Lecture 1 - Intro to Microbiology, History - Part 1

Microbiology

• The study of organisms too small to be seen with the unaided eye

“microscopes = new eyes"

Why should we study Microbiology?

1. Ubiquitous = “microbes are everywhere”

2. Beneficial effects

3. Harmful effects

Ubiquitous

THEY ARE EVERYWHERE

“microbes are adapted for each type of environment, not just warm and moist”

Studying Microbiology: Beneficial Effects

• Maintain ecological balance

• Human digestion and vitamin synthesis

• Commercial applications

Beneficial Effects: Maintain Ecological Balance

1. Basis of the food chain

   1. “very small!! larger organisms eat them, then larger ones eat those organisms”

2. Photosynthesis - provide oxygen

   1. “Take CO₂ from environment and turn into sugars”

   2. “70-80% of O₂ in atmosphere from microbes”

      1. -”usually marine algae”

3. Decomposers - recycle nutrients

   1. “help breakdown organic material”

Beneficial Effects: Human Digestion and Vitamin Synthesis

• “colon”

• “B12, biotin, folic acid, thymine, etc.”

Beneficial Effects: Commercial Applications

1. Food and beverage

   1. Ex: pickles, sauerkraut, soy sauce, yogurt, bread, alcohol, cheese

2. Antibiotics

3. Vaccines

4. Genetic Engineering

   1. “manipulate microorganisms using their genetic info”

      1. “subclone genes, splice things, cut DNA b/c of enzymes, etc.”

Studying Microbiology: Harmful Effects

• Pathogenic: disease causing

• Food spoilage

  • “Could lead to digestive diseases as well”

• Breakdown/damage useful material

Nomenclature

Naming organisms

• Established by Carolus Linnaeus in 1735

• Binomial: two names

  • “Latin naming system”

  • Genus: CAPITALIZED, underlined (“when handwriting”) or italics (typed)

  • Scientific epithet (species): lower cased, underlined (handwritten) or italics (typed)

• Names can describe organism, habitat, or identify researcher, etc…

Types of Microorganisms

1. Prokaryotes

2. Eukaryotes

3. Acellular forms

   1. “different organisms that lack a cell”

Types of Prokaryotes

• Bacteria

  • “main focus in lab, we manipulate and grow”

• Archaea

Structure of Bacteria

• Unicellular

  • “single-celled organisms”

• Prokaryote: lack of true nucleus or membrane bound organelles

• Shape:

  • Cocci (spherical)

  • Bacillus (rod)

  • Spiral (corkscrew “or slinky”)

• Cell wall: peptidoglycan

  • “part protein, part sugar”

• Additional structures: some have flagella (motility)

Reproduction of Bacteria

Binary fission: dividing into 2 equal cells

Nutrition of Bacteria

• Heterotrophic: requires organic carbon source (most)

• Saprophytic: uses dead organic matter nutrients

• Autotrophic: uses carbon dioxide (“inorganic”) as main carbon source (some)

Size of Bacteria

micrometers

= “1/1000th of mm”

Examples of Bacteria

• MRSA

• Helicobacter pylori

• Bacillus anthracis

• Clostridium botulinum

ORGANISM PROFILE: Staphylococcus aureus

*refer to Slide 15

Type: bacteria, Gram (+) cocci

Disease: skin infections with pus, boils, impetigo

Pathogenesis: (opportunistic pathogen)

• Break in skin allows for infection

• Production of toxins that:

  • Inhibit phagocytosis (cell eating; WBC eat bacteria)

  • Cause pus formation

  • Separate dermis from epidermis (exfoliative toxin) → sloughing skin

Treatment: Non-penicillin antibiotic if (MRSA), vancomycin

Staphylococcus aureus - Type

bacteria, Gram (+) cocci

Staphylococcus aureus - Disease

skin infections with pus, boils, impetigo

Staphylococcus aureus - Pathogenesis

(opportunistic pathogen)

• Break in skin allows for infection

• Production of toxins that:

  • Inhibit phagocytosis (cell eating; WBC eat bacteria)

  • Cause pus formation

  • Separate dermis from epidermis (exfoliative toxin) → sloughing skin

Staphylococcus aureus - Treatment

Non-penicillin antibiotic if (MRSA), vancomycin

Structure of Archaea

• Unicellular

• Prokaryote

• Cell wall: lacks peptidoglycan

Three Main Groups of Archaea

1. Methanogens: methane as waste product of respiration

2. Extreme halophiles: live in extreme salty environments

   1. “salt-loving”

3. Extreme thermophiles: live in hot environments

Reproduction of Archaea

Binary fission

Nutrition of Archaea

• Heterotrophic

  • “organic carbon source”

• Autotrophic

  • “using CO2 or a non-organic carbon source”

Size of Archaea

micrometers

Examples of Archaea

• Halobacterium salinarum

Types of Eukaryotes

1. Fungi

2. Algae

3. Protozoa

4. Helminths

Structure of Fungi

• Unicellular (yeasts) or multicellular (molds)

