Microbial Genetics and Immune Systems

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Questions and Answers

What is a primary disadvantage of sexual reproduction compared to asexual reproduction?

Slower to produce offspring (correct)

Generates fewer mutations

Requires more energy to perform

Produces identical offspring

Which of the following processes involves the transfer of DNA through a virus?

Transduction (correct)

Binary fission

Conjugation

Transformation

In horizontal transmission of genetic material, which mechanism involves a physical connection between two bacteria?

Conjugation (correct)

Transduction

Mitosis

Transformation

What is a limitation of transformation as a method for introducing genetic diversity?

Dependent on the availability of environmental DNA Signup and view all the answers

What characterizes generalized transduction?

Transfers random pieces of DNA Signup and view all the answers

What is the primary role of the conjugation pilus in bacterial gene transfer?

To facilitate direct cell-to-cell contact for gene transfer Signup and view all the answers

Which statement regarding specialized transduction is correct?

It results in the transfer of specific bacterial genes associated with the viral DNA. Signup and view all the answers

What defines the core genome in bacterial populations?

The genetic material shared by all strains of a species Signup and view all the answers

What is a characteristic feature of dysbiosis in the human microbiome?

Dominance of pathogenic bacteria and decreased microbial diversity Signup and view all the answers

How do chromosomal islands provide evidence for foreign origin in bacterial genomes?

Their nucleotide composition differs from the rest of the genome and often contains inverted repeats. Signup and view all the answers

What role do the epithelial cells in alveoli play in the immune defense of the lungs?

They produce surfactant, which can act as an antimicrobial agent. Signup and view all the answers

Which statement accurately describes the microbial environment of the skin?

Antimicrobials produced by skin bacteria help control S.aureus colonization. Signup and view all the answers

How can the gut microbiota stimulate the immune system in healthy individuals?

By stimulating the production of mucosal antimicrobial compounds. Signup and view all the answers

What is a characteristic feature of microbiota in the urogenital tract of women?

A weakly acidic environment is created by the fermentation of glycogen into lactic acid. Signup and view all the answers

What happens in the gastrointestinal tract when there is a decrease in stomach acidity?

Pathogenic bacteria are more likely to establish infections. Signup and view all the answers

What primary impact does a high-fiber diet have on the gut microbiome?

It increases gut motility and helps diversify the microbiome. Signup and view all the answers

Which of the following factors is least likely to contribute to dysbiosis?

Living in an area with diverse flora. Signup and view all the answers

How do short-chain fatty acids (SCFA) affect gut health?

They can modulate immune responses and promote tissue repair. Signup and view all the answers

What characterizes the role of Archaea in the gut microbiome?

They produce methane, which can increase acetate and potentially favor pro-obesity conditions. Signup and view all the answers

What limitation is associated with using mouse models to study human gut microbiota?

Differences in gut anatomy prevent accurate comparisons. Signup and view all the answers

Which mechanism allows pathogens to evade phagocytosis by using a protective layer around themselves?

Capsule Signup and view all the answers

Which enzyme helps pathogens to break down connective tissue and facilitate further invasion into host tissues?

Hyaluronidase Signup and view all the answers

Which type of secretion system allows bacteria to inject proteins directly into the host cell?

Type III Signup and view all the answers

What role do adhesins play in the pathogenicity of bacteria?

They facilitate the attachment to host cells. Signup and view all the answers

What is a potential drawback of using prebiotics to promote gut health?

They can also nourish harmful bacteria. Signup and view all the answers

Which of the following correctly describes the role of exotoxins?

They are proteins that can disrupt host cell functions. Signup and view all the answers

In the context of bacterial virulence, what does LD50 signify?

The lethal dosage required to kill 50% of infected hosts. Signup and view all the answers

How does botulinum toxin affect muscle contraction?

It prevents vesicle fusion, reducing muscle contraction. Signup and view all the answers

What is the outcome of a pathogen that can remain inside the phagosome without fusing with a lysosome?

It can be carried into the circulatory system without being digested. Signup and view all the answers

Which statement correctly defines bacteremia?

It can be caused by mundane activities like dental work. Signup and view all the answers

What is the primary mechanism of action for cholera toxin?

It increases cAMP levels, affecting ion transport. Signup and view all the answers

What effect does diphtheria toxin have on host tissues?

It blocks protein synthesis, causing tissue death. Signup and view all the answers

Which of the following best describes the term 'cytotoxin'?

