Exam 1 (Ch.1-3)

Microorganisms

are microscopic forms of life—organisms that are too small to see with the unaided eye.

Viruses

are not living, but they are microscopic; they use biological molecules and cellular machinery (borrowed from their host) to replicate, and they can cause infectious diseases like some microorganisms.

microbes

a more general term that includes microorganisms and viruses

Microbiology

the study of microbes.

definition of “life” that distinguishes living organisms from non‐living objects.

1. living organisms are composed of cells

2. living organisms are capable of:

   1. Metabolism:

   2. Growth:

   3. Reproduction

Metabolism

A controlled set of chemical reactions that extract energy and nutrients from the environment and transform them into new biological materials.

Growth:

An increase in the mass of biological material.

Reproduction:

The production of new copies of the organism.

What are the domains of life?

• Bacteria

• Archaea

• Eurarya

By comparing the sequences of _______________, researchers now classify all living organisms into one of three domains

small subunit (SSU) ribosomal RNA gene sequences

• They are all based off of 16SrRNA

Bacteria V. Archaea V. Eukarya

Nuclear Membrane

Bacteria

• No

Archaea

• No

Eukarya

• Yes

Bacteria V. Archaea V. Eukarya

Membrane Bound Organelles

Bacteria

• Rare, a few types found in a few species

Archaea

• Rare, a few types found in a few species

Eukarya

• Multiple distinct types, found in all species

Bacteria V. Archaea V. Eukarya

Plasma Membrane

Bacteria

• Similar to Eukarya

Archaea

• Different from Bacteria and Eukarya

Eukarya

• Similar to Bacteria

Bacteria V. Archaea V. Eukarya

Cell Wall

Bacteria

• Found in nearly all species, constructed of peptidoglycan

Archaea

• Found in nearly all species, constructed of various materials

Eukarya

• Found in some species, constructed of various materials

Bacteria V. Archaea V. Eukarya

RNA Polymerase

Bacteria

• Single polymerase

Archaea

• Single polymerase, eukaryal‐like RNA pol II

Eukarya

• Three main polymerases (RNA pol I, II, and III)

Bacteria V. Archaea V. Eukarya

Histones

Bacteria

• Histone‐like proteins

Archaea

• Yes

Eukarya

• Yes

Prokaryotes V. Eukaryotes

Prokaryotes:

• No membrane-bound nucleus

• usually contain a single circular chromosomal DNA molecule

• possess a single copy of their genetic material

• Lack membrane-bound organelles

• Typically smaller

• 70S ribosomes

• Nonflexible, hollow helical filaments made of flagellin. Rotate like a propeller powered by a proton motive force

• binary fission / simple asexual division

Eukaryotes

• membrane‐enclosed nucleus

• usually contain multiple linear DNA molecules

• most eukaryal organisms have two copies, or a 2n complement, of their genetic material

• Contain complex membrane-bound organelles

• Typically Larger

• 80S cytoplasmic ribosomes

• Covered by the plasma membrane with a microtubule array (axoneme). Bends in a whip-like motion powered by ATP hydrolysis via dynein motors

• mitosis and meiosis

Paramecium

A single-celled protozoan (ciliate) covered in cilia used for locomotion and feeding

Amoeba

A unicellular protozoan that moves and feeds using pseudopods

Euglena

A single-celled flagellated protist (euglenid) classified under the clade Excavata

• possesses a red eyespot at one end of the cell that detects light, along with one or two long flagella for motion

Giardia

parasitic protozoan that lacks traditional mitochondria (an amitochondriate) and causes human gastrointestinal disease

• Supergroup Excavata —> Diplomonads

encase themselves in tough outer coverings called cysts, which allow them to survive harsh environmental conditions, including the low pH of the stomach

Dictyostelium

large organisms that exhibit complex life cycles and morphological changes

• Supergroup Unikonta —> Amoebozoans

Saccharomyces cerevisiae

A unicellular fungus (yeast) with chitin cell walls, widely used as a model organism and in baking and brewing

• Fungi

Penicillium

multicellular, filamentous fungus (mold)

• Fungi

Escherichia coli (E. coli)

A rod-shaped (bacillus) Gram-negative bacterium with peritrichous flagella distributed around the cell

• Domain Bacteria (Prokaryotic Microbes)

Myxococcus

A Gram-negative bacterium known for gliding motility and forming multicellular fruiting bodies upon starvation

• Domain Bacteria (Prokaryotic Microbes)

Staphylococcus aureus

A spherical (coccus) Gram-positive bacterium arranged in clusters

• Domain Bacteria (Prokaryotic Microbes)

Bacillus subtilis

A rod-shaped (bacillus) Gram-positive bacterium

• Domain Bacteria (Prokaryotic Microbes)

Bacillus anthracis

A rod-shaped (bacillus) Gram-positive bacterium

• Domain Bacteria (Prokaryotic Microbes)

Pseudomonas aeruginosa

A rod-shaped (bacillus) bacterium with a single polar flagellum (monotrichous)

• Domain Bacteria (Prokaryotic Microbes)

What is the human microbiome?

