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SB20103 MICROBE DIVERSITY
Week 4: MICROBIAL IDENTIFICATION METHODS
Jaya Seelan Sathiya Seelan PhD
Institute for Tropical Biology and Conservation, UMS
OBJECTIVE
• To introduce students to the basic
tools and techniques used to identify
and characterize microorganisms.
OUTLINE
• Identification of Bacteria
• Identification of Fungi
• Identification of Algae
• Identification of Virus
IDENTIFICATION OF BACTERIA
• Methods used to identify bacteria to the level
of genus and species
• Phenotypic methods
• Morphology
• Physiology or biochemistry
• Immunologic method
• Serological analysis
• Genotypic techniques
• Genetic markers (18S/16S ribosomal gene) for
identifying bacteria
PHENOTYPIC METHODS
•Microscopic morphology
•Macroscopic morphology
•Physiological/Biochemical characteristics
•Chemical analysis
MICROSCOPIC MORPHOLOGY
•Cell shape and size
•Gram stain reaction
•Acid fast reaction
•Special structures
SHAPE AND SIZES
GRAM STAINING METHODS
Gram +ve
Gram -ve
DIFFERENCES BETWEEN GRAM -/+
*Important to classify between gram -/+
MACROSCOPIC MORPHOLOGY
•Colony appearance
•Speed of growth
•Patterns of growth
COLONY GROWTH FORM
PHYSIOLOGICAL/BIOCHEMICAL
CHARACTERISTICS
• Traditional bacterial identification
• Diagnostic tests for determining the presence of
specific enzymes and assessing nutritional and
metabolic activities
• Examples
• Fermentation of sugars
• Capacity to metabolize complex polymers
• Production of gas
• Presence of enzymes
• Sensitivity to antimicrobial drugs
BIOCHEMICAL TEST
• Presence/absence of
selective
sugars/proteins/amino acids
API Kit for Rapid Test
CHEMICAL ANALYSIS
• Analyzing the types of specific
structural substances that the
microorganism contains
• Examples
• Chemical composition of
peptides in the cell wall
• Lipids in membranes
• Antibiogram
• Where do you find these
bacteria?
• As a microbiologist, how
do you interpret this
chart?
• Can you ID the species
level?
Critical thinking
GENOTYPIC METHODS
•Primary advantage over phenotypic
methods:
•Hybridization
•Nucleic Acid Sequencing and rRNA Analysis
•Polymerase Chain Reaction (PCR)-Multiplex
PCR
IMMUNOLOGIC METHODS
•Antibody response to antigens
•Blood testing- often easier than testing
for the microbe itself
•Serology
•Laboratory kits available for immediate
identification of a number of pathogens
• Characteristics of antibodies
can reveal the history of a
patient’s contact with
microorganisms or other
antigens
Serology
• Deals with in vitro diagnostic
testing of the serum
FUNGI IDENTIFICATION
Single cell-Yeasts
- Basidiomycetes
Unicellular-Chytrid fungi
Multicellular
Ascomycetes
HOW TO IDENTIFY FUNGI?
• Morphology: under different media; growth
forms, colony appearance, growth rates, spore
shapes and sized
• Physiology: pH, Temperature and etc.
• Chemical: Secondary metabolites, toxins
• Phylogeny: Very important and up to date
(Fungal Barcode DNA, ITS)
Colonies on different media & Microscopic
Aspergillus & Penicillium
IDENTIFICATION OF ALGAE
•Color
•Type of photosynthetic food reserve
•Flagella type, cell wall structure and
composition
•Morphology vs phylogeny methods
Where do you look for Algae?
IDENTIFICATION OF VIRUS
Morphology: Helical/ Icosahedral
shapes
Microscopy in cell cultures
Immunofluorescence
(IF) Assay
• Real-time RT-PCR assays for influenza virus detection
• Immunofluorescence Foci Assay (IFA)
• Immunoblotting
Methods
• Hemagglutination Assay (HA)
Lecture: Virus (more details)
GAME: WHAT AM I?
• In this game, each group will be given a
microbe (card) to discuss.
• Identify your microbe
• You may find all the relevant information
from the web.
• Identify their scientific name, where you
can find them, their role and etc. (Be
concise)
• Describe the identification methods.
• Be creative!
Learning objective
• Appreciate the vast
abundance and
diversity of microbes
• Able to classify microbes
based on their
characters
• Understand that most
microbes are not just
harmful
EXAMPLE
• Gram-negative (bacteria)
• Facultative anaerobic
• Rod shape
• Genus/species: Escherichia coli
• Found in lower intestine; in soil
• Harmless: producing vitamin K2
• Pathogenic to human: gastroenteritis, urinary tract infections, and neonatal meningitis
• E.coli #0157:H7, that produces a toxin called the Shiga toxin (classified as a bioterrorist agent)
• Have been used in vaccine development, bioremediation, production of biofuels, lighting, and production of
immobilized enzymes
Identification method: E.coli
Rapid test
-EMB Agar- glowing
colonies
Indole test (+)
• Glucose fermentation with
gas production, urea and
H2S
• Lactose
• Sucrose; mannitol
cellobiose
• Citric Acid
-
+
-
-

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SB20103 Microbe Diversity: Microbe Identification Methods

  • 1. SB20103 MICROBE DIVERSITY Week 4: MICROBIAL IDENTIFICATION METHODS Jaya Seelan Sathiya Seelan PhD Institute for Tropical Biology and Conservation, UMS
  • 2. OBJECTIVE • To introduce students to the basic tools and techniques used to identify and characterize microorganisms.