A toxin that causes cell lysis by targeting cell membranes. Signup and view all the answers

Which statement most accurately describes the differences between exotoxins and endotoxins?

Exotoxins can directly kill cells, whereas endotoxins primarily stimulate immune reactions. Signup and view all the answers

What role do peptidoglycan layers play in bacterial cell walls?

They provide shape and rigidity while resisting osmotic stress. Signup and view all the answers

How does the structure of gram-negative bacteria differ from that of gram-positive bacteria?

Gram-negative bacteria possess an outer membrane containing LPS; gram-positive bacteria do not. Signup and view all the answers

Which bacterial structure is primarily responsible for maintaining cell morphology during division?

Bacterial cytoskeleton proteins Signup and view all the answers

What protects the DNA within bacterial endospores from environmental stress?

The calcium-dipicolonic acid complex Signup and view all the answers

Which protein is involved in the segregation of chromosomes during bacterial cell division?

ParM Signup and view all the answers

The function of the capsule in bacteria primarily relates to which of the following?

Preventing dehydration and enhancing pathogenicity. Signup and view all the answers

What role do alveolar macrophages play in the immune defense of the lungs?

They directly engulf and destroy pathogens. Signup and view all the answers

How do resident bacteria in the vagina help maintain its acidic environment?

By fermenting glycogen to produce lactic acid. Signup and view all the answers

What is a consequence of taking antibiotics for women concerning their vaginal microbiota?

Rise in commensal bacteria that could cause infections. Signup and view all the answers

What does an Hfr strain indicate about the genetic makeup of the bacterial cell?

The F plasmid is integrated into the host chromosome. Signup and view all the answers

Which characteristic of the gut microbiome plays a role in energy generation for humans?

Fermentation of sugars leading to short-chain fatty acids. Signup and view all the answers

What contributes to the sterility of the kidney and bladder?

Effective immune response from epithelial cells. Signup and view all the answers

How does specialized transduction differ from generalized transduction in phage-mediated gene transfer?

Generalized transduction can transfer any bacterial DNA segment. Signup and view all the answers

What is a key characteristic of chromosomal islands that suggests they originate from foreign DNA?

They have differing nucleotide compositions from the core genome. Signup and view all the answers

What effect can dysbiosis have on the immune system?

It can cause increased inflammation and immune disorders. Signup and view all the answers

In human microbiome dynamics, what primarily distinguishes a healthy state from a diseased state?

The diversity and balance of microbial populations. Signup and view all the answers

What is a potential long-term impact of dysbiosis on human health?

Active promotion of inflammatory diseases Signup and view all the answers

Which factor is most likely to promote the development of a healthy gut microbiota?

High-fiber diet with a variety of fiber sources Signup and view all the answers

How might the presence of Archaea in the gut microbiome influence obesity?

By producing methane that leads to increased acetate production Signup and view all the answers

What is a critical condition required for inflammation to occur in the gut?

Stimulation of innate immune cells due to a physical barrier breach Signup and view all the answers

What distinguishes probiotics from prebiotics in terms of their function?

Probiotics directly affect gut health; prebiotics feed existing bacteria Signup and view all the answers

What is a primary benefit of sexual reproduction compared to asexual reproduction?

It generates genetic diversity. Signup and view all the answers

What process describes the uptake of naked DNA from the environment by bacteria?

Transformation Signup and view all the answers

In generalized transduction, what determines the genes that can be transferred between bacteria?

The size of the bacteriophage's capsid Signup and view all the answers

What is a significant downside of asexual reproduction in bacteria?

It results in offspring with identical genomes. Signup and view all the answers

What term defines the transfer of DNA between species that are not directly related?

Horizontal transmission Signup and view all the answers

Which of the following mechanisms is NOT typically used by bacteria to colonize host tissues?

Activation of host immune cells to enhance pathogen invasion Signup and view all the answers

What is the primary role of hyaluronidase in the context of bacterial infections?

To break down hyaluronic acid, facilitating tissue invasion Signup and view all the answers

Which of the following statements about Type III secretion systems is correct?

They facilitate direct interaction between bacterial proteins and host cells Signup and view all the answers

Which of the following is a potential consequence of a bacterial capsule?

Inhibition of the host's immune response by preventing phagocytosis Signup and view all the answers

What is one of the limitations of using prebiotics in gut health?

