Microbial Genetics and Genomics Quiz
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Questions and Answers

What is the primary advantage of sexual reproduction compared to asexual reproduction?

  • Generation of genetic diversity (correct)
  • No requirement for a partner
  • Identical genetic makeup
  • Faster production of offspring
  • Which statement best describes horizontal transmission of genetic material?

  • Transfer of genetic material between unrelated species (correct)
  • Transfer of genetic material from parent to offspring
  • Replication of genetic material within the same organism
  • Integration of environmental DNA into the bacterial genome
  • What is the role of the pilus in bacterial transformation?

  • It binds and transports naked DNA into the cell (correct)
  • It protects the ssDNA from nucleases
  • It facilitates the replication of plasmids
  • It degrades the double stranded DNA
  • In generalized transduction, what limits the amount of DNA transferred between bacteria?

    <p>The capacity of the phage head (A)</p> Signup and view all the answers

    What is a significant downfall of asexual reproduction in terms of genetic diversity?

    <p>It leads to the accumulation of harmful mutations (B)</p> Signup and view all the answers

    What role do alveolar macrophages have in the alveoli?

    <p>They act as a first line of defense by detecting pathogens. (C)</p> Signup and view all the answers

    Which factor primarily causes changes in the vaginal microbiota in women?

    <p>Hormonal fluctuations related to the menstrual cycle. (A)</p> Signup and view all the answers

    Which microbial interaction is critical for maintaining the skin microbiome's balance?

    <p>Competition for nutrients between bacteria. (B)</p> Signup and view all the answers

    What is the primary reason that the colon is more diverse in microbial species compared to the stomach?

    <p>Higher pH levels that favor more bacterial growth. (C)</p> Signup and view all the answers

    How do commensal bacteria in the gut help in developing the local immune response?

    <p>By stimulating the activation of naive T cells. (B)</p> Signup and view all the answers

    What distinguishes specialized transduction from generalized transduction?

    <p>Specialized transduction incorporates viral DNA directly into the bacterial chromosome. (B)</p> Signup and view all the answers

    Why do F- cells lack the ability to form a sex pilus?

    <p>They lack the plasmid that encodes for the formation of the sex pilus. (A)</p> Signup and view all the answers

    What role do chromosomal islands play in bacterial evolution?

    <p>They contribute to increased bacterial fitness for specific environments and are of foreign origin. (B)</p> Signup and view all the answers

    Which statement correctly describes dysbiosis?

    <p>Dysbiosis leads to an imbalance with pathogen overgrowth causing various health issues. (B)</p> Signup and view all the answers

    What distinguishes core genome from pan genome in bacterial species?

    <p>Pan genome includes the core genome plus genes unique to certain strains. (A)</p> Signup and view all the answers

    What function does a high-fiber diet serve in maintaining gut health?

    <p>It diversifies the microbiome by supporting beneficial bacteria. (C)</p> Signup and view all the answers

    Which of the following factors can contribute to the development of dysbiosis?

    <p>Genetics. (C)</p> Signup and view all the answers

    How do pathogens disrupt the balance of gut microbiota?

    <p>By outcompeting commensal bacteria for resources. (D)</p> Signup and view all the answers

    Which statement accurately describes short-chain fatty acids (SCFA)?

    <p>They play a role in regulating inflammation and gut health. (D)</p> Signup and view all the answers

    What is one limitation of using mouse models to study human gut microbiota?

    <p>Many human microbial taxa do not colonize the mouse gut. (B)</p> Signup and view all the answers

    What is the role of adhesins in bacterial infection?

    <p>To chemically recognize and bind to host cell adhesion receptors (A)</p> Signup and view all the answers

    Which enzyme is involved in facilitating the spread of bacteria through breaking down clots?

    <p>Streptokinase (A)</p> Signup and view all the answers

    What mechanism do bacterial capsules primarily utilize to evade the immune system?

    <p>Hiding the Fc antibody from phagocyte recognition (B)</p> Signup and view all the answers

    What is the primary purpose of Type III secretion systems in bacteria?