  • 3. OUTLINE • Identification of Bacteria • Identification of Fungi • Identification of Algae • Identification of Virus
  • 4. IDENTIFICATION OF BACTERIA • Methods used to identify bacteria to the level of genus and species • Phenotypic methods • Morphology • Physiology or biochemistry • Immunologic method • Serological analysis • Genotypic techniques • Genetic markers (18S/16S ribosomal gene) for identifying bacteria
  • 5. PHENOTYPIC METHODS •Microscopic morphology •Macroscopic morphology •Physiological/Biochemical characteristics •Chemical analysis
  • 6. MICROSCOPIC MORPHOLOGY •Cell shape and size •Gram stain reaction •Acid fast reaction •Special structures
  • 9. DIFFERENCES BETWEEN GRAM -/+ *Important to classify between gram -/+
  • 10. MACROSCOPIC MORPHOLOGY •Colony appearance •Speed of growth •Patterns of growth
  • 12. PHYSIOLOGICAL/BIOCHEMICAL CHARACTERISTICS • Traditional bacterial identification • Diagnostic tests for determining the presence of specific enzymes and assessing nutritional and metabolic activities • Examples • Fermentation of sugars • Capacity to metabolize complex polymers • Production of gas • Presence of enzymes • Sensitivity to antimicrobial drugs
  • 13. BIOCHEMICAL TEST • Presence/absence of selective sugars/proteins/amino acids API Kit for Rapid Test
  • 14. CHEMICAL ANALYSIS • Analyzing the types of specific structural substances that the microorganism contains • Examples • Chemical composition of peptides in the cell wall • Lipids in membranes • Antibiogram
  • 15. • Where do you find these bacteria? • As a microbiologist, how do you interpret this chart? • Can you ID the species level? Critical thinking
  • 16. GENOTYPIC METHODS •Primary advantage over phenotypic methods: •Hybridization •Nucleic Acid Sequencing and rRNA Analysis •Polymerase Chain Reaction (PCR)-Multiplex PCR
  • 17. IMMUNOLOGIC METHODS •Antibody response to antigens •Blood testing- often easier than testing for the microbe itself •Serology •Laboratory kits available for immediate identification of a number of pathogens
  • 18. • Characteristics of antibodies can reveal the history of a patient’s contact with microorganisms or other antigens Serology • Deals with in vitro diagnostic testing of the serum
  • 19. FUNGI IDENTIFICATION Single cell-Yeasts - Basidiomycetes Unicellular-Chytrid fungi Multicellular Ascomycetes
  • 20. HOW TO IDENTIFY FUNGI? • Morphology: under different media; growth forms, colony appearance, growth rates, spore shapes and sized • Physiology: pH, Temperature and etc. • Chemical: Secondary metabolites, toxins • Phylogeny: Very important and up to date (Fungal Barcode DNA, ITS)
  • 21. Colonies on different media & Microscopic Aspergillus & Penicillium
  • 22. IDENTIFICATION OF ALGAE •Color •Type of photosynthetic food reserve •Flagella type, cell wall structure and composition •Morphology vs phylogeny methods Where do you look for Algae?
  • 23.
  • 24. IDENTIFICATION OF VIRUS Morphology: Helical/ Icosahedral shapes Microscopy in cell cultures Immunofluorescence (IF) Assay • Real-time RT-PCR assays for influenza virus detection • Immunofluorescence Foci Assay (IFA) • Immunoblotting Methods • Hemagglutination Assay (HA) Lecture: Virus (more details)
  • 25. GAME: WHAT AM I? • In this game, each group will be given a microbe (card) to discuss. • Identify your microbe • You may find all the relevant information from the web. • Identify their scientific name, where you can find them, their role and etc. (Be concise) • Describe the identification methods. • Be creative! Learning objective • Appreciate the vast abundance and diversity of microbes • Able to classify microbes based on their characters • Understand that most microbes are not just harmful
  • 26. EXAMPLE • Gram-negative (bacteria) • Facultative anaerobic • Rod shape • Genus/species: Escherichia coli • Found in lower intestine; in soil • Harmless: producing vitamin K2 • Pathogenic to human: gastroenteritis, urinary tract infections, and neonatal meningitis • E.coli #0157:H7, that produces a toxin called the Shiga toxin (classified as a bioterrorist agent) • Have been used in vaccine development, bioremediation, production of biofuels, lighting, and production of immobilized enzymes Identification method: E.coli Rapid test -EMB Agar- glowing colonies Indole test (+) • Glucose fermentation with gas production, urea and H2S • Lactose • Sucrose; mannitol cellobiose • Citric Acid - + - -