They may inadvertently support the growth of harmful bacteria Signup and view all the answers

What is the primary consequence of the lipid A component of the LPS molecule in gram-negative bacteria?

It triggers a strong immune reaction in the host. Signup and view all the answers

Which function does the glycocalyx primarily serve for pathogenic bacteria?

Enhancing virulence by adhering to surfaces. Signup and view all the answers

The formation of endospores is a characteristic feature of which type of bacteria?

Gram-positive bacteria Signup and view all the answers

How does the structure of the cell wall in gram-negative bacteria differ from that in gram-positive bacteria?

Gram-negative bacteria possess an outer membrane with lipid A. Signup and view all the answers

Which protein is primarily involved in the septation process during bacterial cell division?

FtsZ Signup and view all the answers

What is the role of dipicolonic acid in bacterial endospores?

It helps protect and stabilize the DNA. Signup and view all the answers

Which of the following statements regarding exotoxins and endotoxins is correct?

Endotoxins cause a strong immune reaction without directly killing cells. Signup and view all the answers

What does the term virulence specifically refer to in relation to pathogens?

The severity of disease caused by a pathogen. Signup and view all the answers

Which of the following best explains the difference between bacteremia and septicemia?

Bacteremia involves localized bacterial presence, while septicemia is a systemic infection. Signup and view all the answers

What is the primary action of the Diphtheria toxin produced by C. diphtheriae?

It blocks protein synthesis within cells. Signup and view all the answers

How does the cholera toxin primarily cause diarrhea in infected individuals?

By increasing cAMP levels, disrupting ion transport. Signup and view all the answers

What is the mechanism by which botulinum toxin affects muscle contraction?

It prevents the uptake of acetylcholine, leading to paralysis. Signup and view all the answers

Which of the following correctly describes the function of exotoxins?

They are secreted proteins that target specific host cells to disrupt their function. Signup and view all the answers

What characterizes the action of cytolytic toxins such as hemolysins?

They form pores in the cell membrane leading to cell lysis. Signup and view all the answers

Which mechanism of horizontal transmission is characterized by the transfer of genetic material through a virus?

Transduction Signup and view all the answers

What is a significant drawback of asexual reproduction in bacteria?

Limited genetic diversity among offspring Signup and view all the answers

In the process of transformation, which part of the bacterial cell binds to the double stranded DNA from the environment?

Pilus Signup and view all the answers

Which type of genetic material transfer includes the integration of DNA into the bacterial chromosome as recombinant DNA?

Transformation Signup and view all the answers

What is the primary function of the F pilus in bacterial conjugation?

To facilitate direct cell-cell contact for gene transfer Signup and view all the answers

Which statement accurately describes specialized transduction?

It results in the simultaneous transfer of both viral and bacterial DNA Signup and view all the answers

How do chromosomal islands differ from the core genome of bacteria?

Chromosomal islands contain specialized functions and are often of foreign origin Signup and view all the answers

What is a significant outcome of dysbiosis in the human microbiome?

Overgrowth of pathogenic bacteria leading to inflammation Signup and view all the answers

What characterizes an Hfr strain of bacteria?

It has integrated the F plasmid into its chromosomal DNA Signup and view all the answers

What characteristic of the vaginal microbiota helps maintain its weakly acidic environment?

Fermentation of glycogen into lactic acid Signup and view all the answers

Which of the following best describes the impact of the stomach's acidity on microbial colonization?

Many bacteria do not survive and colonize the stomach. Signup and view all the answers

What role do Peyer's patches play in the immune response of the gastrointestinal tract?

They detect bacteria in the gut and present information to the local immune system. Signup and view all the answers

Which feature of skin microbiota helps to limit the colonization of Staphylococcus aureus?

Production of antimicrobial compounds by resident bacteria Signup and view all the answers

How does decreased stomach acidity potentially lead to infections in the gastrointestinal tract?

It allows more pathogens from food to survive passage to the intestines. Signup and view all the answers

How does a high-fiber diet specifically support a diverse gut microbiome?

By providing various fiber sources that feed beneficial bacteria. Signup and view all the answers

What is the consequence of a high-fat diet on gut health?

It can lead to increased absorption of endotoxins. Signup and view all the answers

What factor is critical in determining the severity of inflammation in the gut?

The relationship between host immune function and pathogen virulence. Signup and view all the answers

Which short-chain fatty acid (SCFA) is primarily associated with promoting a pro-obesity phenotype?