    <p>To inject bacterial proteins directly into host cells (B)</p> Signup and view all the answers

    Which of the following statements about prebiotics is most accurate?

    <p>They provide nutrition for gut bacteria to potentially enhance helpful bacterial growth. (B)</p> Signup and view all the answers

    What is the primary role of the capsule in bacterial pathogens?

    <p>Adhesion and biofilm formation (D)</p> Signup and view all the answers

    Which characteristic is NOT associated with gram-negative bacteria?

    <p>Presence of mycolic acid (D)</p> Signup and view all the answers

    How does the Shiga-like toxin affect bacterial pathogenicity compared to the labile toxin?

    <p>It inhibits protein synthesis, leading to cell death. (B)</p> Signup and view all the answers

    Which of the following statements regarding the bacterial plasma membrane is accurate?

    <p>It generates a proton motive force for ATP synthesis. (C)</p> Signup and view all the answers

    What is the main difference in cell wall structure between gram-positive and gram-negative bacteria?

    <p>Gram-positive bacteria have teichoic acids present. (B)</p> Signup and view all the answers

    Which protein is responsible for maintaining the diameter of bacterial cells during cell division?

    <p>FtsZ (C)</p> Signup and view all the answers

    What defines the feature of endospores in gram-positive bacteria?

    <p>They are highly resistant to extreme conditions. (A)</p> Signup and view all the answers

    What is one mechanism used by pathogens to resist digestion inside phagocytes after phagocytosis?

    <p>They prevent fusion of the lysosome and phagosome. (C)</p> Signup and view all the answers

    What characterizes septicemia compared to bacteremia?

    <p>Septicemia involves a systemic inflammatory response. (D)</p> Signup and view all the answers

    How does the botulinum toxin affect muscle contraction?

    <p>It destroys SNARE proteins preventing vesicle fusion. (B)</p> Signup and view all the answers

    What defines virulence in the context of a pathogen’s ability to cause disease?

    <p>It combines infectivity, severity, and genetic factors. (B)</p> Signup and view all the answers

    What distinguishes exotoxins from endotoxins?

    <p>Exotoxins can be denatured by heat, while endotoxins cannot. (C)</p> Signup and view all the answers

    What is the primary action of cholera toxin once inside host cells?

    <p>To disrupt ion channels and increase cAMP levels. (A)</p> Signup and view all the answers

    Why is LD50 an important measure of a pathogen’s virulence?

    <p>It represents the dosage required to kill 50% of a population. (D)</p> Signup and view all the answers

    Which statement about cytotoxins is true?

    <p>Cytotoxins kill host cells by disrupting their membrane integrity. (C)</p> Signup and view all the answers

    Which of the following statements accurately describes a benefit of sexual reproduction?

    <p>It generates genetic diversity through chromosomal crossover. (B)</p> Signup and view all the answers

    What is the main purpose of horizontal transmission of genetic material in bacteria?

    <p>To enable genetic diversity among unrelated species. (B)</p> Signup and view all the answers

    Which mechanism is least effective for introducing genetic diversity in bacteria?

    <p>Transformation of naked DNA from the environment. (A)</p> Signup and view all the answers

    Which of the following best describes generalized transduction?

    <p>It randomly incorporates any piece of the bacterial genome during virus infection. (A)</p> Signup and view all the answers

    What is a significant limitation of asexual reproduction in bacteria concerning genetic diversity?

    <p>It only passes down identical DNA with minimal mutation opportunities. (C)</p> Signup and view all the answers

    Which aspect distinguishes specialized transduction from generalized transduction?

    <p>Specialized transduction results in the transfer of specific bacterial genes. (C)</p> Signup and view all the answers

    What is the consequence of F+ to F- conjugation in bacterial cells?

    <p>The F- cell acquires the ability to form a conjugation pilus. (B)</p> Signup and view all the answers

    What is a primary mechanism by which chromosomal islands are believed to originate?

    <p>Incorporation through specialized transduction. (D)</p> Signup and view all the answers

    Which statement accurately reflects dysbiosis in the human microbiome?

    <p>Dysbiosis can lead to intestinal barrier damage and immune disorders. (B)</p> Signup and view all the answers

    What defines an Hfr strain in bacterial genetics?