Microbes are all of the small organisms that can’t be seen with the naked eye from bacteria to viruses. So, a microbiome is a collection of these microbes in a region, but the regions can vary in size. The human microbiome is the variety of microbes that exist across the entire human body from skin to intestines. The microbes in the human body help with metabolic activities, like in the gut.

Where do we get our microbiomes?

You don’t really start to get your body’s microbes till you start interacting with the world. Most of your microbes will come from contacting other people, like during birth, breast feeding, and being held as a baby. Then as they start to get older you start to get microbes from expanding your diet, social circle, and environment.

How is our microbiome beneficial?

Microbiome is located anywhere that there is a connection to the outside environment, like the skin, mouth, nose, guts, and more. Each microbiome location has different conditions, so there could be varying amounts of microbes with different roles. For example the gut microbes help with digestion.

How does our microbiome change?

During your first two years of life your microbiome will change, because this is your first time interacting with most of the world, so you are picking up all kinds of new microbes. Your microbiome can also change as an adult when being introduced to new things like a change in diet, antibiotics, and a change in environment.

How are changes in human microbiome composition linked to disease? Ex: Clostridium difficile infection, inflammatory bowel disease, diabetes, obesity, autoimmune disease

There has been a correlation between having less diverse microbiomes and having health issues like diabetes or obesity. However, it is unknown if these diseases affect your microbiome or your microbiome causes these disorders, or both. But your microbiome can help with metabolic processes and when it’s disturbed you will experience health issues.

Is everyone’s microbiome the same?

Every person has a different microbiome, however they usually carry out similar functions. The main thing that differs with the microbiome is the amount and diversity of species from person to person.

How can I take care of my microbial partners?

One of the easiest ways is through your diet by eating beneficial carbs, prebiotics, and probiotics, which gives your microbes the nutrients they need. You can also eat microbes in fermented food, which can help to change your microbiome.

What are Probiotics?

• Beneficial Microbes

  • Ex) yogurt

• live bacteria and yeasts that provide health benefits when you consume or apply them in sufficient amounts

What are Prebiotics?

• Food for the good microbes

• non-digestible food ingredients, mostly specialized plant fibers, that act as food for the beneficial bacteria in your gut

What are Synbiotics?

• Probiotics and Prebiotics

• mixtures of live beneficial microorganisms (probiotics) and specialized food substrates (prebiotics)

What are Postbiotics?

• The products made by the microbes

• preparations of non-living microorganisms and/or their cellular components that confer a health benefit on the host

What are Antibiotics?

powerful medications that fight bacterial infections by either killing bacteria directly or stopping them from growing and multiplying

Microbiome

All the microbes in or on a system

Things that affect our Microbiomes:

• Diet

• Age

• Alcohol

• Exercise

• Antibiotics

• Pets

• Environment

• Birth Type

• Social Life

• Disease/health

Baby’s gut microbiome is most similar to…

an adult vaginal microbiome, then skin, then its gut microbiome develops

gnotobiotic animals

Animals that don’t have microbiomes (they are very unhealthy)

What is referred to as the second brain

ENS (enteric Nervous System)

Everyone has a different microbiome, but…

they have similar functions

How is 16S rRNA gene sequencing used to identify bacteria?

targeting a universal gene that contains both highly conserved and rapidly changing regions

What is the workflow for a metagenomics project?

a step-by-step path from physical sample collection to wet-lab processing and computer-based data analysis

1. Sample Collection

2. DNA Extraction

3. Library Preparation

4. Sequencing

5. Quality Control (QC)

6. Host Decontamination

7. Assembly or Profiling

8. Binning and Annotation

9. Statistical and Diversity Analysis

What is a fecal transplant?

You take fecal matter from a donor (healthy) and gives it to another patient to grow their microbiome.