Acetate, which stimulates lipid synthesis and storage. Signup and view all the answers

What is one major limitation of using human-microbiota-associated mouse models?

Human microbiota effectively resist mouse gut environments. Signup and view all the answers

What is the function of adhesins in bacterial pathogenesis?

They facilitate the attachment of bacteria to host cells and tissues. Signup and view all the answers

Which of the following statements best describes the role of hyaluronidase in bacterial invasion?

It degrades connective tissue, facilitating deeper tissue invasion. Signup and view all the answers

What characteristic of Type III secretion systems distinguishes them from Type II systems?

They secrete proteins from the bacterial cytoplasm directly into host cells. Signup and view all the answers

Which mechanism allows bacteria to alter their growth conditions and evade the host immune response?

The use of antiphagocytic proteins that inhibit phagocytosis. Signup and view all the answers

How do various types of pili contribute to bacterial adherence to host tissues?

Type 1 pili create a strong attachment through carbohydrate binding. Signup and view all the answers

What is the primary role of lipopolysaccharide (LPS) in gram-negative bacteria?

To act as an endotoxin triggering immune response Signup and view all the answers

What effect does the presence of thick peptidoglycan layers in gram-positive bacteria have?

Strengthens cell wall integrity Signup and view all the answers

Which of the following describes the action of the Shiga-like toxin produced by certain E. coli strains?

It inhibits protein synthesis resulting in cell death. Signup and view all the answers

What characterizes the structure of an endospore in gram-positive bacteria?

Multiple protective layers including a spore coat and dipicolonic acid Signup and view all the answers

Which bacterial structural component is primarily responsible for maintaining morphology during cell division?

FtsZ protein Signup and view all the answers

In contrast to exotoxins, what is a critical feature of endotoxins during an immune reaction?

They primarily potentiate inflammation without immediate cell lysis Signup and view all the answers

What is the primary function of the glycocalyx in bacterial cells?

Providing adherence and protecting against dehydration Signup and view all the answers

What is a primary mechanism by which a pathogen evades digestion inside a macrophage?

By resisting lysosomal enzymes and multiplying within Signup and view all the answers

What distinguishes septicemia from bacteremia?

Septicemia involves a systemic infection affecting the bloodstream Signup and view all the answers

Which statement best describes the mechanism of cholera toxin?

It disrupts ion transport by increasing cAMP levels Signup and view all the answers

How does the tetanus toxin affect muscle contraction?

By blocking the degradation of acetylcholine at synapses Signup and view all the answers

What does LD50 measure in terms of pathogenicity?

The lethality of a substance to kill 50% of a test group Signup and view all the answers

Which of the following statements about exotoxins is true?

Exotoxins are proteins that can be denatured by heat Signup and view all the answers

What virulence factor allows a pathogen to mimic cytokines and alter host immune responses?

Surface proteins that mimic immune signaling Signup and view all the answers

What is the primary effect of diphtheria toxin on host tissues?

Blocking protein synthesis leading to tissue death Signup and view all the answers

Which type of bacteria has a thick peptidoglycan layer and appears purple when stained?

Gram-positive bacteria Signup and view all the answers

What structural component is present in the outer membrane of gram-negative bacteria that contributes to its characteristics?

Lipopolysaccharide Signup and view all the answers

Which protein is essential for the organization of cell wall extension in bacterial cells?

MreB protein Signup and view all the answers

What is one primary function of the glycocalyx in bacteria?

Facilitating attachment to surfaces Signup and view all the answers

Which structural feature distinguishes acid-fast bacteria from other types of bacteria?

Waxy outer coating of mycolic acid Signup and view all the answers

How do lysozymes affect the bacterial cell wall?

They cleave glycosidic bonds between sugars. Signup and view all the answers

What role does FtsZ play in bacterial cell division?

It maintains the cell's diameter and forms a ring around the septum. Signup and view all the answers

Which component of endospores provides protection against environmental stresses?

Spore coat enriched with dipicolonic acid Signup and view all the answers

How do archaea differ from bacteria in terms of their plasma membrane structure?

Archaea contain ether-linked lipids instead of ester-linked lipids. Signup and view all the answers

What is the primary function of MreB in bacterial cells?

To assist with the cell's elongation. Signup and view all the answers

Which feature distinguishes the endospore production process from typical bacterial division?

