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Questions and Answers
What is the primary composition of most microbiota?
What is the primary composition of most microbiota?
Which statement about dysbiosis is true?
Which statement about dysbiosis is true?
What term refers to the balance of microbial communities in the microbiota?
What term refers to the balance of microbial communities in the microbiota?
Which of the following can lead to dysbiosis?
Which of the following can lead to dysbiosis?
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What is a characteristic of pathogenic bacteria in terms of biofilm formation?
What is a characteristic of pathogenic bacteria in terms of biofilm formation?
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Which type of microbiota is characterized by its persistence in the body?
Which type of microbiota is characterized by its persistence in the body?
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What condition is believed to be influenced by GI microbiota?
What condition is believed to be influenced by GI microbiota?
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How does excessive hygiene potentially affect the microbiota?
How does excessive hygiene potentially affect the microbiota?
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What type of biofilms do pathogenic bacteria commonly form on medical devices?
What type of biofilms do pathogenic bacteria commonly form on medical devices?
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Which factors do NOT influence the composition of microbiota?
Which factors do NOT influence the composition of microbiota?
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How does the size of the plasmid affect its migration through agarose gel?
How does the size of the plasmid affect its migration through agarose gel?
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What is a characteristic of broad host range plasmids?
What is a characteristic of broad host range plasmids?
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What role do CRISPR-Cas systems play in bacteria?
What role do CRISPR-Cas systems play in bacteria?
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Why do commensal bacteria generally avoid acquiring extra genetic material?
Why do commensal bacteria generally avoid acquiring extra genetic material?
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What typically happens to pathogens in terms of genetic material compared to commensal bacteria?
What typically happens to pathogens in terms of genetic material compared to commensal bacteria?
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What is the role of a capsule in Streptococcus pneumoniae?
What is the role of a capsule in Streptococcus pneumoniae?
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What happens to avirulent S.pneumoniae when injected with killed encapsulated virulent bacteria?
What happens to avirulent S.pneumoniae when injected with killed encapsulated virulent bacteria?
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Transformation is a genetic mechanism primarily associated with which process?
Transformation is a genetic mechanism primarily associated with which process?
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What characterizes plasmids in relation to the chromosome?
What characterizes plasmids in relation to the chromosome?
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Which is a consequence of S.pneumoniae lacking a capsule?
Which is a consequence of S.pneumoniae lacking a capsule?
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What initiates the replication process of both chromosomes and plasmids?
What initiates the replication process of both chromosomes and plasmids?
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What is the primary function of the DNA polymerase during replication?
What is the primary function of the DNA polymerase during replication?
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Why is S.pneumoniae considered virulent?
Why is S.pneumoniae considered virulent?
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Avirulent S.pneumoniae strains are characterized by what genetic feature?
Avirulent S.pneumoniae strains are characterized by what genetic feature?
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What is formed when replication initiation proteins bind to the origin of replication?
What is formed when replication initiation proteins bind to the origin of replication?
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Which condition is mentioned as not largely influenced by microbiota?
Which condition is mentioned as not largely influenced by microbiota?
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What psychological aspect may be influenced by the GI microbiota?
What psychological aspect may be influenced by the GI microbiota?
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What nerve connects the brain and the digestive tract?
What nerve connects the brain and the digestive tract?
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What is the primary role of pathogens found in the microbiome?
What is the primary role of pathogens found in the microbiome?
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Which taxonomic rank is found at the end of the branching hierarchy of bacteria?
Which taxonomic rank is found at the end of the branching hierarchy of bacteria?
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What assumption does phylogeny typically rely upon?
What assumption does phylogeny typically rely upon?
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How many kingdoms are established based on ribosomal rRNA gene phylogeny?
How many kingdoms are established based on ribosomal rRNA gene phylogeny?
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Which of the following is NOT a level of bacterial classification?
Which of the following is NOT a level of bacterial classification?
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Which of these diseases is associated with the influence of GI microbiota?
Which of these diseases is associated with the influence of GI microbiota?
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What signifies that there needs to be a mark to go through evolution?
What signifies that there needs to be a mark to go through evolution?
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What is transformation in the context of horizontal gene transfer?
What is transformation in the context of horizontal gene transfer?
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Which statement is correct about the competence of bacteria?
Which statement is correct about the competence of bacteria?
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What role does RecA play in homologous recombination?
What role does RecA play in homologous recombination?
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What must be true for ssDNA to be incorporated into a bacterial genome?
What must be true for ssDNA to be incorporated into a bacterial genome?
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What is the primary challenge to DNA uptake during transformation?
What is the primary challenge to DNA uptake during transformation?
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Which of the following statements describes a pan genome?
Which of the following statements describes a pan genome?
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What is the function of ssDNA binding proteins during transformation?
What is the function of ssDNA binding proteins during transformation?
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What is the main type of DNA that is taken up during the transformation process?
What is the main type of DNA that is taken up during the transformation process?
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Why are the genes of a supragenome important for bacterial diversity?
Why are the genes of a supragenome important for bacterial diversity?
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Which mechanism is NOT a form of horizontal gene transfer?
Which mechanism is NOT a form of horizontal gene transfer?
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What is the hallmark of transformation in laboratory experiments?
What is the hallmark of transformation in laboratory experiments?
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What is required for RecA to facilitate strand exchange during homologous recombination?
