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

Flashcards

Priming Immune System

The activation of the body's defenses against pathogens.

Exclusionary Effect

A phenomenon where one treatment or pathogen can inhibit the effects of another, often demonstrated by antibiotics.

Nutritional Digestion

The process by which food is broken down to absorb nutrients, affecting health.

Next Generation Sequencing (NGS)

A method for sequencing DNA quickly and efficiently through massively parallel technology.

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PCR Amplification

A technique to make multiple copies of a specific DNA segment, used in sequencing.

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Library Preparation

A process where DNA fragments are prepared for sequencing, including the addition of adapters.

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Bridge Amplification

A technique used in NGS to create clusters of DNA sequences on a surface.

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Cluster Formation

The grouping of many identical DNA sequences into clusters for sequencing analysis.

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Sequencing by Synthesis

A method of determining DNA sequences through the addition of labeled nucleotides.

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Multiplexed Approach

A technique that allows multiple DNA samples to be sequenced simultaneously using barcoding.

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Indigenous microbiota

Microorganisms that naturally inhabit a specific environment within a host.

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Symbiosis

Biological association between two or more species that can benefit either or both.

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Commensalism

A relationship where one species benefits and the other is unharmed.

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Mutualism

A symbiotic relationship where both species benefit.

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Parasitism

A relationship where one species benefits at the expense of the other.

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Microbiota diversity

Variation in types of microorganisms found in different environments.

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Opportunistic pathogens

Microorganisms that exploit a weakened host to cause disease.

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Factors influencing microbiota

Local physiology, ecological factors, and microbial interactions dictate microbiota composition.

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Colonic microbiota

Predominantly anaerobic bacteria found in the colon, essential for digestion.

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Neonate microbiota

The initial microbial community established in a newborn after birth.

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Isothermal Bridge Amplification

A technique used in NGS to create DNA clusters through amplification at constant temperature.

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Template Extraction

The process of isolating DNA or RNA samples for sequencing.

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Hybridization of Sequencing Primers

The binding of sequencing primers to DNA templates for sequencing reactions.

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Reverse Strand Cleavage

The removal of the reverse strand from double-stranded DNA during sequencing preparation.

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Flow Cell

A device that contains numerous DNA clusters for sequencing on the Illumina platform.

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Sequencing Clusters

Groupings of identical DNA sequences created during NGS for reading.

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Denaturation in Sequencing

The process of breaking double-stranded DNA into single strands for sequencing.

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Barcoding in DNA Libraries

A method of labeling DNA samples to identify and track them during sequencing.

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16S rRNA Target Sequence

A specific region of DNA used for the identification of bacterial species via sequencing.

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Polymicrobial Samples

Samples containing multiple microbial species that can be analyzed to determine community composition.

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Single Molecule Templates

Isolated DNA fragments used to form clusters in sequencing.

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Sequencing Primer

Short DNA sequences that initiate the DNA synthesis during sequencing.

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Microbiota Colonization

The process by which microorganisms establish themselves in a new environment.

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Neonate Microbiota Formation

The establishment of microbiota in newborns influenced by birth and environment.

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Microbial Interactions

The relationships between different microorganisms that influence microbiota composition.

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Microbiota at Different Sites

The variation of microbial populations in various body locations.

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Transmission of Microbiota

The process by which microbiota colonize and multiply in a host.

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Commensal Relationship

A symbiotic relationship where one species benefits and the other is not harmed.

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Origin of Microbiota

Newborns begin with sterile microbiota; colonization occurs from birth and environment.

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Skin Microbiota

Microorganisms like Staphylococcus epidermidis inhabit the skin, protecting against pathogens.

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Intestinal Microbiota

A diverse microbial population in the intestines crucial for digestion, especially in the colon.

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Respiratory Microbiota

Microorganisms residing in the respiratory tract, important for health and immunity.

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Genitourinary Microbiota

Microbes in the urinary and vaginal tracts that vary with age and hormonal changes.

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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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