The mother cell is lysed to release the spore. Signup and view all the answers

Which structure is involved in the movement of genetic material between bacteria during conjugation?

Pili Signup and view all the answers

What is the primary advantage of endospore formation for bacteria in unfavorable conditions?

Preserves genetic material while minimizing active metabolism. Signup and view all the answers

What mechanism do archaea use to rotate their archaella?

ATP energy Signup and view all the answers

What key feature distinguishes a retrovirus from other viruses?

It uses reverse transcriptase Signup and view all the answers

Which of the following is a method that bacteria use to defend against viral infections?

Restriction endonucleases Signup and view all the answers

What is the primary function of ABC transporters in bacteria?

Transporting nutrients and antibiotics Signup and view all the answers

In what way do animal viruses enter host cells compared to bacteriophages?

Animal viruses can use receptor-mediated endocytosis Signup and view all the answers

Which statement accurately describes the lytic cycle of bacteriophages?

Phage DNA is replicated, proteins synthesized, leading to cell lysis Signup and view all the answers

What characteristic of archaeal DNA distinguishes it from bacterial DNA?

Presence of histones Signup and view all the answers

Which mechanism is primarily responsible for the adaptation of bacteria to resist viral infection via genetic changes?

CRISPR-Cas system Signup and view all the answers

What adaptation helps thermophilic bacteria stabilize their proteins at elevated temperatures?

Formation of more ionic bonds on protein surfaces Signup and view all the answers

How do halophiles adapt to high salinity environments?

By using a sodium motive force to balance ion concentrations Signup and view all the answers

What is a characteristic feature of microaerophiles?

They require lower levels of oxygen than what is present in the atmosphere. Signup and view all the answers

Which mechanism do bacteria use to communicate cell density in quorum sensing?

Synthesizing and releasing autoinducers Signup and view all the answers

What role do exopolysaccharides play in biofilm formation?

They anchor bacteria to surfaces and provide structural integrity. Signup and view all the answers

How do obligate anaerobes cope with the toxic effects of oxygen?

By producing enzymes to break down reactive oxygen species Signup and view all the answers

In the context of biofilms, what is an autolysin's primary function?

To aid in the release of DNA during cell death Signup and view all the answers

What is a primary benefit of cell-to-cell communication in quorum sensing for bacterial populations?

Enables bacteria to function as a coordinated collective. Signup and view all the answers

What is the primary difference between substrate-level phosphorylation and oxidative phosphorylation?

Substrate-level phosphorylation does not require oxygen while oxidative phosphorylation does and generates more ATP. Signup and view all the answers

In which of the following conditions would fermentation be utilized over aerobic respiration?

When no terminal electron acceptor is available. Signup and view all the answers

What unfavorable condition is likely to affect microbial growth in cold environments?

Decreased enzymatic function. Signup and view all the answers

Which statement accurately describes the proton-motive force?

It is the energy stored from the movement of ions across a gradient and influences ATP production. Signup and view all the answers

What phenomenon occurs during the stationary phase of bacterial growth?

The number of reproducing bacteria and dying bacteria are roughly equal. Signup and view all the answers

Which category of microbe would require organic carbon sources as a primary nutrient?

Chemotroph Signup and view all the answers

Which type of respiratory process relies on an alternative acceptor for electrons other than oxygen?

Anaerobic respiration Signup and view all the answers

What is a common challenge faced when culturing hyperthermophilic organisms?

Ensuring the integrity of proteins at elevated temperatures. Signup and view all the answers

What differentiates sessile growth from planktonic growth in microbial populations?

Sessile growth is associated with nutrient-rich environments. Signup and view all the answers

Which statement about NAD+ in cellular metabolism is correct?

NAD+ is crucial for the transfer of electrons in metabolic reactions. Signup and view all the answers