    <p>It has a high frequency of recombination due to plasmid integration into the chromosome. (C)</p> Signup and view all the answers

    Which factor is crucial for a pathogen to successfully invade human tissues?

    <p>The pathogen needs to adhere to host cells effectively. (D)</p> Signup and view all the answers

    What role does hyaluronidase play in bacterial infection?

    <p>It breaks down barriers between cells to facilitate tissue invasion. (B)</p> Signup and view all the answers

    How does a high-fiber diet contribute to maintaining gut microbiota health?

    <p>It encourages microbial diversity and enhances gut motility. (C)</p> Signup and view all the answers

    How do capsules contribute to a bacterial pathogen's virulence?

    <p>By hiding bacteria from phagocytosis. (C)</p> Signup and view all the answers

    What role does the gut microbiota play in energy metabolism and obesity?

    <p>It metabolizes sugars into short-chain fatty acids, contributing to energy intake. (C)</p> Signup and view all the answers

    What is a major limitation of using mouse models to study human gut microbiota and diseases?

    <p>Many gut microbial taxa do not colonize the mouse gut, leading to bias. (C)</p> Signup and view all the answers

    Which secretion system is specifically designed to inject bacterial proteins directly into host cells?

    <p>Type III secretion system (B)</p> Signup and view all the answers

    What is a primary limitation of using carbohydrates as prebiotics in promoting gut health?

    <p>They may inadvertently feed harmful bacteria. (B)</p> Signup and view all the answers

    Which of the following factors is NOT associated with promoting a healthy gut microbiota?

    <p>Consistent consumption of high-fat foods. (A)</p> Signup and view all the answers

    Which short-chain fatty acid is primarily associated with anti-obesity effects?

    <p>Butyrate (C)</p> Signup and view all the answers

    What role does the mucus in the gastrointestinal tract play in the interaction with the microbiota?

    <p>It forms a barrier separating microbes from the epithelial cells. (C)</p> Signup and view all the answers

    Which factor is crucial in maintaining the weakly acidic environment of the vagina, thereby influencing its microbiota?

    <p>The fermentation of glycogen by resident bacteria. (D)</p> Signup and view all the answers

    What factor contributes to the increased risk of yeast infections in women following antibiotic treatment?

    <p>Reduction in lactic acid production by vaginal bacteria. (A)</p> Signup and view all the answers

    Which component in the skin microbiome is primarily responsible for suppressing the colonization of S. aureus?

    <p>Antimicrobial proteins produced by skin cells. (B)</p> Signup and view all the answers

    How does the gut microbiota influence the host's immune response?

    <p>By influencing the balance between tolerance and inflammation based on microbial antigens. (A)</p> Signup and view all the answers

    Which feature is characteristic of endospores formed by gram-positive bacteria?

    <p>They contain dipicolonic acid to stabilize DNA. (D)</p> Signup and view all the answers

    How do exotoxins and endotoxins primarily differ in their effects on the host?

    <p>Endotoxins trigger immune responses, while exotoxins typically cause cell death. (B)</p> Signup and view all the answers

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

    <p>Enhancing pathogenicity by aiding in adhesion. (D)</p> Signup and view all the answers

    Which statement accurately describes the structure of gram-negative bacteria cell walls?

    <p>They have two membranes with a thin peptidoglycan layer between. (D)</p> Signup and view all the answers

    Which component of the bacterial plasma membrane is primarily involved in generating a proton motive force?

    <p>ATP synthases. (A)</p> Signup and view all the answers

    What role does the protein MreB play in bacterial cell morphology?

    <p>It maintains the cell's diameter and shape. (C)</p> Signup and view all the answers

    Which process describes the mechanism of action of the labile toxin produced by E. coli?

    <p>Activation of cyclic AMP synthesis causing fluid loss. (C)</p> Signup and view all the answers

    What is a characteristic mechanism by which a pathogen can evade immune response after entering a phagosome?

    <p>It can remain within the phagosome and prevent lysosome fusion. (A)</p> Signup and view all the answers

    How does the cholera toxin affect ion transport in host cells?

