BASIC CONCEPTS IN MICROBIOLOGY • Carl von Linne/ Carolus Linnaeus

(BACTERIOLOGY) o Binomial system (basic rules for taxonomic

categories)
Microbiology
Taxonomy- Classification
• Study of organisms naked to the human eye
• Bacteria, Viruses, Fungi, Parasites, etc. • Organization of microorganisms based on
• Collectively known as microbes similarities in morphology, physiology, and genetic
traits
• DOMAIN- Bacteria, Archaea, Eukarya
History • KINGDOM- Similarities in DNA, RNA
• PHYLUM
1. Anton van Leeuwenhoek
• CLASS
a. Father of microbiology
b. Observed microorganisms; termed • ORDER
“animalcules” under a self-made • FAMILY- “-aceae” exception to Enterobacteriaceae
microscope which is named after “enteric” group
2. Lazzaro Spallanzani • GENUS- based on genetic and phenotypic
a. Sterilization of broth by boiling characteristics
b. Contamination of broth if exposed to open • SPECIES- most basic taxonomic groups; define as
air collection of bacterial strains sharing physiologic
3. Louis Pasteur and genetic features
a. Formulated aseptic technique (use of heat • SUBSPECIES- further division of bacteria
in killing microorganisms according to biotype, serotype, or genotype
b. Proved that air does not generate
MNEMONIC! Dear King Philip Came Over For Good
microbes but is naturally present and can
Soup
contaminate sterile solutions
4. John Tyndall
a. Supported Pasteur’s theory
b. Tyndallization- uses moist heat for 3 days Taxonomy- Nomenclature
to kill off vegetative cells and endospores
• Naming of organisms according to established rules
5. Ferdinand Julius Cohn
and guidelines by the International Code of
a. Classified bacteria according to shape
Nomenclature of Bacteria or by Bacteriological
b. Proved the existence of endospores in Code (BC)
Bacillus
• Genus and species are used- binomial system
6. Robert Koch
• Eg. Staphylococcus aureus, S. aureus
a. Proved that bacteria cause diseases
b. Discovered Bacillus anthracis and • When written: Staphylococcus aureus, S. aureus
Mycobacterium tuberculosis • When bacteria are written as a group, names are
c. Developed culture media from boiled not capitalized or underlined
potatoes, gelatin, meat extracts, and
protein
d. Formulated Koch’s Postulates Taxonomy- Identification
i. The microorganism must be found in
abundance in all organisms suffering from the • Key features of bacteria are analyzed
disease, but should not be found in healthy
organisms. • 2 Characteristic Identification
ii. The microorganism must be isolated from a o 1. Phenotypic (Observable)
diseased organism and grown in pure culture. ▪ Macroscopic morphology
iii. The cultured microorganism should cause
disease when introduced into a healthy ▪ Microscopic morphology
organism. ▪ Staining characteristics
iv. The microorganism must be reisolated from
the inoculated, diseased experimental host
▪ Environmental requirements
and identified as being identical to the original ▪ Nutritional requirements
specific causative agent. ▪ Resistance profiles
Taxonomy ▪ Subcellular properties
▪ Chemotaxonomic properties
Taxonomy o 2. Genotypic
▪ DNA base composition
• Area of biologic science comprising interrelated ▪ DNA/RNA base sequences
studies: classification, nomenclature, &
identification
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L. J. Gumahad, RMT 2024 1st Ed.
Prokaryotes 5. Nocardia
▪ Bacteria without cell walls
• Prokaryotes • Contain sterols in cell
1. Organisms that do not contain true membranes
nucleus and organelles • Eg. Mycoplasma &
2. Functions take place at cytoplasm Ureaplasma
3. “Pro”- before 2. Plasma Membrane
4. “Karyon”- nucleus, nut, or kernel ▪ Semi-permeable phospholipid
• Bacteria bilayer embedded by proteins
1. Unicellular organisms- do not have true ▪ Separates the interior and
nucleus, nuclear membrane, & membrane exterior environment of bacteria
bound organelles ▪ Osmotic barrier
2. Reproduction by binary fission ▪ Functions as mitochondria, Golgi
3. Chromosome is not located in a complex, & lysosome
membrane-bound organelle • Cytoplasmic structure
1. Cytoplasm
▪ Gel-like structure inside the cell
Bacteria Cell Structure ▪ Contains other parts of the
bacteria
2. Nucleoid
▪ Region within the bacteria that
contains most of genetic material
3. Ribosomes
▪ Responsible for protein synthesis
▪ Consists of 30s and 50s
4. Genome
▪ Single, circular chromosome that
is present in the nucleoid
5. Inclusion bodies
▪ Storage of nutrients and energy
eg. Glycogen, lipids, phosphate
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eria_cell_drawing-5786db0a5f9b5831b54f017c.jpg

• Cell Envelope QUICK RECALL!