• people want it if they had C.diff (clostridium difficile)

clostridium difficile

a bacterium that causes severe diarrhea and inflammation of the colon

Who coined the term cell?

Robert Hooke (1635–1703) was the first to describe cells based upon his microscopic observations of cork. This illustration was published in his work Micrographia.

Antoni Van Leeuwenhoek

First observed single-celled organisms in 1674 using a microscope

Louis Pasteur

Definitively refuted the long-standing theory of spontaneous generation through his swan-neck flask experiments and discovered microbial fermentation while investigating the causes of spoilage in beer and wine

swan-neck flask experiments by Pasteur features

The unique swan-neck feature of the flasks used in Pasteur’s experiment allowed air to enter the flask but prevented the entry of bacterial and fungal spores

Swan-neck flask experiments by Pasteur procedure

Pasteur’s experiment consisted of two parts. In the first part, the broth in the flask was boiled to sterilize it. When this broth was cooled, it remained free of contamination. In the second part of the experiment, the flask was boiled and then the neck was broken off. The broth in this flask became contaminated.

Robert Koch

Established a systematic protocol to link specific microorganisms to infectious diseases, determining the causative agents for numerous bacterial infections and advancing the germ theory of disease

Who discovered causative agents for many bacterial infections

Robert Koch

Alexander Fleming

discovered penicillin, the world's first antibiotic

Ignaz Semmelweis

Demonstrated that physician handwashing significantly reduced the transmission of puerperal infections between patients

Joseph Lister

Pioneered antiseptic surgical practices by developing procedures for sterilizing surgical instruments, caring for surgical wounds, and using carbolic acid as a disinfectant

Sergei Winogradsky

The Winogradsky Column: He invented this simple column device using mud and water to grow and display diverse microbial communities and their natural chemical gradients

John Snow

• Father of Epidemiology

• Demonstrated that cholera was transmitted through contaminated drinking water, laying the groundwork for modern epidemiological tracking

Father of Epidemiology

John Snow

What is the theory of spontaneous generation?

The theory of spontaneous generation was the long-held historical belief that living organisms could arise spontaneously from nonliving matter or decaying organic material through a hypothetical "life force"

• Proven wrong by Francesco Redi's Container Experiments

Francesco Redi's Container Experiments

Redi challenged the idea that maggots spontaneously generated from rotting meat. He set up open jars, cork-sealed jars, and gauze-covered jars containing meat. Maggots only formed on the meat in the open containers where flies could lay eggs (as well as on the outer gauze), demonstrating that maggots were the offspring of flies rather than products of spontaneous generation.

John Needham vs. Lazzaro Spallanzani

• Needham argued in favor of spontaneous generation, contending that boiling broth could still give rise to microbes via a "life force"

• Spallanzani countered Needham by conducting broth experiments specifically designed to disprove his results and show that microbes did not arise spontaneously

How did Louis Pasteur refute the idea of spontaneous generation?

• Louis Pasteur's Swan-Neck Flask Experiments:

Pasteur definitively disproved the theory of spontaneous generation in 1862. He boiled nutrient broth in swan-neck flasks, which allowed air to enter while trapping airborne bacterial and fungal spores in the curved neck. The sterile broth remained free of microbial growth indefinitely until the neck was broken off, allowing airborne microbes to enter and contaminate the broth

endosymbiotic theory

• mitochondria and chloroplasts are each derived from the uptake of bacteria.

• These bacteria established a symbiotic relationship with

• their host cell that eventually led to the bacteria evolving into mitochondria and chloroplasts

germ theory of disease

states that infectious diseases are caused by specific microscopic organisms—such as bacteria, fungi, or protists—invading a host organism, rather than arising spontaneously or from foul air

Girolamo Fracastoro (1546):

Formulated an early proposal of germ theory in De Contagione et Contagiosis Morbis, suggesting that diseases are spread by transferable contagious entities

Ignaz Semmelweis (1847):

Demonstrated that physician handwashing dramatically reduced the transmission of puerperal (childbed) fever between hospital patients

John Snow (1854):

Demonstrated that cholera was transmitted through contaminated drinking water rather than miasma, proving environmental vector transmission

Louis Pasteur (1856–1862):

Connected microbes to fermentation and spoilage, and definitively disproved spontaneous generation using swan-neck flasks, establishing that microorganisms only originate from existing microbes

Joseph Lister (1867):

Developed antiseptic surgical procedures using carbolic acid to sterilize surgical tools and clean wounds, dramatically reducing post-operative surgical infections

Robert Koch (1876–1906):

Formulated a standardized experimental protocol to definitively prove that a specific microbe causes a specific disease, identifying the causative bacterial agents for diseases like anthrax, cholera, and tuberculosis

Koch's postulates

are a set of four standardized scientific criteria established by Robert Koch to determine the causative agent of a specific infectious disease—definitively linking a particular microorganism to a particular illness

The 4 Koch Postulates

1. Association: The suspected pathogen must be present in every organism suffering from the disease, but absent from healthy individuals.