    <p>By increasing cAMP levels, leading to excessive secretion of ions. (A)</p> Signup and view all the answers

    What distinguishes bacteremia from septicemia?

    <p>Septicemia involves a systemic immune response that can lead to shock. (C)</p> Signup and view all the answers

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

    <p>It blocks protein synthesis, leading to tissue death. (B)</p> Signup and view all the answers

    Which term describes the ability of a pathogen to cause disease severity and not merely infection?

    <p>Virulence (D)</p> Signup and view all the answers

    Which statement correctly describes the function of exotoxins compared to endotoxins?

    <p>Exotoxins are secreted proteins that can be toxic, while endotoxins are components of the bacterial cell wall. (B)</p> Signup and view all the answers

    Which mechanism do botulinum and tetanus toxins share despite their opposite effects?

    <p>They both disrupt normal neurotransmitter transport. (B)</p> Signup and view all the answers

    What does the term LD50 refer to in the context of pathogen virulence?

    <p>The lethal dose required to kill 50% of a test population. (B)</p> Signup and view all the answers

    Flashcards

    Sexual Reproduction

    Reproduction where two organisms combine their DNA to create offspring with varied genetic material.

    Asexual Reproduction

    Reproduction where one organism creates an offspring with identical genetic material.

    Horizontal Gene Transfer

    The transfer of genetic material between different organisms, without being passed down through generations.

    Transformation

    A horizontal gene transfer method where bacteria take up free DNA from the environment.

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    Transduction

    A horizontal gene transfer method where DNA is transferred between bacteria by a virus.

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    Specialized Transduction

    A type of viral-mediated gene transfer where a specific piece of bacterial DNA is packaged within a phage and transferred to a new bacterial cell. This transfer often depends on the phage's integration site in the bacterial chromosome.

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    Conjugation Pilus

    A protein appendage, also known as the F pilus, that extends from a bacterial cell and allows for direct contact with another bacterium, facilitating the transfer of genetic material during conjugation.

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    Hfr Strain

    A bacterial cell where the F plasmid has integrated into the bacterial chromosome. This integration allows for the transfer of chromosomal genes during conjugation, leading to high frequency of recombination.

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    Generalized Transduction

    A type of transduction where random bacterial DNA fragments are packaged within phage particles and transferred to new bacterial cells. This occurs when a phage accidentally packages bacterial DNA instead of its own.

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    Chromosomal Island

    A cluster of genes in a bacterial chromosome that have a distinct origin from the rest of the genome. These islands often encode specialized functions like pathogenicity or antibiotic resistance.

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    Mucociliary Escalator

    A defense mechanism in the respiratory system that sweeps foreign particles, including microbes, out of the lungs and back through the mouth.

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    Alveolar Defense Mechanisms

    The epithelial cells of alveoli have various ways to defend themselves against microbes, including surfactant with antimicrobial properties, mucus secretion, alveolar macrophages, and dendritic cells.

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    Urogenital Tract Microbiota

    The urogenital tract has a specific microbial community that varies depending on location and factors like pH and hormones. The vagina, for example, is usually acidic due to lactic acid produced by bacteria, while the bladder and kidneys are typically sterile.

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    Skin Microhabitat

    The skin microbiome is influenced by its diverse microhabitats, including dry, acidic epidermis and oily, anaerobic dermis. This environment favors gram-positive bacteria due to their resistance to salt and dryness.

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    Gut Microbiota Benefits

    The gut microbiota plays crucial roles in digestion, immune system development, and overall health. It aids in breaking down complex carbohydrates, producing short-chain fatty acids, and preventing pathogens from colonizing.

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    What are the conditions for infection?

    For an infection to occur, a pathogen must be exposed to a host, adhere to the host's surface, invade through the epithelial barrier, grow and multiply, and cause damage to tissues.

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    Adhesins

    Glycoproteins or lipoproteins on a bacterial cell wall that recognize and bind to host cell receptors, enabling attachment.

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    Capsule

    A polysaccharide coat that surrounds bacteria, preventing phagocytosis by hiding them from immune cells.