Study Notes

Microbial Genetics and Genomics

Sexual vs. Asexual Reproduction:
- Both transmit genetic material vertically (parent to offspring).
- Sexual reproduction combines DNA from two parents, generating genetic diversity via chromosomal crossover. This increases the frequency of mutations, potentially advantageous in changing environments. However, it is slower.
- Asexual reproduction creates identical offspring from a single parent, lacking genetic diversity (mutations are random and rare). It is faster.
Vertical vs. Horizontal Transmission:
- Vertical transmission is the transfer of genetic material from one generation to the next (e.g., mother cell to daughter cell).
- Horizontal transmission (HT) involves transferring small DNA fragments between closely or distantly related species. This is a mechanism for asexual organisms like bacteria to gain genetic diversity. Examples include transformation, transduction, and conjugation.
Transformation:
- Uptake of naked DNA from the environment.
- A pilus binds to double-stranded DNA (dsDNA) and pulls it into the periplasm.
- DsDNA becomes single stranded (ssDNA), and the other strand degrades.
- ssDNA integrates into the bacterial chromosome.
- Bacteria have nucleases to degrade dsDNA but are ineffective against ssDNA.
- Not a very efficient method of genetic diversity as environmental DNA is often scarce, and nucleases can degrade ssDNA.
- Can occur when bacteria are dead.
Transduction:
- Gene transfer via a virus (phage).
- Generalized: Phage DNA transfer is random from one cell to another in infected host cells.
- Specialized: Phage DNA incorporates into the host's chromosome in a specific location.
- The genes transferred are limited by the space in the phage's head.
- Bacteria must be alive to be infected.
Conjugation:
- Direct cell-to-cell contact via a conjugation pilus (sex pilus) to transfer genes.
- The ability to form a pilus is encoded on a plasmid.
- F+ to F- conjugation:
  - Pilus formation and retraction brings cells together.
  - One plasmid strand is cut, transferred, and the complementary strand is synthesized in both cells.
  - The recipient cell becomes F+.
- Hfr (high frequency of recombination): F plasmid integrates into host chromosome. Genes closest to the integration site are transferred first. May not become F+ but still transfer genetic information. Bacteria must be alive.
Generalized vs. Specialized Transduction:
- Generalized transduction: Random transfer of bacterial DNA by a virus. The host's DNA can be packaged into viral particles and transferred to another bacterium - Specialized transduction: Specific portions of DNA are transferred. The specific location from where the DNA was integrated from was transferred to the new bacteria.
Consequences of Genetic Diversity:
- Transduction: V. cholera can acquire genes for cholera toxin via a CTX phage (specialized transduction), transitioning from non-pathogenic to pathogenic.
Pan and Core Genomes:
- Core genome: Shared genes across all strains of a species.
- Pan genome: Includes core genome plus additional genes unique to certain strains.
Chromosomal Islands:
- Clusters of genes for specialized functions (e.g., pathogenicity) not essential for survival.
- Often of foreign origin from horizontal gene transfer (HGT) due to differences in nucleotide composition from the core genome and often containing inverted repeats.
Microbial Diversity Evolution: Mechanisms like horizontal gene transfer and the transfer of functional genes via transduction create microbial diversity.

Microbial Symbiosis with Humans

Diversity and Dynamics of Microbial Populations:
- Most microbes are harmless and beneficial to the host, with different microhabitats supporting distinct microbial communities.
Dysbiosis:
- Symbiosis: A healthy gut microbiome involves symbiotic bacteria producing metabolites and antigens, supporting tolerance. - Dysbiosis: Pathogenic bacteria can disrupt healthy microbiota. They secrete antigens and toxins, stimulating immune cells to increase inflammation. This continuous inflammation can lead to pathogenic colonization, intestinal damage, immune disorders, and metabolic dysfunction (immunopathology).
Oral Cavity and Airways:
- Saliva and immune responses combat microbes in the upper respiratory tract.
- Low microbial presence in the lower respiratory tract, with mucociliary escalator and alveolar defenses.
Urogenital Tract:
- Kidney/bladder are normally sterile.
- Vaginal acidity and glycogen fermentation by resident bacteria maintain a healthy environment.
- Microbiota composition varies with hormonal changes.
Skin:
- Microbiota composition varies by environmental conditions (dryness, acidity).
- Mostly gram-positive bacteria reside on the skin.
- Antimicrobial peptides and healthy bacteria help to lower S. aureus colonization.
Gut Microbiota Roles:
- Fermentation producing SCFA for energy.
- Prevent pathogenic colonization via antimicrobial compounds and nutrient competition.
- Development of immune response (tolerance or inflammation) and stimulation of naïve T cells.
- Supporting Vitamin K, and chemical compound digestion (i.e. medications).
Gut Microbiota Alterations:
- Microbiome development begins before birth, influenced by factors like birth method (vaginal vs. C-section), feeding (breast milk vs. formula), diet, and age. Microbiota diversity decreases with aging and some dietary choices and other factors.