1. Cell Wall Bacteria with inclusion bodies:
▪ Peptidoglycan layer (Murein
Layer) 1. Corynebacterium- Babes-Ernst bodies
▪ Maintains shape of cell- structural 2. Mycobacterium- Much’s granules
support 3. Nocardia & Actinomyces- Sulfur granules
▪ Main target of antimicrobial 4. Pasteurella & Bordetella- Bipolar bodies
agents
▪ Distinguishes gram-positive and 6. Endospores
gram-negative, acid-fast, absence ▪ Aids in the survival of bacteria
of cell wall against external conditions
▪ Acid-fast cell wall ▪ Not all bacteria have endospores
• Has similar structure of a ▪ Bacteria that can form
gram-positive cell wall endospores
• Additional layer of • Bacillus
glycolipids and fatty • Clostridium
acids (mycolic acid) 7. Plasmid
▪ Extrachromosomal double-
QUICK RECALL! stranded element of DNA
(associated with virulence)
Some important acid-fast organisms:
▪ Usual site of gene coding for
1. Mycobacterium spp. antibiotic resistance and toxin
2. Isospora production
3. Legionella micdadei
4. Cryptosporidium
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L. J. Gumahad, RMT 2024 1st Ed.
 • Appendages (provides motility and attachment; not MNEMONIC! Some Nasty Killers Have Some Capsular
present in all bacteria) Protection
1. Glycocalyx
▪ Capsule Bacterial Growth Curve
• Virulence factor
• Made of organized
polysaccharide elements
• Resist phagocytosis and
acts as a defense
mechanism
• Special staining
methods:
o Hiss stain
o India ink stain
▪ Slime
• Aids in adherence of
bacteria to hosts
• Made of unorganized 1. Lag phase
polysaccharide elements a. No multiplication of bacteria
• Inhibits phagocytosis b. Adjustment and adaptation period to new
2. Pili environment
▪ Proteinaceous, filamentous 2. Log phase
polymeric organelles (Pilins) a. AKA: Exponential phase
present on the surface of the b. Bacteria are actively multiplying and
bacteria dividing
▪ Considered as a virulence factor c. Phase in which bacteria is utilized for
▪ Aids in the attachment of bacteria physiological and biochemical testing
to surfaces d. Phase in which bacteria is sensitive to
▪ Fimbriae- shorter than pili; similar antimicrobials
functions 3. Stationary phase
3. Flagella a. During this phase, nutrients from the host/
▪ Long-whip like appendages environment has been fully utilized or
involves in bacterial motility exhausted
(mode of actions: rotation) b. Accumulation of toxic metabolic wastes
▪ Types of Flagella starts
• Atrichous- no flagella 4. Death phase
a. Cessation of bacterial growth
• Monotrichous- single
b. Viable count of organisms decline
flagellum at one pole;
common Nutrition Requirement
• Amphitrichous- single
flagellum at each pole For all bacteria:
• Lophotrichous- tuft of • Carbon source
flagella at one or both
• Nitrogen source
poles
• Energy source: ATP
• Peritrichious- flagella all
• Trace elements
over organism; common
Oxygen growth requirement
QUICK RECALL!
• Aerobes
Some important encapsulated microorganisms:
o Require oxygen and grow in room air
1. Streptococcus pnuemoniae o Eg. Bordatella, Mycobacteria,
2. Neisseria meningitidis Pseudomonas, Brucella
3. Klebsiella pnuemoniae • Anaerobes
4. Haemophilus influenzae o Facultative anaerobe
5. Salmonella typhi ▪ Bacteria that may grow in the
6. Cryptococcus neoformans absence or presence of oxygen
7. Pseudomonas aeruginosa ▪ May not require oxygen but grows
better withit
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L. J. Gumahad, RMT 2024 1st Ed.
 ▪ Eg. Enterobacteriaceae o Light as energy source
o Aerotolerant anaerobe • Chemotrophs
▪ Can tolerate low levels of oxygen o Utilize energy from organic or inorganic
but cannot perform metabolic compounds
functions
▪ Metabolic functions are best at Salt concentration requirement
anaerobic conditions • Halophiles
▪ Eg. Propionibacterium acnes o Need an increased concentration of NaCl
o Obligate anaerobe for growth
▪ Dies in the prolonged exposure to o Eg. Staphylococcus aureus & Listeria
oxygen or air monocytogenes
▪ Eg. Clostridium & Bacteriodes
o Microaerophilic Staining Principle
▪ Needs a small amount (2-10 %)
oxygen for growth 1. Gram- stain
▪ Eg. Campylobacter spp. & T. a. Most commonly used
pallidum b. Method by fixing specimen on to slide
i. Heating
Temperature requirement ii. Methanol
1. Preserves morphology
• Cryophiles of host cells & bacteria
o 0-20 degrees Celsius 2. Slide is overlaid with
• Mesophiles 95% methanol for 1
o 20- 45 degrees Celsius minute and rinsed off
• Thermophiles c. Steps in gram staining
o 50- 125 degrees Celsius i. Primary stain- crystal violet
o Eg. Bacillus stearothermophilus ii. Gram’s iodine
• Extremophiles 1. Chemically bons alkaline
o Organisms that survive in very extreme dye to the iodine which
conditions (absence of oxygen, high creates a cross-linking
temperature, & living below ground complex in cell wall
surface) iii. Decolorization
o Eg. Bacillus infernus 1. Distinguishing factor for
gram-positive & gram-
negative bacteria
QUICK RECALL! 2. Most critical step
iv. Counter stain- safranin pink
Bacteria used as control for effectiveness in autoclaving:
Bacillus stearothermophilus
New name: Geobacillus stearothermophilus

