GI: microbiome and enteral nutrition Flashcards
Name 4 of the major bacteria phyla identified in the healthy gut of dogs and cats
Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria, and Actinobacteria
One of the major metabolic functions of the GI microbiome is to ferment non-digestible dietary residues into volatile fatty acids. Name the short chain volatile fatty acids
Acetate, propionate, butyrate
What short chain fatty acid is the major energy source for colonocytes?
Butyrate
Name 3 vitamins synthesized by the microbiome
Biotin, folate, vitamin K
Name 3 minerals that the microbiome assists in the absorption of
Calcium, magnesium, iron
Name 2 ways that the microbiome contributes to host mucosal immunity
1) Colonization by bacteria after birth influences T cell repertoires and Th1/Th2 cytokine profiles
2) Form a biofilm to prevent pathogenic bacterial colonization - displacement, competition for nutrients, production of antimicrobial substances (lactic acid, bacteriocins)
Surface enterocytes sense danger signals within the intestinal lumen and respond by secreting what products?
Defensins, IgA, chemokines and cytokines
What are M cells?
Specialized epithelial cells that overlie lymphoid follicles. Sample luminal antigens and deliver them to DCs for antigen presentation
What are two pattern recognition receptor (PRR) systems used by the mucosal immune system to recognize pathogens? Where are they located?
Toll like receptors (TLRs) - transmembrane
Nucleotide-binding oligomerization domain (NOD1 and NOD2) - intracellular
Immune responses to commensal bacteria in IBD may be driven by what TLR/antigen?
Flagellin activating TLR5
Increased numbers of intestinal bacteria can cause malabsorption and diarrhea through what mechanisms?
1) Competition for nutrients - such as bacterial binding of cobalamin, which prevents absorption
2) Metabolism of nutrients into products that promote colonic secretion/diarrhea
3) Biochemical injury to the brush border, decreasing enzyme activity
Selective IgA deficiency leading to bacterial overgrowth occurs in what breed?
German Shepherds
What is the difference between microbiota and microbiome?
Microbiota = taxonomy (who is there)
Microbiome = the gene content and function (what are they doing)
Why is bacterial culture less useful for evaluating the microbiome?
Majority of bacteria (especially in the colon) are anaerobes; a reduction in beneficial bacteria is often more relevant than overgrowth of one species - difficult to identify on culture
What is DNA shotgun sequencing or metagenomics?
A technique that aims to sequence extracted DNA in a sample without prior PCR amplification on a high throughout sequencer - allows assessment of taxonomy and functional gene categories
What are 3 advantages of DNA shotgun sequencing over 16S RNA sequencing?
- Better resolution at the bacterial species and strain level
- Can identify archaea, fungi, and DNA viruses
- Can provide more detailed info on virulence genes and antimicrobial resistance genes
What are disadvantages of DNA shotgun sequencing over 16S RNA sequencing?
High cost, advanced bioinformatics needed to assemble the data
What is the 16S rRNA gene?
Several bacteria variable gene regions that are flanked by conserved regions
What is 16S rRNA gene sequencing?
DNA is extracted from a sample, and bacterial universal primers are used to amplify the conserved regions consisting of the 16S gene. PCR amplicons are sequenced using a high throughput sequencer
What is alpha diversity?
The richness and diversity of a sample - how many taxa are in one sample
What is beta diversity?
How similar one sample is to another sample based on the taxa present