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
What are the advantages of 16S rRNA gene sequencing?
- Useful to detect overall differences in microbiota composition between groups; cannot detect the exact bacterial species (semi-quantitative)
- Relatively inexpensive
What are the disadvantages of 16S rRNA gene sequencing?
- Changes in taxonomic databases and bioinformatics pipelines over time make comparing results across studies difficult
- Some taxa will differ significantly depending on the extraction/amplification technique used
- Gives you relative abundance of bacteria (not exact quantities)
What method does the dysbiosis index use?
Quantitative PCR for specific taxa that have been identified as clinically relevant based on prior sequencing studies
What percent of dogs and cats with chronic enteropathies have decreased abundance of C. hirononis?
50-60% of dogs, 30% of cats
In one study, cats with small cell intestinal lymphoma had increased numbers of what bacteria attached to the mucosa in the ileum and colon compared to cats with IBD?
Fusobacterium sp.
What is metabolomics?
Analysis of microbial-derived metabolites (SCFA, fecal bile acids, etc)
Tryptophan is converted by bacteria into indole metabolites. What are their function in the GI tract?
Indoles can be anti-inflammatory (decrease IL-8 expression), induce mucin gene expression, and strengthen tight junctions
Fecal concentrations of what short chain fatty acids were lower in dogs with chronic enteropathy than healthy controls?
Acetate and propionate
What does richness refer to?
The overall number of unique operational taxonomic units (proxy for species) in a sample
What does diversity refer to?
A measure of the variability of the microbiome, considering both the richness (number of unique species) and relative abundance of those species
Puppies up to 5 to 6 weeks of age had what changes in their microbiome compared to older dogs?
Increased dysbiosis index, increased C. difficile, decreased C. hiranonis and secondary bile acids
Administration of metronidazole for 14 days caused what changes to the microbiome in dogs? How long did it take for those changes to reverse?
Decreased richness, decreased Fusobacterium, increased dysbiosis index, increased fecal lactate and decreased secondary bile acids. Took 4 weeks to recover
In a study of dogs with steroid responsive CE, how much lower were secondary fecal bile acids in affected dogs compared to control dogs? How did steroids affect it?
29% vs 88%; improved to 94% with steroid treatment
In a study of dogs with steroid responsive CE, did the dogs’ dysbiosis index improve with steroid treatment?
No - remained increased despite clinical resolution of disease. C hiranonis did improve though
In a study of 773 shelter dogs, administration of a synbiotic reduced the occurrence of diarrhea in the first 14 days by what percent?
From 27% in the control group to 18% in the synbiotic group
In a study of 773 shelter dogs, administration of a synbiotic reduced the occurrence of >2 consecutive days of diarrhea by what percent?
8% in the control, 4.6% in the synbiotic group
In healthy cats given clindamycin, concurrent administration of a synbiotic had what beneficial effects?
Administration of synbiotics decreased hyporexia and vomiting
For puppies with Parvovirus, administration of an FMT improved what measures of disease?
Faster resolution of diarrhea, shorter hospitalization (3 days vs 6 days), decreased mortality (21% vs 36%)
What effects did tylosin (administered for 7 days) have on the microbiome?
Decreased bacterial diversity (some resolved, some didn’t), increase in primary bile acids (lasted until day 63)
What enzymatic process is required to convert primary to secondary bile acids?
7-alpha-dehydroxylation
In healthy research dogs given enrofloxacin and metronidazole, what effect did giving a synbiotic have?
Reduced hyporexia, no difference in vomiting or diarrhea
Based on multiple cross over studies, how long do the effects of synbiotics last?
At least 8-9 weeks (affected second study period too)
Administration of Fortiflora to healthy dogs had what effect on cobalamin and folate?
Decrease in cobalamin with moderate hypocobalaminemia developing in 40%. No effect on folate
When given to puppies for one year, Enterococcus faecium (Fortiflora), induced what changes?
Increased fecal and serum IgA levels, increased vaccine associated IgA and IgG levels
Name the primary bile acids. What are they conjugated to?
Cholic acid, chenodeoxycholic acid - synthesized in the liver from cholesterol and conjugated to taurine or glycine
Name the secondary bile acids
Deoxycholic acid, lithocholic acid
What bacteria has been associated with AHDS?
Toxin-producing C. perfringens (potentially the netF toxin gene)
Helicobacter species produce what enzyme that is used to buffer gastric acid?
Urease - converts urea to ammonia
How does omeprazole administration change the gastric microbiota?
Decreases Helicobacter (from 98% of gastric bacteria to 92%), allowing for growth of Firmicutes/Fusobacteria. Increases total number of bacteria in the duodenum
In patients with an esophagojejunal feeding tube placed fluoroscopically with wire guidance, post pyloric access was gained in what percent of cases? What was the mean duration of the procedure?
95%
63 minutes
Dogs and cats receiving corticosteroids when a PEG tube is placed had what percent complication rate compared to controls?
43% vs 18% - included infection of the site, PEG tube dislodgment, and chewing of the tube around the stoma
In a retrospective study evaluating E tube complications in 123 patients, what percent experienced a complication related to tube placement?
44% (same in dogs and cats)
- 14-17% infection at the E tube site (mostly Enterococcus and E coli)
- Regurgitation of food through the stoma noted in 7 dogs and 1 cat
- 10-13% required re-suturing due to loose sutures
- 5-6% dislodgment
In a retrospective study evaluating E tube complications in 248 cats, what percent of cats had complications and what were they?
35.8% complication rate
- Tube dislodgment 14%
- Stoma site infections 12% - increased risk while on glucocorticoids or oncolytic agents