Carbon dioxide requirement

• Capnophiles
o Require 5-10% carbon dioxide for growth
o Eg. Haemophilus influenzae, Neisseria https://labster-image-manager.s3.amazonaws.com/bd7be05a-dd65-4273-a739-ff9801800aad/GRM_The_Gram_stain_procedure_overview_THEORY.en.x1024.png
gonorrhoeae, Streptococcus pneumoniae
Carbon source requirement 2. Acid fast stain
• Autotrophs a. Designed for bacteria with long chain fatty
o Can use carbon dioxide as a sole source acids on cell walls (mycolic acid)
of carbon b. Stain used for Mycobacterium spp.
o Self-sufficient c. Other spp.: Nocardia spp. &
Cryptosporidium spp.
• Heterotrophs
d. Steps in acid-fast staining
o Needs an external source of carbon
i. Carbol fucshin
Energy source requirement ii. Acid Alcohol
iii. Alkaline Methylene Blue
• Phototrophs
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L. J. Gumahad, RMT 2024 1st Ed.
 e. For hot method: Heat allows primary stain different densities or thickness (refractive
to enter waxy structure index)
f. Modification of acid-fast stain: Kinyoun’s • Fluorescent Microscope
stain o Uses dyes: fluorochromes/ fluorophores
g. Other acid-fast stain methods o Excitation light excites dyes to stain
i. Pappenheim method specimen
1. Differentiates M. o Fluorescing objects appear brightly lit
smegmatis from M. against dark background
tuberculosis o Samples of fluorescing dyes: acridine
ii. Baumgarten method orange, auramine, fluorescein
1. Differentiates M. leprae isothiocyanate, calcofluor white
from M. tuberculosis • Dark Field Microscope
iii. Auramine-rhodamine method o Alteration of microscopic technique rather
1. For AFB cell wall than the use of dyes or stains to achieve
staining contrast
https://laboratoryintern.com/wp-content/uploads/2023/07/Non-Acid-Fast-Bacteria-vs-acid-fast-bacteria.jpg o Does not allow light to pass directly
through the specimen
o Commonly used for detection of
Treponema pallidum
QUICK RECALL!
Treponema pallidum is the causative agent of syphilis- one
of the sexually transmitted diseases
• Electron Microscope
o Uses electrons instead of light to visualize
small objects
o Allows magnification up to 100,000,000
times
o Fixative: glutaraldehyde/ osmium
tetraoxide
o Dehydrating agent: Alcohol/ acetone
o Stains: Lead citrate & uranyl acetate
o Types of electron microscope
▪ Transmission E.M.
• Passes electron beam
https://www.shutterstock.com/image-photo/show-microbacterium-tuberculosis-tb-positive-600nw-491157913.jpg through objects & allow
visualization of internal
structures
Microscopy ▪ Scanning E.M.
• Uses electron beams to
• Light Microscope scan the surface of
o Visible light passes through the specimen objects & provides 3D
by series of lenses which then reflects light views of surface
o Uses fixed smear structures
o Lenses: ocular (10x), and objectives
lenses: LPO (10x), HPO (40x), OIO (100x)
o Cedarwood oil (Immersion oil)
▪ Enhance visuality of organism by
filling the gaps of the lens to the
slide
• Phase-contrast Microscope
o Does not use fixed smear
o Used in wet mount
o Spx: Usually non viscous liquid (eg. Urine)
o Uses beam of light passing through the
specimen that are partially defected by

