Introduction & Classification of Human Microbiota Flashcards
According to the current system ‘The Tree of Life’, what 3 domains can all the living organisms on the planet be placed into?
- Bacteria 2. Archaea 3. Eukarya (eukaryotes)
Why are ‘viruses’ and ‘prions’ not included in the ‘Tree of Life’?
These “infectious particles” do not satisfy the criteria for a living organism
What is taxonomy?
The science of naming, describing and classifying organisms and includes all plants, animals and microorganisms of the world
What are the 8 levels of taxonomy?
The taxonomic hierarchy has eight ranks from general to specific: 1. Domain 2. Kingdom 3. Phylum 4. Class 5. Order 6. Family 7. Genus 8. Species
What is a ‘domain’? What are the 3 ‘domains’?
A domain is the highest (most general) rank of organisms. There are 3 domains of life: 1. Bacteria 2. Archaea 3. Eukaryota
Regarding ‘Escherichia coli’ as an example, what does each part of the name denote?
‘Escherichia’ - genus ‘Coli’ - species
How is it decided where bacterial species are placed in the tree of life? How is this used?
Focus on the DNA 16S rRNA sequence –> you can classify bacteria into groups depending on how similar this piece of DNA is I.e. bacteria that are closely related will have a very similar 16S
Why is the 16s rRNA sequence used?
A piece of DNA that is present in all bacteria and is highly conserved
What are bacteria? Do they have a membrane bound nucleus?
Simple, single cell organisms They lack a membrane bound nueclues
Prokaryote vs eukaryote?
Prokaryotes are organisms made up of cells that lack a cell nucleus or any membrane-encased organelles. Eukaryotes are organisms made up of cells that possess a membrane-bound nucleus that holds genetic material as well as membrane-bound organelles
Are bacteria pro or eukaryotes? Why?
Prokaryotes as lack a membrane bound nucleus
Diagram of bacteria. What are the noticeable features?
- Nucleoid (including chromosomal DNA)
- Capsule (if present)
- Cell envelope
- Plasma membrane
- Polysomes
- Plasmid DNA
- Fimbriae
- Flagellum
What is the flagella? What is it responsible for?
- Long tail-like structure
- Responsible for locomotion (motility)
E.g. bladder infection –> ability of bacteria to move up the urethra
The number and location of flagella can vary. What are the different options?
- Monotrichous (A)
- Lophotrichous (B)
- Amphitrichous (C)
- Peritrichous (D)
What bacteria is the main cause of UTIs?
E. coli
What is the ‘H antigen’? What is this used for?
Flagella is the whole structure, while the slender threadlike portion of the flagella is called the H antigen.
Used for the identification of the certain pathogens
What are fimbriae? How do they differ from pili?
Both are structures exposed to the extracellular space (very similar)
Fimbriae:
- Bristle like short fibres occurs on the surface of bacteria
- Present on both Gram positive and Gram negative bacteria
Pili:
- Long hair like tubular microfibres like structures present on the surface of bacteria.
- Present only on some Gram negative bacteria.
What is the importance of fimbriae/pili to bacteria?
Aid adhesion to host cells and colonisation (helpful in ability to cause an infection)
What is the capsule of bacteria? Are they present in all bacteria?
It is a polysaccharide layer that lies outside the cell envelope, and is deemed part of the outer envelope of a bacterial cell.
Present in most but not all bacteria.
What is purpose of capsule of bacteria?
- Polysaccharide material protection from
- Phagocytosis/immune attack
- Dessication
- Antibiotics
Difference between a slime layer and a capsule?
Slime layer:
- Loosely associated with the bacterium
- Can be easily washed off
Capsule:
- Attached tightly to the bacterium
- Has definite boundaries
What are bacteria biofilms?
Community of bacteria surrounded by extracellular polymeric substances (layer) –> another example of polysaccharide protection
What is an endospore?
An endospore is a dormant, tough, and non-reproductive structure produced by certain bacteria.
What is purpose of endospores?
Resistant to many forms of environmental stress (allow bacteria to persist):
- Dessication
- UV radiation
- Temperature extremes
- Certain antiseptic agents
What are Genus Bacillus and Genus Clostridium examples of?
Endospore-producing bacteria
What 4 types of cell wall are encountered in bacteria?