What is required for RecA to facilitate strand exchange during homologous recombination?
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What is one key characteristic of competent bacteria?
What is one key characteristic of competent bacteria?
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What happens to the ssDNA within the bacterial cell once taken up?
What happens to the ssDNA within the bacterial cell once taken up?
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Which is true regarding DNA incorporation into a bacterial genome?
Which is true regarding DNA incorporation into a bacterial genome?
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Study Notes
Bacterial Microbiota
- Bacteria live in multispecies biofilms in the microbiota
- Pathogenic bacteria often form monospecies biofilms and sometimes multispecies biofilms on indwelling devices (e.g., catheters, joint replacements)
- Most microbiota is mixed species
- The microbiota makes up a highly adapted ecology of bacteria
- Microbiota often contains biofilms
- Resident microbiota is the own microbiota
- Transient microbiota comes and goes
- Dysbiosis represents a microbial imbalance in the microbiota
- Diet, exercise, antibiotics, and hygiene influence the microbiota
- Dysbiosis can lead to changes in immune status including inflammation (hyperimmunity) and immunodeficiencies, as well as possibly autoimmune diseases
- Dysbiosis can lead to chronic systemic inflammation and metabolic disease
- Hygiene means too much hygiene
- GI microbiota is being associated with multiple conditions
- GI microbiota contributes to systemic conditions such as diabetes
- Obesity is not largely influenced by microbiota
- Local conditions, such as Crohn's disease and colon cancer, are associated with GI microbiota
- The Gut-Brain Axis, GI microbiota may influence psychological conditions as well Parkinson's disease
- The Vagus nerve connects the brain and the gut
- Pathogens are found in the microbiome meant to murder
Bacterial Phylogeny
- To be marked by phylogeny, a mark to go through evolution is needed
- Phylogeny assumes an ancestor and uses evolution to change gene sequences
- The bacteria are organized into Kingdom, Phylum, Class, Order, Family, Genus, Species
- Species are at the end of each branch
- There are three kingdoms based on ribosomal rRNA gene phylogeny.
Mechanisms of Horizontal Gene Transfer (HGT)
- Stress causes bacterial DNA to fragment (e.g., oxidative burst by immune cells)
- Starvation in deep layers of a biofilm is a stressor
- Error-prone polymerases do not proofread
- Transformation is the uptake of DNA from the environment by competent bacteria
- DNA is free in the environment, making it susceptible to DNase
- DNase inhibition of DNA uptake during laboratory experiments is a hallmark of transformation
- Only competent bacteria can take up DNA
- Competence is a naturally occurring state
- Competence can be chemically induced in some bacteria
- Single-strand of DNA (ssDNA) is taken up by the DNA uptake machinery
- Pili are often associated with DNA uptake machinery
- RecA protein coats ssDNA, performs homology searches, and replaces it with the chromosome
- Once inside the cell, DNA is protected by ssDNA binding proteins
- RecA recombinase binds to the ssDNA and mediates homologous recombination
- The ssDNA must have regions of homology to DNA already in the chromosome
- The DNA binds in these stretches and RecA mediates strand exchange
- If DNA is not cleaved by restriction enzymes (enzymes that cleave DNA), it is incorporated into the genome
- Numerous additional genes can be introduced into the chromosome as long as they are flanked by regions of homology
- A bacterial species with a supragenome (pan genome) will have a core genome shared by all the bacteria (comprises 60-70% of the genome)
- Distributed genes are present in only some of the bacteria in the population, giving rise to different strains
- Genes encode unique functions — alternate metabolism, virulence factors, etc.
- Transformation is one genetic mechanism that can give rise to this type of genome structure in a species
- Transformation of competent cells led to the discovery of DNA
- Streptococcus pneumoniae is a virulent bacteria that will kill mice
- S. pneumoniae requires a capsule to keep it from being killed by the immune system
- Without a capsule S. pneumoniae is avirulent (cannot cause disease)
- If killed encapsulated virulent bacteria are injected into a mouse along with live avirulent unencapsulated bacteria, the mouse will die. The live bacteria pick up the capsule gene via transformation
Plasmids
- Plasmids replicate separately from the chromosome — autonomous replicons
- Replication initiation proteins bind to the origin of replication to initiate replication
- Bound replication initiation protein recruits DNA polymerase (which replicates the chromosome) to replicate the plasmid.
Plasmids and Horizontal Gene Transfer
- Plasmids can be used to transfer genes between organisms.
- The size of the plasmid impacts its migration speed in agarose gel electrophoresis.
- Large plasmids migrate slower than chromosomes
- Small plasmids migrate faster than chromosomes
- Broad host range plasmids can transfer genes between different genera and species through horizontal gene transfer.
CRISPR-Cas System
- CRISPR-Cas systems are used for gene editing in bacteria.
- The CRISPR-Cas system protects commensal bacteria from acquiring genes from horizontal gene transfer.
- Commensal bacteria are highly adapted to their niche environments.
- Commensal bacteria do not want the added burden of extra genetic material.
- Pathogenic bacteria often acquire antibiotic resistance genes and virulence factors from mobile genetic elements.
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Description
Explore the complexities of bacterial microbiota in this quiz. Learn about the differences between resident and transient microbiota, the significance of biofilms, and how dysbiosis can affect overall health. Understand the influence of diet, hygiene, and other factors on your microbiota.