2. Isolation: The suspected pathogen must be isolated from a diseased host and grown in a pure culture.

3. Inoculation (Causation): The cultured pathogen must cause the same specific disease when inoculated into a healthy, susceptible host.

4. Re-isolation: The pathogen must be re-isolated from the experimentally infected host and shown to be identical to the original isolated pathogen.

A typical prokaryotic cell contains

• cell membrane

• chromosomal DNA that is concentrated in a nucleoid

• ribosomes

• cell wall

• Some prokaryotic cells may also possess

  • flagella, pili, fimbriae, and capsules

colony

A macroscopic cluster of cells appearing on a solid medium, each arising from the multiplication of a single cell

What is a bacterial lawn?

a dense, uniform, and continuous sheet of bacterial growth covering the entire surface of an agar plate

A typical bacterial cell is composed of

• Nucleoid

• Cytoplasm

• Ribosomes

• Plasmids

• Inclusion Bodies, Specialized Inclusions (Gas Vesicles, Magnetosomes), Bacterial Cytoskeleton

• Plasma Membrane

• Cell Wall

• Capsule / Glycocalyx

• Fimbriae & Pili

• Flagella

Nucleoid (Bacteria)

The irregular region within the cytoplasm containing the bacterial genome. It is not enclosed by a membrane and typically houses a single, circular chromosome of double-stranded DNA coated with packaging proteins and nascent RNA

Cytoplasm (bacteria)

The internal fluid environment containing dissolved enzymes, nutrients, and structural components

Ribosomes (bacteria)

The cellular machinery responsible for translation (protein synthesis). Bacterial ribosomes are 70S, composed of a 30S small subunit and a 50S large subunit made of rRNA and protein

Plasmids (bacteria)

Small, extrachromosomal circular DNA molecules that replicate independently and encode non-essential or specialized genes (such as antibiotic resistance)

Inclusion Bodies (bacteria)

Polymer storage structures that accumulate nutrients such as polyhydroxybutyrate (PHB) for carbon, volutin (phosphate), or sulfur granules

Gas Vesicles (bacteria)

Protein-walled structures that provide buoyancy in aquatic environments

• Specialized Inclusion

Magnetosomes (bacteria)

Membrane-bound iron particles that align the bacterial cell along magnetic fields

• Specialized Inclusions

Bacterial Cytoskeleton (bacteria)

Internal protein scaffolding that organizes cell division and maintains cell shape. Key proteins include FtsZ (forms a Z-ring during cell division), MreB (directs cell wall synthesis and maintains rod shape), and ParM (partitions plasmids during division)

Plasma Membrane (bacteria)

A phospholipid bilayer with ester linkages and embedded proteins that regulates selective transport and maintains homeostasis. Unlike eukaryotic membranes, bacterial membranes generally lack sterols

Cell Wall (bacteria)

A rigid outer layer composed of peptidoglycan (alternating NAG and NAM sugar chains cross-linked by peptide bridges) that gives the cell its shape and prevents lysis from osmotic pressure

• Gram positive and negative

Gram-Positive

Features a thick peptidoglycan layer containing teichoic acids

Gram-Negative

Features a thin peptidoglycan layer enclosed by an outer membrane containing lipopolysaccharide (LPS) and porins

Capsule / Glycocalyx (bacteria)

An organized outer polysaccharide layer that protects against desiccation, aids in surface adherence, and resists host immune clearance

Fimbriae & Pili (bacteria)

Thin, hair-like protein filaments made of pilin extending from the cell surface used for attachment to surfaces, tissues, or host cells. Specialized sex pili facilitate horizontal gene transfer

Flagella (bacteria)

Long, rigid helical protein filaments made of flagellin anchored into the cell envelope via a basal body motor. They rotate like a propeller powered by a proton motive force to drive cell motility (runs and tumbles)

Coccus (pl. cocci):

Round or spherical cells

Bacillus (pl. bacilli):

Rod-shaped cells