- Gram-positive
- Gram-negative
- Mycobacterial (‘acid-fast’)
- No peptidoglycan (‘atypical)
Why are bacteria cell walls important?
Helps decide what antibiotic to prescribe
What colour is gram-positive bacteria stained?
The staining method uses crystal violet dye, which is retained by the thick peptidoglycan cell wall found in gram-positive organisms. This reaction gives gram-positive organisms a blue color when viewed under a microscope.
What colour is gram-negative bacteria stained?
Red
What type of cell wall are Staphylococcus, Streptococcus, Bacillus and Clostridium examples of?
Gram-positive
What cell walls are E. coli, Acinetobacter, Klebsiella and Neisseria examples of?
Gram-negative
What cell walls are Mycobacterium and Rhodococcus examples of?
Mycobacterial (acid-fast)
What type of cell wall is Chlamydia and Mycoplasma examples of?
No peptidoglycan
Bacteria can be divided into 3 groups during a Gram reaction. What are these 3 groups?
- Gram-positive
- Gram-negative
- Colourless
What dye is used in Gram reaction?
Crystal violet-iodine dye complex following acetone/alcohol treatment
What colour is Gram-positive bacteria stained?
Retain the complex, appear blue/purple when visualised
What colour is Gram-negative bacteria stained?
Loss of complex, appear red/pink
Why do some bacteria appear colourless during Gram stain?
Stains unable to penetrate mycolic acid layer (e.g. Mycobacteria)
Bacteria are categorised based on their shapes into three classes. What are these classes?
- Cocci (spherical-shaped)
- Bacillus (rod-shaped)
- Spirochetes (spiral-shaped) cells
Examples of cocci shape:
Example of bacilli shape:
What do most bacteria rely on for replication (vertical gene transfer)?
Binary fission
What is binary fission?
A cell just needs to grow to twice its starting size and then split in two. Before binary fission occurs, the cell must copy its genetic material (DNA) and segregate these copies to opposite ends of the cell.
Is binary fission sexual or asexual reproduction?
Asexual
Process of binary fission
Bacteria cell replicates its genetic material –> 2 different chromosomes will separate into opposite sides of cell –> cell then separates
What is result of binary fission?
2 identical cells
Why is the growth of a bacterial population exponential?
As every time a cell separates, the population doubles (provided sufficient nutrients are available)
What type of gene transfer is binary fission/replication?
Vertical
Bacteria undergo horizontal gene transfer too. What is the important for?
Important for acquisition of DNA –> important in acquisition of virulence and antibiotic resistance determinants
What are the 3 main mechanisms by which horizontal gene transfer in bacteria can occur?
- Conjugation
- Transformation
- Transduction
What is involved in ‘conjugation’ in horizontal gene transfer? What form is the genetic material typically in?
- Conjugation is the process by which one bacterium transfers genetic material to another through direct contact via pilus.
- During conjugation, one bacterium serves as the donor of the genetic material, and the other serves as the recipient.
- Genetic information that is transferred by conjugation is plasmid DNA
- Really important in passing on antibiotic resistant genes
What is involved in transformation in horizontal gene transfer?
- Involves uptake of short fragments of naked DNA (free DNA in the environment) by naturally transformable bacteria
- Cells that are capable of this are ‘competent’
- DNA binding proteins on the edge of cell will bind to any extracellular DNA
- This is then taken into the cell and integrated into the chromosome
What is involved in transduction in horizontal gene transfer?
Transduction involves transfer of DNA from one bacterium into another via a virus
What is a phage?
a virus which parasitizes a bacterium by infecting it and reproducing inside it
Describe process of transduction
- Virus binds to bacteria and injects its DNA into cell
- Host cell replicates that DNA along with its own
Is fungi eukaryotic or prokaryotic?
Eukaryotic
Do fungi have a cell wall? What is it made of?
Most do - made of chitin
What are 3 examples of disease-causing fungi?
- Yeasts
- Filamentous (moulds)
- Dimorphic (yeast & mould)
What is oral candidiasis an example of?
Thrush –> yeast infection
What is dysbiosis?
a microbial imbalance or maladaptation on or inside the body
Structure of yeast
- Nucleus
- Mitochondria
- Lipid granule
- Vacuole
- Cell wall (chitin)
- Membrane
- Bud scar
How does yeast mainly replicate?
