerobic)
  • Cyanobacteria (blue-green algae, now blue-green bacteria; derived energy from photosynthesis)
• Eukaryotes


  • Animals
  • Plants
  • Fungi
  • Protozoa
  • Algae
• Points of differentiation between prokaryotes and eukaryotes

  • Nuclear Body
  • Cell Division
  • Cell Wall
  • Cytoplasmic Membrane
  • Site for CHON (protein) synthesis
  • Organelles
  • Size
  • Energy/ATP Synthesis
• 70% alcohol is better than 95% alcohol because it has longer contact time because of its 30% water content; according to CDC, denaturation of protein is faster if the agent has water
• Three main parts of a bacterial cell

  • Cell wall
  • Parts lying internal to cell wall
  • Parts lying external to cell wall
• Bacterial Cell Wall


  • Made up of peptidoglycan layer/murein layer/mucopeptide layer with alternating backbone of NAG and NAM
• Functions of the bacterial cell wall

  • Gives shapes/rigidity
  • Responsible for antigenic property
  • Pathogenicity
  • Responsible for staining property
• M protein


  Found in the cell wall of Streptococcus pyogenes; inhibits phagocytosis (engulfment of a foreign material)
• Mycolic acid


  Can be found in acid-fast organisms (AFO) or in Mycobacterium tuberculosis; resists digestion during phagocytosis and just multiply
• Gram stain step and function


  • Primary dye / stain
  • Mordant / Accentuator
  • Decolorizer / Differentiator
  • Secondary dye / Counterstain
• Gram stain reagents and their effects on gram-positive and gram-negative bacteria

  • Crystal violet (primary dye/stain)
  • Gram's iodine (mordant/accentuator)
  • Acetone +95% ethanol (decolorizer/differentiator)
  • Safranin o / safranin red (secondary dye/counterstain)
• Gram stain general rules

  • All cocci (spherical) are Gram (+) except...
  • All bacilli (rod-shaped) are Gram (-) except...
  • Mycobacterium tuberculosis (AFO) are expected as Gram (+), however, in actual staining it is gram-ghost or gram-neutral
  • Spirals/Spirochetes are not stainable using gram staining; however, some are Gram (-) because they use special stains
  • Mycoplasma and Ureaplasma are cell wall deficient so it will stain as Gram (-); it will take up the last stain applied to the smear; not true Gram (-)
  • Yeasts are Gram (+)
• Acid fast stain step and function


  • Primary dye / stain
  • Mordant / Accentuator
  • Decolorizer / Differentiator
  • Secondary dye / Counterstan
• Acid fast stain reagents and their effects on acid fast and non-acid fast organisms

  • Carbol fuchsin (primary dye/stain)
  • Heat / tergitol (mordant/accentuator)
  • Acid alcohol (decolorizer/differentiator)
  • Methylene blue / malachite green (secondary dye/counterstain)
• Other acid fast organisms (with mycolic acid)

  • Legionella micdadei
  • Rhodococcus
  • Nocardia (partial acid fast)
  • Cryptosporidium parvum
  • Isospora belli
  • Cyclospora
• Parts lying internal to the bacterial cell wall

  • Cytoplasmic Membrane
  • Mesosomes
  • Free Ribosomes
  • Inclusion Bodies
• Much granules


  Contains a lot of lipids; seen in Mycobacterium tuberculosis
• Bipolar bodies


  Seen in Yersinia pestis (causative agent of plague)
• Mycobacterium gordonae


  Also known as Tap Water Bacillus; non-pathogenic; important contaminant of water yields a false (+) staining reaction
• Other AFO (with mycolic acid)

  • Legionella micdadei
  • Rhodococcus
  • Nocardia – partial acid fast
  • Cryptosporidium parvum – protozoa under Coccidian family
  • Isospora belli – protozoa under Coccidian family
  • Cyclospora
• Parts Lying Internal to Cell Wall

  • Cytoplasmic Membrane – site of energy production; maintains the viability of the cell; selectively permeable
  • Mesosomes – folds or invagination that serves as point of attachment for chromosome during conjugation process (transfer of genetic material from one bacterial cell to another cell); extension of cytoplasmic membrane
  • Free Ribosomes – site of protein synthesis
  • Inclusion Bodies – food and nutrient storage/reserve
  • Much granules – contains a lot of lipids; seen in Mycobacterium tuberculosis
  • Bipolar bodies – seen in Yersinia pestis (causative agent of Bubonic plague/Black death); uses Wayson stain (stains the bipolar bodies which resembles a safety pin appearance, color red)
  • Babes-Erns/Volutin/Metachromatic granules – seen in C. diphtheria
  • Endospores/Bacterial Spores – not used for reproduction; serves as the resting stage/hibernating stage of bacteria for survival once they are exposed to unfavorable condition (drying, dessication, extreme temperature); heat-resistant; consists of two components: Dipicolinic acid and calcium ions (calcium Dipicolinate complex)
• Spore-forming bacilli