• Eukaryote: contains true nucleus and membrane-bound organelles

• Cell wall: chitin

• Shape:

  • Yeast: ovoid

    • “Like an oval-like shape”

  • Mold: filamentous hyphae

    • “long, thin tubes”

Reproduction of Fungi

Asexually or sexually

• “depends on type of fungus”

Nutrition of Fungi

Heterotrophic

“need an organic carbon source, a lot are saprophytic”

Size of Fungi

Micrometers to millimeters

Examples of Fungi

• Candida albicans

  • “white yeast”

• Cryptococcus neoformans

  • “Causes lung infections”

ORGANISM PROFILE: Candida albicans

*Refer to Slide 24

Type: fungi, dimorphic yeast/mold

Disease: candidiasis (yeast infection), thrush

Pathogenesis:

• Opportunist, can invade when immune system is weak or bacterial normal flora is killed due to antibiotics

  • “if you are immuno-compromised: you may have more yeast infections or thrush more often”

• Hyphal (“filamentous”) forms invades tissues

  • “moves faster and can get more distance”

Treatment: topical anti-fungal creams, Amphotericin B.

Candida albicans - Type

fungi, dimorphic yeast/mold

Candida albicans - Disease

candidiasis (yeast infection), thrush

Candida albicans - Pathogenesis

• Opportunist, can invade when immune system is weak or bacterial normal flora is killed due to antibiotics

  • “if you are immuno-compromised: you may have more yeast infections or thrush more often”

• Hyphal (“filamentous”) forms invades tissues

  • “moves faster and can get more distance”

Candida albicans - Treatment

topical anti-fungal creams, Amphotericin B.

Structure of Algae

• Unicellular or multicellular

• Eukaryote

• Cell wall: cellulose

• Additional structures: chloroplasts (photosynthesis)

Reproduction of Algae

Asexually or sexually

Nutrition of Algae

Autotrophic - “uses CO2 as main carbon source and makes own sugars”

• Photoautotrophic: requires light, water, and carbon dioxide

  • “to generate sugars”

Size of Algae

Micrometers to millimeters

Examples of Algae

• Volvox aureus

  • “golden-ish color”

Structure of Protozoa

• Unicellular

• Eukaryote

• Cell wall: NONE

• Additional structures:

  • pseudopods (“fake foot, grab surface & glide over it”)

  • flagella

  • cilia (“shorter flagella”) (motility)

Reproduction of Protozoa

Asexually or sexually

Nutrition of Protozoa

Heterotrophic: “requires organic carbon source”

Size of Protozoa

micrometers

Examples of Protozoa

• Giardia lamblia

• Plasmodium falciparum

  • “causes malaria”

ORGANISM PROFILE: Giardia lamblia

*Refer to Slide 31

Type: protozoa

Disease: giardiasis - diarrhea, inability to absorb fatty foods

Pathogenesis:

• Cyst ingested and becomes trophozoite in small intestines

• Trophozoites attach to epithelial tissue → inflammation

• Interferes with absorption of (fatty) food and fluids

Treatment: metronidazole (anti-protozoan drug)

Giardia lamblia - Type

protozoa

Giardia lamblia - Disease

giardiasis - diarrhea, inability to absorb fatty foods

Giardia lamblia - Pathogenesis

• Cyst ingested and becomes trophozoite in small intestines

• Trophozoites attach to epithelial tissue → inflammation

• Interferes with absorption of (fatty) food and fluids

Giardia lamblia - Treatment

metronidazole (anti-protozoan drug)

Structure of Helminths

• Multicellular (round and flat worms)

• Eukaryote

• Cell wall: NONE

  • “type of animal”

Reproduction of Helminths

Asexual or sexual

• dioecious

  • “male/female form”

• hermaphroditic

  • “organism has both male and female parts”

Nutrition of Helminths

Heterotrophic

“requires organic carbon source”

Size of Helminths

• MACROSCOPIC

• Microscopic at certain stages of life cycle

Examples of Helminths

• Taenia solium

  • “pork tape worm”

• Enterobius vermicularis

  • “pinworm”

ORGANISM PROFILE: Enterobius vermicularis

*Refer to Slide 35

Type: helminth, pinworm

Disease: enterobiasis - intestinal infection, nocturnal anal itch

Pathogenesis:

• Eggs ingested and hatch in duodenum

• Females emerge at night and lay eggs around anus → itching

Treatment: mebendazole (oral anti-helminth drug)

Enterobius vermicularis - Type

helminth, pinworm

Enterobius vermicularis - Disease

enterobiasis - intestinal infection, nocturnal anal itch

Enterobius vermicularis - Pathogenesis

• Eggs ingested and hatch in duodenum

• Females emerge at night and lay eggs around anus → itching

Enterobius vermicularis - Treatment

mebendazole (oral anti-helminth drug)

Types of Acellular Forms

1. Viruses

2. Viroids

   1. “like a virus”

