microbiome

Question 1

define commensals

Answer 1

normal flora aka microbiota. An interaction between two species in which one benefits, one is unaffected

Question 2

define microbiome

Answer 2

collective microbial genome

Question 3

define dysbiosis

Answer 3

Abnormal composition of a microbiome.

Question 4

define gnotobiotic

Answer 4

Growth in a germ-free environment

Question 5

define immune homeostasis

Answer 5

Balance between a hyper-reactive and unresponsive immune system

Question 6

Beneficial Functions of the GI Microbiota

Answer 6

I. Protective Functions: Pathogen exclusion, Nutrient/receptor competition act as Antimicrobials (lactic acid, H2O2, pH, bacteriocins). II. Structural: barrier fortification, immune development, tight junctions. III metabolic: ferment non-digestible polysaccharides and mucus, synthesize vitamins B3, B5, B6, B12, K, biotin, folate and sequesters metals

Question 7

how do commensals affect immune function

Answer 7

A germ free environment can lead to less development of small intestine immunological cells (peyers patches, germinal centers, etc), less T cells, less production of IgA, reduced expression of MHC II

Question 8

How are bacteria transported throught the intestinal epithelium

Answer 8

M cells

Question 9

GI immune response elicited by B fragilis

Answer 9

Direct activation of Tregs and activation of Th17 via segmented filamentous bacteria

Question 10

What percentage of our calories is provided by microbiome and how?

Answer 10

10% - by breaking indigestible polysaccharides into absorbable short-chain fatty acids (e.g., butyrate, acetate):

Question 11

obesity predisposing microbiome

Answer 11

higher abundances of Firmicutes (a phylum of Gram positive organisms) may lead to obesity. Transfer of microbes from obese to lean animals increases adiposity and weight gain.

Question 12

Gold standard for molecular phylogenetic analysis

Answer 12

ribosomal RNA sequences. Ribosomes are present in all cellular organisms, and the sequences of their constituent RNAs (rRNA) differ from organism to organism.

Question 13

2. Outline the large-scale organization of cellular life and name the primary Domains.

Answer 13

Bacteria: Unicellular organisms – usually what we think of for microbial life. Eucarya: Nucleated cells of unicellular and multicellular organisms. Includes plants and animals as well as microbes (e.g., Giardia). Archaea: Unicellular organisms unrelated to Bacteria. Includes extremophiles capable of life at high temperature (>100°C) and high salinity.

Question 14

what are the commensals in the small/ large intestine

Answer 14

Obligate anaerobes of the phyla Firmicutes and Bacteroidetes

Question 15

list common pathogens in the firmicutes phyla

Answer 15

Faecalibacterium prasunitzii (beneficial) and Clostridium difficile, Staphylococcus aureus, Streptococcus pneumoniae, bac. Anthracis, listeria monocytogenes, strep pyogenes, clostridium botulinum and tetani

Question 16

List common pathogens in actinobacteria phyla

Answer 16

Mycobacterium tuberculosis, Corynebacterium diptheriae, mycobacterium leprae

Question 17

6. Discuss the natural history of the infant microbiome.

Answer 17

Within days after birth, the gut is colonized
by trillions of bacteria. In a matter of weeks,
the overall bacterial load rises to that typical of an adult. However, the weeks and months following birth are characterized by profound
changes in the types of microbes present in
the gut microbiome. Development of the
immune system occurs in parallel and is likely to be influenced by the microbiome

Question 18

Which bacteria are found in an infants gut

Answer 18

during first week, actinobacteria and proteobacteria colonize the gut, but they decrease dramatically in number by 1 year. Firmicutes and bacteroides increase steadily from birth

Question 19

how does C section vs vaginal delivery affect infant microbiome

Answer 19

C section: bacteria from hospital environment. Clostridium difficile is increased, bacteriodes fragilis and bifidobacteria are decreased. Vaginal: fecal and vagina bacteria from mom. Elevated bifidobacteria and bacteroides, but low clostridium

Question 20

How does breast feeding vs formula affect microbiome of infant

Answer 20

breastfed: increased bifidobacteria, strep, staph, enterococci, lactobacilli, enterobacteria. Formula: increased bacteroides fragilis, enterobacteria, and c. diff

Question 21

diseases caused by imbalanced microbiomes

Answer 21

Inflammatory Bowel Disease, Antibiotic associated diarrhea, C. difficile, Obesity, Bacterial Vaginosis, “Non-bacterial” Prostatitis, Pouchitis, Type 1 Diabetes, Mother-to-child HIV transmission, MRSA colonization and infection

Question 22

bacterial vaginosis cause

Answer 22

Bacterial vaginosis is characterized by loss of
protective species, such as lactobacilli, and gain of diverse anaerobes (e.g., Prevotella,
Gardnerella).

Question 23

Crohns disease associated bacteria/genes

Answer 23

Diminished levels of beneficial Clostridium and Bacteroides species. The ideal microbiome correlates with innate immune genes NOD2, ATG16L1 and people with certain alleles are at risk for crohns

Question 24

microbiome in c. diff

Answer 24

recurrent c. diff usually has decreased bacteroides