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    Hyaluronidase

    An enzyme produced by bacteria that breaks down hyaluronic acid, a substance that holds cells together, facilitating tissue invasion.

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    Type III Secretion System

    A virulence factor that directly injects bacterial proteins from the bacterial cytoplasm into the host cell upon contact.

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    Gut Microbiome Diversity

    The variety of different types of bacteria living in the gut. A diverse microbiome is generally healthier, as it promotes competition and prevents harmful bacteria from dominating.

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    Dysbiosis

    An imbalance in the gut microbiota, where the proportion of harmful bacteria increases, leading to potential health problems.

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    How does fiber strengthen gut health?

    Fiber acts as fuel for beneficial bacteria, promoting their growth and outcompeting harmful bacteria. It also increases gut motility, preventing harmful bacteria from sticking to the gut wall and causing infections. Additionally, it stimulates the production of SCFAs, which promote immune system health and reduce inflammation.

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    What are SCFAs? How do they impact health?

    Short-chain fatty acids (SCFAs) are produced by gut bacteria when they ferment fiber. They have various health benefits, including promoting satiety, reducing inflammation, strengthening the gut barrier, and enhancing immune function.

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    What are probiotics?

    Living microorganisms, like bacteria or yeast, that are intentionally ingested to improve gut health by restoring a healthy balance of bacteria.

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    Intracellular Immune Avoidance

    Pathogens that have been engulfed by phagocytes can avoid digestion and continue to thrive within the host cell. This involves various strategies like preventing lysosome fusion, escaping the phagosome, or mimicking host signals to disrupt immune responses.

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    Inclusion Bodies

    A strategy used by pathogens to avoid digestion inside a phagosome. They resist breakdown, multiply, and form visible aggregates within the host cell.

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    Infection vs. Disease

    Infection refers to the presence and growth of microbes in a host, whether they are causing symptoms or not. Disease occurs when the infection leads to noticeable symptoms and harm.

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    Bacteremia vs. Septicemia

    Bacteremia is the presence of bacteria in the bloodstream, often transient and harmless. Septicemia is a systemic blood infection with a massive immune response, leading to potentially fatal septic shock.

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    Virulence

    The severity of the disease caused by a pathogen. It encompasses how easily a pathogen can cause infection (infectivity), the severity of the disease (virulence) and the genetic makeup.

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    LD50

    The lethal dose 50. The amount of a pathogen needed to kill 50% of a test group of animals.

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    Exotoxin vs. Endotoxin

    Exotoxins are proteins secreted by bacteria, often highly toxic. Endotoxins are components of bacterial cell walls, mainly LPS in gram-negative bacteria. Both can cause harm but through different mechanisms.

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    Cytotoxin

    A type of exotoxin that targets and destroys cells. Often acts by disrupting cell membranes, leading to cell death.

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    Bacterial Shapes

    Bacteria come in three main shapes: rods (bacilli), spheres (cocci), and spiral (spirochetes).

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    Glycocalyx Function

    The glycocalyx, a capsule or slime layer, helps bacteria stick to surfaces, resist phagocytosis, and survive dehydration.

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    Gram Staining - Key Difference

    Gram-positive bacteria have a thick peptidoglycan layer that retains crystal violet dye, appearing purple. Gram-negative bacteria have a thin peptidoglycan layer and an outer membrane, retaining safranin dye, appearing pink.

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    Acid-Fast Bacteria

    Acid-fast bacteria have a waxy outer coating of mycolic acid, making them resistant to staining and harder for the immune system to recognize.

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    Bacterial Plasma Membrane

    The bacterial plasma membrane acts as a barrier, anchors proteins, and generates energy through ATP synthases. It also contains lipids that help bacteria adapt to different temperatures.

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    Bacterial Cytoskeleton

    The bacterial cytoskeleton, composed of proteins like FtsZ, MreB, and Crescentin, helps maintain cell shape, organize cell division, and move molecules throughout the cell.

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    Endospores: Bacterial Survival

    Endospores are dormant, resistant structures formed by some bacteria when conditions are unfavorable. They contain DNA, dipicolonic acid, and other protective layers, allowing them to survive harsh environments.

