microbiome Flashcards
define commensals
normal flora aka microbiota. An interaction between two species in which one benefits, one is unaffected
define microbiome
collective microbial genome
define dysbiosis
Abnormal composition of a microbiome.
define gnotobiotic
Growth in a germ-free environment
define immune homeostasis
Balance between a hyper-reactive and unresponsive immune system
Beneficial Functions of the GI Microbiota
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
how do commensals affect immune function
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
How are bacteria transported throught the intestinal epithelium
M cells
GI immune response elicited by B fragilis
Direct activation of Tregs and activation of Th17 via segmented filamentous bacteria
What percentage of our calories is provided by microbiome and how?
10% - by breaking indigestible polysaccharides into absorbable short-chain fatty acids (e.g., butyrate, acetate):
obesity predisposing microbiome
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.
Gold standard for molecular phylogenetic analysis
ribosomal RNA sequences. Ribosomes are present in all cellular organisms, and the sequences of their constituent RNAs (rRNA) differ from organism to organism.
- Outline the large-scale organization of cellular life and name the primary Domains.
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.
what are the commensals in the small/ large intestine
Obligate anaerobes of the phyla Firmicutes and Bacteroidetes
list common pathogens in the firmicutes phyla
Faecalibacterium prasunitzii (beneficial) and Clostridium difficile, Staphylococcus aureus, Streptococcus pneumoniae, bac. Anthracis, listeria monocytogenes, strep pyogenes, clostridium botulinum and tetani
List common pathogens in actinobacteria phyla
Mycobacterium tuberculosis, Corynebacterium diptheriae, mycobacterium leprae
- Discuss the natural history of the infant microbiome.
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
Which bacteria are found in an infants gut
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
how does C section vs vaginal delivery affect infant microbiome
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
How does breast feeding vs formula affect microbiome of infant
breastfed: increased bifidobacteria, strep, staph, enterococci, lactobacilli, enterobacteria. Formula: increased bacteroides fragilis, enterobacteria, and c. diff
diseases caused by imbalanced microbiomes
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
bacterial vaginosis cause
Bacterial vaginosis is characterized by loss of
protective species, such as lactobacilli, and gain of diverse anaerobes (e.g., Prevotella,
Gardnerella).
Crohns disease associated bacteria/genes
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
microbiome in c. diff
recurrent c. diff usually has decreased bacteroides
