Indigenous Microbiota Quiz
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Questions and Answers

What is the typical microbial population density in the colon?

  • 10e3 bacteria/ml
  • 10e10 to 10e11 bacteria/ml (correct)
  • 10e1 bacteria/ml
  • 10e7 bacteria/ml

    • In what area of the body is the mucociliary escalator found, which helps to protect against microbial infections?

  • Skin
  • Oral cavity
  • Larynx and below (correct)
  • Conjunctiva

    • Which of the following is a common inhabitant of the skin microbiota?

  • Streptococcus pneumoniae
  • Bifidobacterium
  • Clostridium perfringens
  • Staphylococcus epidermidis (correct)
  • Bacteroides

    • Which of the following is NOT a factor determining the nature of microbiota at a particular site?

    <p>Temperature outside the body (A)</p> Signup and view all the answers

    What is the primary type of bacteria found in the vagina during childbearing years?

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

    What is the term used to describe a relationship between two species where one benefits and the other is neither helped nor harmed?

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

    What is the primary source of microbiota for a newborn infant?

    <p>All of the above (E)</p> Signup and view all the answers

    What is the relationship between the microbiota and the host known as?

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

    Which of the following bacteria is a common inhabitant of the nasopharynx?

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

    The presence of which bacteria in the human gut is associated with healthy digestion in infants?

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

    What is the purpose of the 'limited PCR amplification' step in next-generation sequencing?

    <p>To create multiple copies of the template DNA for sequencing. (D)</p> Signup and view all the answers

    What is the significance of the 'exclusionary effect' mentioned in the context of the beneficial effects of the microbiome?

    <p>The microbiome prevents the growth of harmful bacteria in the gut. (B)</p> Signup and view all the answers

    What is the main benefit of the 'multiplexed approach' in next-generation sequencing?

    <p>It reduces the cost of sequencing per sample. (A)</p> Signup and view all the answers

    How do the 'capture oligonucleotides' contribute to the cluster formation process in Illumina sequencing?

    <p>They bind to specific sequences in the template DNA, immobilizing it on the flow cell. (A)</p> Signup and view all the answers

    What is the purpose of the '3’-protection' step in cluster generation?

    <p>To ensure that the 3' end of the DNA strand can be sequenced without interference. (A)</p> Signup and view all the answers

    What is the significance of comparing the sequences obtained from next-generation sequencing with sequences from phenotypically validated isolates?

    <p>To identify the specific strains of bacteria present in a sample. (B), To understand the phylogeny (evolutionary relationships) and taxonomy (classification) of the microbes (C)</p> Signup and view all the answers

    Which of the following is NOT a benefit of using next-generation sequencing to study the microbiome?

    <p>The ability to isolate and purify specific microbial species for further study. (A)</p> Signup and view all the answers

    What is the most labor-intensive part of the next-generation sequencing process?

    <p>Data analysis. (B)</p> Signup and view all the answers

    What are the main roles of the microbiome in the human body?

    <p>All of the above. (D)</p> Signup and view all the answers

    Which of the following is NOT a factor that determines the nature of microbiota at a particular site?

    <p>Genetic background of the host (B)</p> Signup and view all the answers

    Which of the following statements accurately describes the relationship between Staphylococcus epidermidis and the host in the context of the skin microbiota?

    <p>It is a commensal relationship, where <em>S. epidermidis</em> benefits and the host is unharmed. (A)</p> Signup and view all the answers

    In the process of next-generation sequencing, what is the main purpose of adding adaptors to the library during sample preparation?

    <p>To facilitate the capture of DNA fragments onto the flow cell. (B)</p> Signup and view all the answers

    Which of the following is NOT a characteristic of the 'bridge amplification' step during Illumina sequencing?

    <p>Linearization of DNA fragments to prevent further branching. (B)</p> Signup and view all the answers

    The statement 'Microbiota: colonize (----> multiply ----->) transmission' suggests which of the following concepts?