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    Vertical Transmission

    Passing genetic material from one generation to the next, like a mother cell to a daughter cell.

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    Horizontal Transmission

    Transferring small pieces of DNA between different organisms, even distantly related ones.

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    Conjugation

    A type of horizontal gene transfer where bacteria share genetic material directly through a pilus.

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    Specialized Transduction: How it Works

    A type of viral-mediated gene transfer where a specific piece of bacterial DNA is packaged within a phage and transferred to a new bacterial cell. This transfer often depends on the phage's integration site in the bacterial chromosome.

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    Conjugation: The Bacterial Sex

    The transfer of genetic material between bacteria through direct cell-cell contact using a conjugation pilus.

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    Hfr Strain: The Master Sharer

    A bacterial cell where the F plasmid has integrated into the bacterial chromosome. This integration allows for the transfer of chromosomal genes during conjugation, leading to high frequency of recombination.

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    Generalized Transduction: Random DNA Delivery

    A type of transduction where random bacterial DNA fragments are packaged within phage particles and transferred to new bacterial cells. This occurs when a phage accidentally packages bacterial DNA instead of its own.

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    Chromosomal Islands: The Foreign Guests

    A cluster of genes in a bacterial chromosome that have a distinct origin from the rest of the genome. These islands often encode specialized functions like pathogenicity or antibiotic resistance.

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    What are the conditions for an infection to occur?

    For an infection to develop, a pathogen must be exposed to a host, adhere to the host's surface, invade through the epithelial barrier, multiply and grow within the host, and cause damage to host tissues.

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    What are the benefits of commensal bacteria in the gut?

    Commensal bacteria in the gut play vital roles in human health, including digestion of complex carbohydrates, production of short-chain fatty acids that provide energy, preventing pathogenic bacteria from colonizing, and contributing to immune system development through tolerance and inflammation regulation.

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    How does gut microbiota composition change?

    The composition of gut microbiota evolves throughout life and is influenced by factors like diet, age, and physiology. For example, breastfed infants have different gut microbiota from formula-fed infants, and a high-fiber diet promotes diverse microbial communities.

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    What are the roles of gut microbiota in healthy people?

    Gut microbiota plays crucial roles in maintaining health and well-being. It acts as a source of energy by breaking down complex carbohydrates humans can't digest, forms a protective barrier against microbial invasion, assists in immune system development, and contributes to vitamin biosynthesis and digestion of chemical compounds.

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    What strengthens gut microbiota?

    A high-fiber diet with diverse fiber types promotes a healthy gut microbiome. It provides food for beneficial bacteria, increases gut motility, and stimulates production of beneficial short-chain fatty acids (SCFAs).

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    Dysbiosis: Gut Imbalance

    Dysbiosis refers to an imbalance in the gut microbiota, where the number of harmful bacteria increases relative to beneficial bacteria. This can lead to various health problems.

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    How do pathogens cause dysbiosis?

    Pathogens can disrupt the balance of the gut microbiota by outcompeting beneficial bacteria for resources and space. This can happen due to factors like antibiotic use, poor diet, and weakened immune system.

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    SCFA's role in obesity

    Short-chain fatty acids (SCFAs) produced by gut bacteria can influence obesity. Some SCFAs, like acetate, may promote obesity, while others, like butyrate, may have anti-obesity effects. The ratio of SCFAs can impact energy metabolism and inflammation.

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    Probiotics vs. Prebiotics

    Probiotics are live microorganisms, like bacteria, that are intentionally introduced into the gut to restore a healthy balance. Prebiotics are non-digestible fibers that act as food for beneficial bacteria, promoting their growth.

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    Biofilms

    A structured community of bacteria attached to a surface, often enclosed in a slimy matrix, providing a protective environment for bacteria.

