Horizontal Gene Transfer & Microbial Interactions

Question 1

segments of DNA that encode enzymes and other proteins that mediate the movement of DNA within genomes (intracellular mobility) or between cells (intercellular mobility)

Answer 1

Mobile genetic elements (MGEs)

Question 2

genes common to all individuals of a species

Answer 2

Core genome

Question 3

genes sporadically present in a species that may also be shared with other species

Answer 3

Pan genome

Question 4

2 requirements of transformation

Answer 4

Competence
Host homologous recombination system

Question 5

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

Answer 5

Generalized

Question 6

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

Answer 6

Specialized

Question 7

Does this describe generalized or specialized transduction:
Homologous recombination is required to integrate the DNA into the recipient genome

Answer 7

Generalized

Question 8

Does this describe generalized or specialized transduction:
Homologous recombination is not required because the DNA is part of the phage

Answer 8

Specialized

Question 9

Broadest host range form of gene transfer

Answer 9

Conjugation

Question 10

Does conjugation require recombination?

Answer 10

Generally does not

Question 11

the most important mechanism of gene transfer in nature

Answer 11

Conjugation

Question 12

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

Answer 12

Plasmids

Question 13

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

Answer 13

Transposons

Question 14

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

Answer 14

Genomic (pathogenicity) islands

Question 15

F plasmid sometimes integrates into the bacterial chromosome by homologous recombination, generating this type of cell

Answer 15

Hfr cell

Question 16

An incorrect excision of the integrated F plasmid brings along a portion of the chromosome, generating this type of cell

Answer 16

F’

Question 17

mobile genetic elements that combine features of bacteriophage, plasmids, and transposons and may include genomic islands

Answer 17

Integrative conjugative elements (ICE)

Question 18

Colonizers are predominately

Answer 18

Anaerobic
Particularly in the GI

Question 19

Microbial density and diversity increases or decreases from proximal to distal gut?

Answer 19

Increases

Question 20

Microbial density and diversity increases or decreases from gut surface to lumen?

Answer 20

Increases

Question 21

Simple sugars are taken up or digest here

Answer 21

Small intestine

Question 22

Complex “indigestible” carbohydrates (fiber) are fermented by bacteria here

Answer 22

Large intestine

Question 23

Does the small intestine have more or less sIgA than the colon?

Answer 23

More

Question 24

Intestinal bacteria can synthesize these 2 vitamins

Answer 24

K and B vitamins

Question 25

Intestinal bacteria can synthesize short chain fatty acids (SCFA), particularly this

Answer 25

Butyrate

Question 26

Capsular polysaccharides and SCFAs stimulate production of these two things

Answer 26

IL-10 and Tregs

Question 27

Segmented filamentous bacteria stimulate this type of T cells important for mucosal immunity to pathogens

Answer 27

Th17

Question 28

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

Answer 28

Butyrate (SCFA)

Question 29

In a normal symbiotic situation, the gut is kept hypoxic by this

Answer 29

Beta oxidation

Question 30

In dysbiosis after treatment with antibiotics, colonocyte metabolism changes to this

Answer 30

Glycolysis Allows the overgrowth of pathogenic bacteria

Question 31

Is gum disease or dental infections associated with this: Higher risk of cardiovascular disease, complications of diabetes, preterm birth

Answer 31

Gum disease

Question 32

Is gum disease or dental infections associated with this: Pneumonia

Answer 32

Dental infections

Question 33

Normal vaginal ecology is predominately this species

Answer 33

Lactobacillus

Question 34

Lactobacillus-free ecology is type #?

Answer 34

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

Question 35

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

Answer 35

Probiotics

Question 36

Probiotics are predominately these 2 species

Answer 36

Lactobacillus and Bifidobacteria

Question 37

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

Answer 37

Live biotherapeutic products (LBPs)

Question 38

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

Answer 38

Prebiotics

Question 39

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

Answer 39

Postbiotics

Question 40

Fecal microbiome transplantation (FMT) is approved for treatment of these infections

Answer 40

C. diff

Question 41

Infections with ________ bacteria are usually acute and severe but relatively brief

Answer 41

Encapsulated

Question 42

Infections with _______ bacteria usually cause infections that are insidious and chronic

Answer 42

Intracellular

Question 43

This microbial component inhibits complement binding

Answer 43

Capsule

Question 44

Exotoxins or endotoxins: Both gram negative and positive

Answer 44

Exotoxins

Question 45

Exotoxins or endotoxins: Can be secreted

Answer 45

Exotoxins

Question 46

Exotoxins or endotoxins: Typically encoded on phages and plasmids

Answer 46

Exotoxins

Question 47

Exotoxins or endotoxins: Most are heat labile

Answer 47

Exotoxins

Question 48

Exotoxins or endotoxins: Only gram negative

Answer 48

Endotoxins

Question 49

Exotoxins or endotoxins: Part of the outer membrane

Answer 49

Gram negative

Question 50

Exotoxins or endotoxins: Encoded on the chromosome

Answer 50

Endotoxins

Question 51

Exotoxins or endotoxins: Heat stable

Answer 51

Endotoxins

Question 52

Hemolysins and cytolysins are _____ forming proteins

Answer 52

Pore Protein or peptide monomers that multimerize in the cell membrane leading to pore formation

Question 53

Part of A-B toxin that binds the toxin molecule to a specific receptor

Answer 53

B (heavy) chain

Question 54

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

Answer 54

A (light) or Active chain

Question 55

Many A-B toxins are on these

Answer 55

Mobile genetic elements

Question 56

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

Answer 56

Type III Secretion systems

Question 57

Type III Secretion systems have only been detected in this type of bacteria

Answer 57

Gram negative

Question 58

Type III Secretion systems are related to these systems

Answer 58

Flagellar

Question 59

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)

Answer 59

Superantigens

Question 60

Many bacterial superantigens are encoded in this

Answer 60

Phage-encoded (lysogenic conversion)

Question 61

Superantigens crosslink the MHC and TCR without this

Answer 61

Without antigen processing

Question 62

Quorum sensing involves this type of feedback loop

Answer 62

Positive

Question 63

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

Answer 63

Quorum sensing

Question 64

Homoserine lactones are examples of autoinducers in gram _______

Answer 64

Negatives

Question 65

Peptides are examples of autoinducers in gram _______

Answer 65

Positives