    <p>The microbiota can be transmitted between individuals and generations. (C)</p> Signup and view all the answers

    In the context of the microbiome, what is the significance of comparing sequences obtained from next-generation sequencing with sequences from phenotypically validated isolates?

    <p>To establish the taxonomic relationships between different microbes. (D)</p> Signup and view all the answers

    Which of the following statements accurately describes the role of the mucociliary escalator in the respiratory tract?

    <p>It helps to prevent the colonization and growth of microbes in the lower respiratory tract. (A)</p> Signup and view all the answers

    Which of the following groups of bacteria typically dominates the vaginal microbiota during childbearing years?

    <p>Lactobacillus and anaerobic GNRs (B)</p> Signup and view all the answers

    Which of the following is a potential consequence of an imbalance in the gut microbiota?

    <p>Increased susceptibility to infections. (C)</p> Signup and view all the answers

    What is the main advantage of using a 'multiplexed approach' in next-generation sequencing of the microbiome?

    <p>It reduces the cost of sequencing per sample. (B)</p> Signup and view all the answers

    What is the primary role of the exclusionary effect in the context of the microbiome?

    <p>Preventing the establishment of harmful microorganisms (D)</p> Signup and view all the answers

    What is the initial step in the next-generation sequencing process?

    <p>Extraction of template (D)</p> Signup and view all the answers

    During bridge amplification in Illumina sequencing, what do the templates hybridize to?

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

    What is a significant advantage of using a multiplexed approach in sequencing?

    <p>Reducing the cost per sample analyzed (A)</p> Signup and view all the answers

    What is the final outcome of repeated denaturation and amplification in cluster generation?

    <p>Creation of dense clusters of DNA molecules (A)</p> Signup and view all the answers

    What does the term 'reverse strand cleavage' refer to in sequencing?

    <p>Cleaving the reverse strand to allow sequencing of the forward strand (C)</p> Signup and view all the answers

    Which of the following best describes the function of the flow cell in next-generation sequencing?

    <p>Enabling the immobilization of DNA clusters for sequencing (D)</p> Signup and view all the answers

    Why is there a need for substantial effort in processing sequencing data?

    <p>To analyze data for quality and accuracy (A)</p> Signup and view all the answers

    What is the importance of hybridizing the sequencing primer to the adapter sequence?

    <p>To initiate the sequencing reaction (B)</p> Signup and view all the answers

    What does the term 'deconvolute polymicrobial samples' refer to?

    <p>Separating the components of mixed microbial populations (A)</p> Signup and view all the answers

    Which of the following accurately describes the relationship between the human host and the microbiota in the nasal cavity?

    <p>A complex and dynamic interaction, where both beneficial and potentially harmful relationships exist. (D)</p> Signup and view all the answers

    Which of the following is NOT a typical inhabitant of the mouth microbiota?

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

    Which of these factors directly influences the composition of the microbiota at different sites in the body?

    <p>All of the above (D)</p> Signup and view all the answers

    Which of the following statements correctly describes the microbiota in the vagina during childbearing years?

    <p>Dominated by Lactobacillus species, contributing to a low pH environment. (D)</p> Signup and view all the answers

    How does the mucociliary escalator contribute to the maintenance of a healthy respiratory system?

    <p>It helps trap and remove pathogens from the respiratory tract. (C)</p> Signup and view all the answers

    Which of the following is a potential consequence of a disruption in the balance of the gut microbiota?

    <p>All of the above (D)</p> Signup and view all the answers

    The term 'carrier state' in relation to microbiota refers to:

    <p>The presence of a particular microbe in a person without causing any illness. (B)</p> Signup and view all the answers

    Which of the following is a factor that contributes to the development of opportunistic infections by microbiota?

    <p>All of the above (D)</p> Signup and view all the answers

    What is the significance of Bifidobacterium in the gut microbiota of human infants?