  • Bacillus – Gram (+) bacilli that can sporulate aerobically (presence of oxygen); catalase (+)
  • Clostridium – Gram (+) bacilli that can sporulate anaerobically (do not have oxygen); catalase (–)
• All spore-forming bacilli are round/oval centrally-located/subterminally-located spores except: Clostridium tetani – round/oval, terminally-located sporulation; lollipop appearance, drumstick, tennis racket bacillus; Clostridium botulinum – subterminally-located sporulation; Bacillus anthracis – centrally-located sporulation
• Parts Lying External to Cell Wall

  • Flagella/Flagellum – are whip-like structure mainly for locomotion; CHONS: Flagellin
  • Pili/Pilus – hair-like projections; CHON: Pilin
  • Glycocalyx – serves as protection and regulation
  • Capsule – organized material firmly attached to cell wall; inhibit phagocytosis; can easily cause meningitis because they can easily cross blood brain barrier; can be serotyped by K (Kapsule) antigen (virulent antigen used only in Salmonella typhi)
  • Slime layer – unorganized material not firmly attached to the cell wall; also inhibit phagocytosis; ex. Staphylococcus epidermidis (normal flora of the skin however, can be an opportunistic pathogen when there is wound infection during open heart surgery)
• Types of Flagella


  • Atrichous – no flagella/flagellum
  • Monotrichous – single flagellum on one-side of bacterial cell; darting motility (ex. Vibrio)
  • Amphitrichous – single flagellum on both sides of bacterial cell
  • Lophotrichous – tuft of flagella on one side of bacterial cell
  • Peritrichous – peri means all over; flagella around the bacterial cell (mainly found in Enterobacteriaceae except Klebsiella and Shigella because they are non-motile)
  • Bilophotrichous – tuft of flagella on both sides of bacterial cell
• Flagella antigen: H (German word Hauch) antigen – important for serotyping Yersinia, Escherichia coli, Salmonella
• Quellung Reaction Test – antigenic specificity to determine if the bacteria has a capsule; Quellung is a German word for swelling
• 5 Encapsulated Bacteria


  • Neisseria meningitids
  • Haemophilus influenzae
  • Klebsiella pneumoniae
  • Streptococcus pneumoniae
  • Bacillus anthracis
• Bacterial Morphology - Spherical or Round Cocci


  • Diplococci (cocci in pairs) – Neisseria, Branhamella, Moraxella (exception: Neisseria elongata, Neisseria bacilliformis, Neisseria weaveri)
  • Flame-lancet-shaped – Streptococcus pneumoniae
  • Packets of four/tetrads/square groups of four cells – Micrococcus tetragenus
  • Packets of 8 cells/cubical/sarcina/sarcinae – Micrococcus luteus
  • Cocci in chains – Streptococcus
  • Cluster of cocci – Staphylococcus
• Bacterial Morphology - Rod or Elongated Bacilli


  • Short plump/stout/small coccobacilli – Family Enterobacteriaceae
  • Large square cut ends chain sporulated – Bacillus anthraxis
  • Small, short bacilli, arranged in school of fish pattern – Haemophilus ducreyi
  • Large rounded end chains non-spore-forming bacilli – Bacteroides (anaerobe)
  • Slender/threadlike/serpentine cord – Mycobacterium tuberculosis
  • Streptobacilli (bacilli in chains) – Arranged at various angles to each other, resembling the letter "V" presenting a cuneiform or Chinese letter arrangement – Corynebacterium diphtheria
  • Curved-shape, small – Vibrio
  • Curved-shaped, S-shaped, C-shaped, sea-gull wing-shaped – Campylobacter, Helicobacter, Arcobacter
• Bacterial Morphology - Hellical or Twisted Shape/Arrangement

  • Spirals – Spirillum minor/minus
  • Spirochetes – Borrelia (loosely twisted), Treponema (tightly twisted resembling corkscrew), Leptospira (tightly twisted but one or both ends are bent into a hook)
• Methods of Studying Bacteria

  • Staining
  • Phenotypic Characterization
  • Genotypic Characterization
  • Animal Inoculation
  • Motility
• Staining Techniques


  • Special/Selective – stains specific bacterial structure
  • Indirect/Negative/Relief
  • Direct/Simple
  • Differential Stain