Horizontal Gene Transfer & Microbial Interactions Flashcards
segments of DNA that encode enzymes and other proteins that mediate the movement of DNA within genomes (intracellular mobility) or between cells (intercellular mobility)
Mobile genetic elements (MGEs)
genes common to all individuals of a species
Core genome
genes sporadically present in a species that may also be shared with other species
Pan genome
2 requirements of transformation
Competence
Host homologous recombination system
Does this describe generalized or specialized transduction:
Occasionally during lysis bacteriophage make a mistake and package host DNA in the capsid instead of bacteriophage DNA
This DNA is then carried passively with the phage head and injected into the next host cell it contacts
Each fragment of host DNA has an equal probability of being packaged
Generalized
Does this describe generalized or specialized transduction:
Generally involves close association between a phage and its host genome in the form of lysogeny
Chromosomal genes closely linked to the prophage may be erroneously packaged with the phage
These genes may become permanent residents within the phage genome leading to lysogenic converting phage
Specialized
Does this describe generalized or specialized transduction:
Homologous recombination is required to integrate the DNA into the recipient genome
Generalized
Does this describe generalized or specialized transduction:
Homologous recombination is not required because the DNA is part of the phage
Specialized
Broadest host range form of gene transfer
Conjugation
Does conjugation require recombination?
Generally does not
the most important mechanism of gene transfer in nature
Conjugation
Genetic elements that are replicated and inherited independently from the bacterial chromosome
Encode a negative regulator circuit (cop) that keeps the copy number within prescribed limits differentiating them from phage
Frequently carry genes for antibiotic resistance and virulence factors
Plasmids
non-replicating genetic elements capable of “hopping” or transposing from one position on the genome to another
Encode an enzyme called transposase that recognizes the ends, cuts them from their initial location and catalyze their movement to a new location
Transposons
clusters of related genes variably present in strains of the same species and associated with bacteriophage-like genes and properties
Have GC contents suggestive of foreign acquisition
Genomic (pathogenicity) islands
F plasmid sometimes integrates into the bacterial chromosome by homologous recombination, generating this type of cell
Hfr cell
An incorrect excision of the integrated F plasmid brings along a portion of the chromosome, generating this type of cell
F’
mobile genetic elements that combine features of bacteriophage, plasmids, and transposons and may include genomic islands
Integrative conjugative elements (ICE)
Colonizers are predominately
Anaerobic
Particularly in the GI
Microbial density and diversity increases or decreases from proximal to distal gut?
Increases
Microbial density and diversity increases or decreases from gut surface to lumen?
Increases
Simple sugars are taken up or digest here
Small intestine
Complex “indigestible” carbohydrates (fiber) are fermented by bacteria here
Large intestine
Does the small intestine have more or less sIgA than the colon?
More
Intestinal bacteria can synthesize these 2 vitamins
K and B vitamins
Intestinal bacteria can synthesize short chain fatty acids (SCFA), particularly this
Butyrate
Capsular polysaccharides and SCFAs stimulate production of these two things
IL-10 and Tregs
Segmented filamentous bacteria stimulate this type of T cells important for mucosal immunity to pathogens
Th17
These are 3 benefits of production of this:
Stimulation of Treg cells to reduce inflammation
Drives colonocyte metabolism to consume oxygen and reduce nitrate production to maintain hypoxia
Stimulation of production of beta defensins
Butyrate (SCFA)
In a normal symbiotic situation, the gut is kept hypoxic by this
Beta oxidation
In dysbiosis after treatment with antibiotics, colonocyte metabolism changes to this
Glycolysis
Allows the overgrowth of pathogenic bacteria
Is gum disease or dental infections associated with this:
Higher risk of cardiovascular disease, complications of diabetes, preterm birth
Gum disease
Is gum disease or dental infections associated with this:
Pneumonia
Dental infections
Normal vaginal ecology is predominately this species
Lactobacillus
Lactobacillus-free ecology is type #?