Gut Microbiota and Disease

Factors influencing Gut Microbiota: Diet, drugs, age, genetics, pre-existing conditions, microbial diversity, lifestyle (e.g., smoking).
Mechanisms of Dysbiosis: High-fiber diets support diversity and outcompete pathogens to maintain a healthy microbiota. High-fat diets promote endotoxin absorption and inflammation dysregulating the healthy microbiota.
Pathogen-Induced Dysbiosis: Disruptions in the balance of commensal and pathogenic bacteria allow pathogens to proliferate.

Host-Pathogen Responses

Infection Conditions: Exposure, adhesion to surfaces, invasion, growth, spread, and tissue/systemic damage.
Virulence Factors:
- Adherence: Molecules like adhesins, pili, fimbriae, capsules for attachment to host cells.
  - Pili: Used in conjugation and adhesion .
- Invasion: Enzymes (hyaluronidase, coagulase, streptokinase) for breaking down tissue barriers.
- Toxicity: Exotoxins (diphtheria toxin, botulinum toxin, tetanus toxin, cholera toxin) or endotoxins for damaging tissues.
- Immune Evasion: Anti-phagocytic proteins, immune inhibitors, and secretion systems.
- Intracellular Avoidance: Bacteria can survive and multiply inside host cells. This can involve resisting digestion, preventing lysosome fusion, exiting the phagosome etc.
Infection vs. Bacteremia vs. Septicemia:
- Infection: Presence of a microorganism.
- Bacteremia: Bacteria in the bloodstream, often transient and not necessarily harmful.
- Septicemia: Systemic infection in the bloodstream, intense immune response to bacteria.
Virulence and LD50/ID50:
- Virulence: Severity of disease by a pathogen.
- LD50: Lethal dose (kills 50% of test animals).
- ID50: Infectious dose (infects 50% of test animals)
Cytotoxins, Endotoxins, Exotoxins, Hemotoxins:
- Cytotoxins: Cell-killing agents
- Exotoxins: Secreted protein toxins (diphtheria, botulinum, cholera).
- Endotoxins: (Lipid component of Gram-negative cell walls).
- Hemotoxins: Affect red blood cells.
- E. coli Toxins:
  - Labile toxin causes watery diarrhea.
  - Shiga-like toxin causes bloody diarrhea .
Virulence mechanisms Specific examples of toxins: Toxins like diphtheria, botulinum, tetanus, cholera, cytolytic toxins (hemolysins), and endotoxins cause specific tissue damage by interfering with cellular mechanisms or by triggering immune responses.

Bacteria

Bacterial Cell Morphologies: Rods (bacilli), spheres (cocci), spirals (spirilla/spirochetes).
Glycocalyx: Capsule or slime layer, for protection, adherence, and biofilm formation.
Cell Walls: Different structures between Gram-positive and Gram-negative bacteria. Gram positive contains a thick layer of peptidoglycan and stains purple. Gram negative has a thin layer of peptidoglycan encased in 2 membranes and stains pink. Acid-fast bacteria have a waxy outer layer making them resistant to stains.
Cytoplasmic Membrane: Permeability barrier, protein anchor, proton motive force generation (energy storage).
Cytoskeleton: MreB (elongation), FtsZ (division), crescentin (shape).
Nucleoid and Ribosomes: Nucleoid houses bacterial chromosome (no membrane), ribosomes synthesize proteins.
Endospores: Dormant forms for survival under harsh conditions .
Sporulation: Complex process creating an endospore, for bacterial survival .
Flagella, Fimbriae, Pili: Used for mobility (flagella) and adhesion/gene transfer (fimbriae/pili).
Bacterial Locomotion: Run (CCW flagellar rotation) and tumble (CW).
Unique Bacterial Structures: Peptidoglycan cell wall, endospores, single chromosome, flagella, fimbriae, pili.
Chemotaxis: Bacteria move in response to chemical gradients by changing flagellar rotation.

Archaea

Archaea as a Separate Domain: Distinctive rRNA sequences, different metabolic pathways, and unique cell wall structures separate archaea from bacteria.
Archaeal Cell Structures: similar to bacteria in basic shapes and functions, but use different molecules for cell wall and lipids.
Cell Walls: Composed of pseudomurein or other unique polysaccharides, different from peptidoglycan.
Plasma Membranes: Ether-linked membrane lipids with isoprene chains (more stable). Can form lipid bilayer or monolayer.
Cytoskeleton: TubZ, crenactin, ESCRT.
Unique Archaeal Structures/Pathways: Hami (attachment), archaella (movement with ATP).