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    Study Notes

    Microbial Genetics and Genomics

    • Sexual reproduction creates genetic diversity through chromosomal crossover between parents, but is slower.
    • Asexual reproduction (e.g., bacteria) is faster but doesn't generate diversity. Mutations are rare and random.
    • Vertical transmission: genetic material passed from a parent generation to the next.
    • Horizontal (lateral) transmission: genetic material transferred between different organisms (e.g., bacteria)
    • This transfer occurs through transformation, transduction, and conjugation. These mechanisms create genetic diversity in asexual bacteria.

    Transformation

    • Naked DNA is absorbed from the environment.
    • A pilus in the bacterial plasma membrane binds and pulls the DNA into the cell.
    • Double-stranded DNA becomes single-stranded, and one strand might be degraded.
    • The remaining single-stranded DNA integrates into the bacterial chromosome.
    • This process is not always efficient due to bacterial nucleases degrading the DNA.

    Transduction

    • Genes are transferred between bacterial cells via a virus (phage).
    • Generalized transduction: Random transfer of a piece of bacterial DNA.
    • Specialized transduction: Specific piece of bacterial DNA transferred. Phage has a preferred insertion site in the chromosome.
    • Bacteria must be alive for transduction to occur.

    Conjugation

    • Bacteria use a conjugation pilus (F pilus) for cell-cell contact to transfer genes.
    • The ability to make F pili is encoded on a plasmid. F+ cells have the plasmid, F- cells do not.
    • F+ to F- conjugation: F+ cell makes contact with F- cell, transfers a strand of the F plasmid by cutting it with a relaxosome and replicating the complementary strand in both. The recipient becomes F+.
    • Hfr (high frequency of recombination) strains: F plasmid integrates into the host chromosome. Genes nearest the integration site are transferred first.

    Generalized vs. Specialized Transduction

    • Generalized: A phage infects a bacterial cell, replicates, and accidentally packages bacterial DNA instead of phage DNA. This DNA can then be injected into another cell. There are many possible pieces of DNA that can be transferred.
    • Specialized: A phage infects a bacterial cell and integrates phage DNA into the host cell chromosome. Only specific genes near the integration site can be transferred.

    Consequences of Genetic Transfer in Bacteria

    • Transduction: The cholera toxin gene can be acquired by specialized transduction. It makes a non-pathogenic bacteria pathogenic.
    • Transformation: Less efficient in introducing genetic diversity since some DNA would get degraded and might be difficult to find sufficient donor environmental DNA to capture.
    • Conjugation: A highly efficient way of introducing genetic diversity with more possibilities.

    Pan and Core Genome

    • Core genome: Genes shared by all strains of a species or strain.
    • Pan genome: The set of all genes present in all strains; this includes the core genome plus additional genes specific to individual strains.

    Chromosomal Islands

    • Chromosomal islands: Clusters of genes involved in specialized functions such as pathogenicity.
    • They have a foreign origin (HGT) because they are not found in all strains and have unique nucleotide compositions and inverted repeats.

    Microbial Symbiosis with Humans

    • The human microbiome is diverse; most microbes are commensal and even beneficial to the host.
    • Symbiosis is a balanced and healthy relationship with microbiota
    • Dysbiosis: Disruption of the beneficial microbiota by pathogens and their products; these can trigger inflammation.

    Oral Cavity/Airways Microbiota

    • Saliva has antimicrobial components that help control microbes.
    • The upper respiratory tract has resident microbes; lower tract is usually sterile.
    • Mucociliary escalator helps clear microbes.

    Urogenital Tract Microbiota

    • Kidneys and bladder are typically sterile.
    • Vaginal acidity, lactic acid production inhibit many microbes (e.g., yeast). Microbiota composition influenced by hormonal changes.
    • Uncircumcised penis can have more anaerobic microbes.

    Skin Microbiota

    • Skin microbiome composition depends on moisture, pH, and oxygen levels.
    • Mostly gram-positive bacteria.
    • Antimicrobials produced by microbes can prevent the colonization of S. aureus (and likely other pathogens) to a lesser extent.

    Interaction Between Microbiota and Pathogens

    • Disturbance of the commensal microbiota can permit opportunistic pathogens to cause disease by outcompeting them for resources.
    • Antibiotics can disrupt microbiota composition.
    • Pathogen exposure, attachment to tissues, and invasion are key to infection and disease initiation.