3. Prions

Structure of Viruses

• Acellular

  • “no cell, can’t reproduce on its own”

• Nucleic acid core (DNA or RNA)

• Capsid: protein coat

  • “protection”

• Envelope: outer membrane (some)

Reproduction of Viruses

• Obligate intracellular parasites

  • “has to be in a cell in order to reproduce; will do damage”

Size of Viruses

• nanometers

  • “1000x smaller than micrometer”

Examples of Viruses

• HIV

• Herpes Simplex Virus (HSV)

• Influenza B

ORGANISM PROFILE: Herpes Simplex Virus I (HSV I)

*Refer to Slide 40

Type: DNA Virus, enveloped

Disease: cold sores - ulcerative lesions on gum and lips (herpes)

Pathogenesis:

• Virus enters through oral contact w/infected host

• Replicates in epithelial cells → vesicles

• Virus ascends sensory neuron to posterior root ganglion

• Remains dormant until future outbreak

Treatment: Acyclovir (anti-viral) before vesicles form

Herpes Simplex Virus I (HSV I) - Type

DNA Virus, enveloped

Herpes Simplex Virus I (HSV I) - Disease

cold sores - ulcerative lesions on gum and lips (herpes)

Herpes Simplex Virus I (HSV I) - Pathogenesis

• Virus enters through oral contact w/infected host

• Replicates in epithelial cells → vesicles

• Virus ascends sensory neuron to posterior root ganglion

• Remains dormant until future outbreak

Herpes Simplex Virus I (HSV I) - Treatment

Acyclovir (anti-viral) before vesicles form

Structure of Viroids

“virus-like structure”

• Acellular

• Linear or circular RNA

• NO CAPSID

Size of Viroids

10x smaller than the smallest virus

Examples of Viroids

Potato Spindle Tuber Viroid (PSTVd)

Structure of Prions

• Acellular

• Self-replicating infectious protein

“hard to destroy”

Size of Prions

100x smaller than the smallest virus

Examples of Prions

• Creutzfeldt Jakobs Disease (CJD)

• Mad cow disease

ORGANISM PROFILE: PrP^Sc prion

*Refer to Slide 45

Type: prion

Disease: Creutzfeldt - Jakob’s Disease (CJD)

• Degeneration of CNS → dementia, abnormal motor function → death

Pathogenesis:

• PrP^Sc (misfolded protein) converts a PrP^C (normal protein) →PrP^Sc

• PrP^Sc aggregate to form deposits in brain → vacuoles (gaps/circles in brain; swiss cheese)

Treatment: NONE

PrP^Sc prion - Type

prion

PrP^Sc prion - Disease

Creutzfeldt - Jakob’s Disease (CJD)

• Degeneration of CNS → dementia, abnormal motor function → death

PrP^Sc prion - Pathogenesis

• PrP^Sc (misfolded protein) converts a PrP^C (normal protein) →PrP^Sc

• PrP^Sc aggregate to form deposits in brain → vacuoles (gaps/circles in brain; swiss cheese)

PrP^Sc prion - Treatment

NONE

Classification Schemes: Taxonomy

System for naming, organizing, and classifying living things

How does Taxonomy work?

1. Identify organism

2. Classify organism

   1. Type of cell structure

      1. “cell wall, size, pro or eukaryote, etc.”

   2. Type of nutrition

      1. “autotrophic, heterotrophic, etc.”

   3. Similarity in nucleic acids

3. Name organism

   1. “Binomial Latin nomenclature”

Who came up with the Three Domain System of Classification?

Carl Woese in 1978!

Three Domain System of Classification

1. Domain Bacteria

2. Domain Archaea

3. Domain Eukarya

“Does not account for acellular forms (viruses, viroids, prions); kept separate

Domain Bacteria

Prokaryotes with cell walls containing peptidoglycan

Domain Archaea

Prokaryotes with cell walls lacking peptidoglycan

Domain Eukarya

1. Protists: slime molds, protozoa, algae

2. Fungi: yeasts, molds, mushrooms

3. Plants: mosses, ferns, conifers, flowering plants

4. Animals: sponges, worms, insects, vertebrates

When naming an organism:

A) the genus is lowercased

B) the scientific epithet is capitalized

C) only the genus should be underlined

D) none of the above

You discover a unicellular prokaryote near underwater volcanic vents. The organism has a cell wall lacking peptidoglycan. Your organism is most likely a(n):

A) bacteria

B) helminth

C) archaea

D) protozoa

Which of the following organisms is most likely the cause of nocturnal anal itching?

A) Staphylococcus aureus

B) Enterobius vermicularis

C) Giardia lamblia

D) PrP^Sc

Prions:

A) are made of only RNA

B) cause thrush

C) are prokaryotes

D) are self-replicating proteins

Which domain does Giardia lamblia belong?

A) Domain Eukarya

B) Domain Fungi

• “does not exist”

C) Domain Bacteria

D) Domain Archaea