    <p>It is a strong competitor against pathogenic bacteria in the infant gut. (A), It plays a role in the digestion and absorption of lactose. (C)</p> Signup and view all the answers

    Which of the following statements accurately describes the role of the skin microbiota in protecting against pathogens?

    <p>All of the above. (D)</p> Signup and view all the answers

    Study Notes

    Indigenous Microbiota

    • Microbiota, sometimes called flora, colonize and multiply, potentially transmitted.
    • Symbiosis is a biological interaction between species; it may or may not benefit both.
    • Commensalism benefits one species and doesn't harm the other.
    • Mutualism benefits both species.
    • Parasitism benefits one species (parasite) at the expense of the other (host).
    • Microbiota can exist as residents, transients, or in a carrier state.
    • A fetus is initially sterile, gaining microbiota from the birth canal, skin, respiratory system of personnel, and environment.
    • Neonates initially have a wide range of microbiota, narrowing based on colonization ability, then aligning with age-group microbiota of environment.
    • Local physiology, microbial attributes, and microbial interactions (competition) influence microbiota composition.

    Microbiota at Different Sites

    • Microbiota are present in blood, tissues, and body fluids.
    • Skin microbiota includes Staphylococcus epidermidis, other Staphylococcus species, Propionibacterium, and diphtheroids.
    • Conjunctiva microbiota includes S. epidermidis and non-pathogenic Corynebacteria.
    • Mouth microbiota contains ~108 organisms/mL saliva; Streptococcus mutans adheres to teeth; Neisseria and Moraxella; strict anaerobes and microaerophilic microbes in gingival crevices are present.
    • Stomach and small intestine have sparse microbiota.
    • Colon microbiota contains ~1010 to 1011 bacteria/mL; feces are ~25% bacteria by weight; 90% are anaerobes (Bacteroides, Fusobacterium, Clostridium perfringens); 10% are facultative (E. coli, other Enterobacteriaceae, enterococci, yeasts such as Candida).
    • Dietary and age factors alter microbiota populations. Bifidobacterium is common in infants.
    • Respiratory tract microbiota varies. Nares are similar to skin and include S. aureus. Nasopharynx is similar to mouth but contains Streptococcus pneumoniae, Neisseria meningitidis, Haemophilus influenzae, while larynx, lungs, and middle ear are generally protected by the mucociliary escalator.
    • Urinary tract microbiota is minimal, mostly in the first cm of the urethra, and generally sterile in healthy individuals above that.
    • Vaginal microbiota varies. Before puberty and after menopause microbiota is mixed and nonspecific: from skin, colon, and perineum. In childbearing years, there are Lactobacillus, anaerobic gram-negative rods, gram-positive cocci, Gardnerella, Mycoplasma, and Ureaplasma.

    Role of Microbiota in Disease

    • Microbiota can be opportunistic pathogens due to quantity and genetic attributes.

    Beneficial Effects of Microbiota

    • Microbiota can prime the immune system.
    • Antibiotic treatments can have an exclusionary effect on microbiota.
    • Microbiota play roles in digestion, nutrient absorption, and vitamin K synthesis; normal function of numerous organs and systems.

    Next-Generation Sequencing

    • Extracting DNA template.
    • Limited PCR amplification of 16S rRNA.
    • Preparing a library with adaptors for sequencing and barcodes.
    • Immobilizing single DNA templates on a flow cell via capture oligonucleotides.
    • Performing isothermal bridge amplification for cluster formation.
    • Sequencing clusters by synthesis using reversible terminators.
    • Deconvoluting polymicrobial samples to identify constituent members of microbiome.
    • Comparing against known pathogens to establish identification and relatedness.
    • Clusters are generated on the Illumina platform through immobilization, 3'-extension, bridge amplification, linearization, 3' protection (blocking), and hybridization of sequencing primers.

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    Description

    Test your knowledge on indigenous microbiota and their interactions. This quiz covers key concepts like symbiosis, colonization, and the diversity of microbiota across different body sites. Explore how microbiota develop from a sterile state to a complex ecosystem.

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