    Gut Microbiota

    • Gut microbiota plays a crucial role in digestion, immunity, and overall health (e.g., vitamin K and digestion of chemicals).
    • Diversity of gut microbiota is influenced by factors like diet, age, and mode of birth.

    Gut Microbiota and Disease

    • Factors that influence gut dysbiosis: diet, drugs, age, genetics, infections, existing conditions, environmental factors.
    • Pathogens can upset the balance in microbiota, leading to dysbiosis and disease.
    • Inflammation requires innate immune cell activation, pathogen stimulation, and a host's response to environmental conditions.
    • Host gut microbiota can cause metabolic disorders; the ratio of Bacteroidetes/Firmicutes may influence SCFA production.

    Mice Models Limitations:

    • Transferring human microbiota to mice often lacks transfer of all human taxa and does not adequately represent human diversity.
    • Differences in anatomy and physiology limit the relevance to human conditions.

    Gut Microbiota and Obesity:

    • Microbiota contributes to energy harvesting; SCFA production influences host energy metabolism, and imbalances tilt toward pro- or anti-obesity properties.

    Probiotics vs Prebiotics

    • Probiotics are live microbes intended to restore gut microbiota balance but often not beneficial as they encounter numerous barriers.
    • Prebiotics are food components that promote microbial growth. But feeding harmful bacteria can be a limitation.

    Host-Pathogen Responses

    • Infection requires exposure, attachment, invasion, multiplication, spread, and host damage, with virulence factors such as adhesions and enzymes, avoiding or evading the host's response.

    Viral Replication

    • Lytic and lysogenic cycles differ in bacteriophages (lytic cycle is for phage DNA replication, lysogenic cycle involves integration of phage genome into bacterial DNA allowing for replication).

    Bacterial Defense

    • Bacteria have genetic resistance, restriction endonucleases, and CRISPR-Cas systems to defend against viruses.

    Animal Virus Entry & Replication

    • Animal viruses have three different entry mechanisms: receptor-mediated endocytosis for non-enveloped, membrane fusion for enveloped, and receptor-mediated endocytosis.

    Retroviruses and Latent Viruses

    • Retroviruses use reverse transcriptase. Latent viruses persist in host cells and can reactivate under certain conditions.

    Bacterial and Archaeal Cells

    • Comparing Bacteria and Archaea cells, their cell walls, membranes, and internal structures differ significantly; Bacteria have peptidoglycan cell walls and ester-linked membranes; Archaea have pseudomurein or protein sheaths and ether-linked membranes.

    Microbial Metabolism

    • Catabolism: Breaking down molecules for energy. Anabolism: Building molecules.
    • Oxidation-Reduction: Essential in metabolism for energy transfer.
    • Substrate-level phosphorylation and oxidative phosphorylation create ATP.
    • ATP, NAD+, and other electron carriers transfer energy in cells.
    • Autotrophs and Heterotrophs use different carbon sources. Phototrophs vs Chemotrophs use different energy sources; Organotrophs vs Lithotrophs use different electron sources.

    Microbial Growth and Biofilms

    • Binary fission: Bacterial cell division.
    • Continuous culture maintains a consistent growth phase.
    • Batch culture phases include lag, log, stationary, and death phases.
    • Biofilms are surface-attached communities, offer protection and survival.
    • Microbes need a variety of temperatures, pH and oxygen conditions. Adaptations include variations to temperature or pH.

    Microbial Regulatory Systems

    • Quorum sensing: Cell-to-cell communication using autoinducers.
    • Two-component systems: Detect environmental signals and regulate gene expression.
    • Operons: Cluster of genes regulated together.
    • Stringent response and stress responses are global regulatory mechanisms to maintain cell function in adverse conditions.
    • Persistence and dormancy traits increase bacteria survival to environmental conditions.

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    Test your knowledge on microbial genetics and genomics, focusing on reproduction methods, genetic diversity mechanisms, and specific processes such as transformation. This quiz covers essential concepts of how bacteria exchange genetic material, both vertically and horizontally. Challenge yourself to understand the complexities of microbial DNA transfer!

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