Viruses

Viral Structure: Nucleic acid (DNA or RNA), protein capsid, some have an envelope.
Bacteriophages, Plant Viruses, Animal Viruses: Differences in host range, entry mechanisms, and replication cycles.
Lytic and Lysogenic Cycles: Lytic cycle results in phage release, lysogenic cycle results in phage incorporation into host's chromosomes.
Bacterial Defense Mechanisms: Genetic resistance, restriction enzymes, CRISPR-Cas.
Animal Virus Entry: Endocytosis, receptor-mediated endocytosis, and membrane fusion.
Animal Virus Replication: Lytic or lysogenic cycle (DNA or RNA polymerase, transcription of viral mRNA, production of new viral particles, release by budding or cell lysis).
Retroviruses: Use reverse transcriptase.
Latent Viruses: Integrate into host's genome, remain inactive until environmental cues trigger replication.

Microbial Metabolism

Nutrient Transport: Passive/active transport, ABC transporters, siderophores, periplasmic binding proteins for uptake.
Catabolism vs. Anabolism:
- Catabolism: Breaking down molecules, releasing energy.
- Anabolism: Building up molecules, requiring energy.
Oxidation-Reduction: Vital for energy transfer in metabolism.
Substrate-Level vs. Oxidative Phosphorylation:
- Substrate-level: Direct ATP generation.
- Oxidative: ATP generation driven by electron transport chain.
Fermentation: Partial breakdown without electron transfer to inorganic acceptors (does not require oxygen) – results in lesser ATP byproducts of different organic compounds.
Aerobic vs. Anaerobic Respiration: Use oxygen or other electron acceptors for energy production.
ATP, NAD+, etc.: Energy carriers for metabolic processes.

Microbial Growth

Binary Fission: Bacterial cell division.
Batch vs. Continuous Culture: Batch culture has a limited nutrient supply. Continuous culture maintains a steady state.
Growth Phases: Lag, log, stationary, death.
Sessile vs. Planktonic Growth: Sessile bacteria attach to surfaces, planktonic bacteria remain free in solution.
Biofilms vs. Cell Mats: Biofilms are surface-attached communities; cell mats are multilayered.
Temperature Adaptations: Microbes adapt to temperature by altering their membrane fluidity, enzyme structure, or by producing heat-shock proteins.
pH Adaptations: Microbes adjust their internal pH based on the external environment.
Oxygen Requirements: Microbes have different oxygen needs including: obligate aerobes, obligate anaerobes, facultative anaerobes, aerotolerant anaerobes, microaerophiles.
Oxidation and ROS: Oxygen can be toxic to some microbes causing oxidative stress and/or damage.
Salinity and Osmotic pressure requirements: microbes have specific needs depending on salt and water in their environments
Bacterial growth: Adapt to different environments including temperature, pH, and oxygen concentrations.

Microbial Regulatory Systems

Quorum Sensing: Cell-to-cell communication in bacteria based on cell density.
Autoinducers: Molecules used in quorum sensing.
Quorum sensing in gram-positive and gram-negative bacteria: The mechanisms of communication difference.
Quorum Quenching: Methods to interfere with bacteria's ability to communicate.
Spatial Organization: MreB, FtsZ, Crescentin, and other proteins that play a role in cell division, maintenance of cellular shape, and localization.
Cell Polarity: Spatial localization of proteins and cellular structures.
Negative vs Positive Gene Regulation: How regulatory proteins either suppress or promote bacterial gene expression.
Operons: Groups of genes transcribed together.
Two-Component Systems: Sensory systems in bacteria.
Chemotaxis in E. coli: How bacteria respond to chemical gradients using proteins such as Che proteins.
Stringent Response: Mechanism to cope with environmental changes, slowing growth to preserve resources.
Global Response Networks and Regulons: Networks that coordinate gene expression in response to stresses.

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Description

This quiz explores key concepts in microbial genetics, focusing on mechanisms of genetic transfer in bacteria as well as the role of the microbiome in human health. It covers topics such as sexual and asexual reproduction, transduction, transformation, and immune defense roles of epithelial cells. Deepen your understanding of how microorganisms interact with their hosts and each other.