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L. J. Gumahad, RMT 2024 1st Ed.
 Gram-positive cell wall Gram-negative cell wall
Peptidoglycan layer Thick (multilayered) Thin
Teichoic acid Present Absent
Gram stain reaction Retain primary dye- crystal violet Decolorized and takes in counter stain-
safranin
Color of bacteria Appears violet/ purple Appears pink or red
Presence of Lipopolysaccharides in Absent Present
outer membrane
Porins Absent Present
Other Characteristics Consist of glycan chain NAG and NAM Outer membrane is also composed of LPS
(N-acetylglucosamine & N- (lipopolysaccharide) lipids, & proteins
acetylmuramic acid) LPS is responsible for endotoxin (due to the
presence of lipid protein A) of gram-negative
bacteria, and are released when cell wall of
bacteria is lysed

Can induces symptoms like fever, chills,

hypotension, granulocytosis, thrombocytopenia,
and DIC

References:
A brief history of microbiology. (n.d.). https://www.cliffsnotes.com/study-guides/biology/microbiology/introduction-to-microbiology/a-brief-history-
of-microbiology
Dhakal, B., Bower, J., Mulvey, M., & Yang, X. (2015). Pili, Fimbriae☆. In Elsevier eBooks. https://doi.org/10.1016/b978-0-12-801238-3.02316-3
Legend Review Center. (2020, May 11). Must-Knows in Bacteriology #1 (FREE handouts below) | Legend Review Center - Medical Technology
[Video]. YouTube. https://www.youtube.com/watch?v=F92qOTF1Ju8
Libretexts. (2022, December 24). 1.1B: History of Microbiology - Hooke, van Leeuwenhoek, and Cohn. Biology LibreTexts.
https://bio.libretexts.org/Bookshelves/Microbiology/Microbiology_(Boundless)/01%3A_Introduction_to_Microbiology/1.01%3A_Introduc
tion_to_Microbiology/1.1B%3A_History_of_Microbiology_-_Hooke_van_Leeuwenhoek_and_Cohn
Malak, H. A., Abulreesh, H. H., Organji, S. R., Elbanna, К., Shaaban, M. R., Samreen, Ahmad, I., Shami, A., Alshehri, W. A., Khalel, A. F.,
Abureesh, H. H., Asiri, F. H., Aldosari, M. S., & Almalki, M. H. (2020). Immune System Evasion Mechanisms in Staphylococcus
aureus: Current Understanding. Journal of Pure and Applied Microbiology, 14(4), 2219–2234. https://doi.org/10.22207/jpam.14.4.01
Rodriguez, M. T. (2016). In Review Handbook in Diagnostic Bacteriology. C & E Publishing.
Society, M. (n.d.). What is Microbiology? Microbiology Society. https://microbiologysociety.org/why-microbiology-matters/what-is-
microbiology.html
4: Bacteria - Cell Walls. (2018, February 6). Biology LibreTexts.
https://bio.libretexts.org/Bookshelves/Microbiology/Microbiology_(Bruslind)/04%3A_Bacteria%3A_Cell_Walls
Bacterial Cell Wall Definition, Function & Composition—Lesson. (n.d.). Study.Com. Retrieved March 23, 2024, from
https://study.com/academy/lesson/bacterial-cell-walls-and-the-gram-stain-test.html
Gram-positive Cell Wall Vs Gram-negative Cell Wall—Differences. (n.d.). BYJUS. Retrieved March 23, 2024, from
https://byjus.com/biology/difference-between-gram-positive-and-gram-negative-cell-wall/

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