By budding –> unusual style of asymmetric division into a large mother cell and a small daughter cell
Is ‘budding’ sexual or asexual?
Asexual
Yeast can also undergo sexual reproduction. What occurs here?
A single yeast cell undergoes meiosis and produces haploid spores; these spores can recombine with other haploid spores, producing a diploid cell – the yeast’s “normal” state.
Do yeast cells reproduce sexually or asexually?
Both
What are Candida, Blastomyces, Histoplasma and Cryptococcus all examples of?
Fungi
What common, superficial infections can moulds cause?
Ringworm, athletes foot
Moulds can also cause uncommon, more severe infections. What are 2 examples of these?
- Aspergillosis
- Mucormycosis
Describe the replication process of moulds
- Moulds reproduce by producing large numbers of small spores, which may contain a single nucleus or be multinucleate.
- Mold spores can be asexual (the products of mitosis) or sexual (the products of meiosis)
What are the 3 classes of parasites that can cause disease in humans?
- Protozoa
- Helminths
- Ectoparasites
Are protozoa multi or uni cellular? What about Helminths (worm)?
Protozoa - unicellular
Helminths - multicellular
Are parasites eukaryotes or prokaryotes?
Eukaryotes
What are 3 examples of intestinal protozoa?
- Entamoeba
- Giardia
- Cryptosporidium
What are 3 examples of non-intestinal protozoa?
- Plasmodium
- Leishmania
- Trypanosoma
What are 3 examples of intestinal Helminths?
- Enterobius (pinworm)
- Taenia (tapeworm)
- Ascaris (roundworm)
What is an example of a non-intestinal Helminths?
•Schistosoma
Is the replication of parasites sexual or asexual?
Sexual and asexual forms
What may parasites require for replication?
- May require multiple hosts to complete lifecycle
- May include cyst formation as a mode of survival
Why are viruses not classed as living organisms?
Cannot exist on their own
Describe the structure of viruses
- Nucleic acid core wrapped in a protein coat
- Some also have a lipid envelope
What does the nucleic acid core of a virus consist of?
DNA or RNA
What are retroviruses?
A retrovirus is a type of virus that inserts a copy of its RNA genome into the DNA of a host cell that it invades, thus changing the genome of that cell. Once inside the host cell’s cytoplasm, the virus uses its own reverse transcriptase enzyme to produce DNA from its RNA genome. The new DNA is then incorporated into the host cell genome. The host cell then treats the viral DNA as part of its own genome.
What are the 6 stages of virus lifecycle?
- Attachment
- Penetration
- Uncoating
- Biosynthesis
- Assembly
- Release
Describe the attachment stage in the virus lifestyle
Attachment is via specific receptors (tropism) –> virus becomes attached to target cell
Describe the penetration stage of the virus lifecycle
Penetration via endocytosis or membrane fusion –> the cell engulfs the virus
Describe the uncoating stage of the virus lifecycle
Viral contents are released –> genetic material targeted to nucleus
Describe the biosynthesis stage of the virus lifecycle
Viral RNA enters the nucleus where it is replicated by the viral RNA polymerase and early viral proteins are produced:
- Polymerase
- Integrase
- Allows genome replication
Describe the assembly stage of the viral lifecycle
Late viral proteins are produced:
- Structure proteins
- Capsid
- Surface proteins
- Assembly of virion
Describe the release stage of the virus lifecycle
Relesae via budding or cell lysis –> New viral particles are made and released into the extracellular fluid. The cell which is not killed in the process continues to make new virus.
HIV lifecycle
What factors is the lifecycle of a virus based on?
- Nature of the nucleic acid: RNA or DNA
- Symmetry of the capsid
- Presence or absence of an envelope
- Dimensions of the virion and capsid
What are prions?
Prions are misfolded proteins with the ability to transmit their misfolded shape onto normal variants of the same protein
Do prions contain genetic material?
No
How can prions be transmitted?
- Inherited
- Spread via contaminated material
- Occur spontaneously
What is effect of prions on native proteins?
Aggregate and cause misfolding of native proteins – chain reaction
What are examples of diseases caused by prions?
- Creutzfeldt-Jakob Disease
- Bovine spongiform encephalopathy
- Scrapie
- Kuru