Type IV
Is associated with higher vaginal pH, higher incidence of vaginosis (Nugent score) and higher incidence of preterm labor, less effective HIV biocide prevention
Products with live bacterial cultures meant to provide benefit while growing in the host (traditional yogurts and fermented dairy products, pills, cosmetics, mattresses, etc.)
Generally regarded as safe (GRAS)
Predominately Lactobacillus and Bifidobacteria species
The majority of studies have failed to show benefit in healthy individuals and they are not recommended by the FDA for treatment of any medical condition
Probiotics
Probiotics are predominately these 2 species
Lactobacillus and Bifidobacteria
Essentially probiotics FDA approved for treatment of specific diseases
Contains live organisms, such as bacteria
Is applicable to the prevention, treatment, or cure of a disease or condition of human beings
Is not a vaccine
May include gut organisms that are not GRAS
May include microorganisms genetically modified to deliver a bioactive compound
None currently available
Live biotherapeutic products (LBPs)
Microbial food, generally carbohydrates, indigestible by the host
Stimulate growth of beneficial microbes that are already present
Are unregulated nutritional supplements
Dietary fiber positively influences gut function, immune function, glucose tolerance, metabolic regulation, and reduces the incidence of colon cancer
Prebiotics
Bacterial or host metabolites that facilitate establishment of a beneficial microbiome, e.g. SCFA
Interference with microbial production of trimethylamine-N-oxide (TMAO) which is associated with cardiovascular disease
Postbiotics
Fecal microbiome transplantation (FMT) is approved for treatment of these infections
C. diff
Infections with ________ bacteria are usually acute and severe but relatively brief
Encapsulated
Infections with _______ bacteria usually cause infections that are insidious and chronic
Intracellular
This microbial component inhibits complement binding
Capsule
Exotoxins or endotoxins:
Both gram negative and positive
Exotoxins
Exotoxins or endotoxins:
Can be secreted
Exotoxins
Exotoxins or endotoxins:
Typically encoded on phages and plasmids
Exotoxins
Exotoxins or endotoxins:
Most are heat labile
Exotoxins
Exotoxins or endotoxins:
Only gram negative
Endotoxins
Exotoxins or endotoxins:
Part of the outer membrane
Gram negative
Exotoxins or endotoxins:
Encoded on the chromosome
Endotoxins
Exotoxins or endotoxins:
Heat stable
Endotoxins
Hemolysins and cytolysins are _____ forming proteins
Pore
Protein or peptide monomers that multimerize in the cell membrane leading to pore formation
Part of A-B toxin that binds the toxin molecule to a specific receptor
B (heavy) chain
Part of A-B toxin that enters the host cell and enzymatically interferes with an essential host function like protein synthesis, signal transduction, or interference with neurotransmitters
A (light) or Active chain
Many A-B toxins are on these
Mobile genetic elements
A nanostructure for delivering bacterial toxins to a host cytoplasm
Related to flagellar systems
Delivered proteins are referred to as effectors and may have various effects including promotion of uptake, interference with signal transduction, and induction or inhibition of apoptosis
So far detected only in gram negative bacteria
Type III Secretion systems
Type III Secretion systems have only been detected in this type of bacteria
Gram negative
Type III Secretion systems are related to these systems
Flagellar
Crosslinks the MHC and TCR without antigen processing
Activates 2-20% of all T cells
Cause a variety of symptoms including shock and vomiting
Many bacterial are phage-encoded (lysogenic conversion)
Superantigens
Many bacterial superantigens are encoded in this
Phage-encoded (lysogenic conversion)
Superantigens crosslink the MHC and TCR without this
Without antigen processing
Quorum sensing involves this type of feedback loop
Positive
Regulating the switch from invasion to toxin production
Biphasic growth: Attachment and immune evasion –> Toxin production and attack
Secreted molecule (autoinducer) inducing a “feed-forward” loop leading to a rapid peak of induction
Quorum sensing
Homoserine lactones are examples of autoinducers in gram _______
Negatives
Peptides are examples of autoinducers in gram _______
Positives
