Microbiome Flashcards
What are diversity, richness and dysbiosis
Diversity = measure of variability, considering richness and relative abundances
alpha = individual sample
beta - between different samples
Richness = measure of overall number of unique species (operation taxonomic units)
Dysbiosis - changes in composition due to disease or other factors
Typically a reduction in diversity and altered metabolic relationships with host
Methods to evaluate Biome
High throughput sequencing platforms - allow identification of bacterial groups using primers targeted at universally conserved regions
Groups of low abundance may be so small they are not identified
Commonly used primer protocols can underestimate the presence of specific bacterial groups
FISH - allows quantification of bacterial groups and visualisation of location of bacteria in relation to epithelium
Metagenomics - DNA extracted is sequenced without prior amplification of specific sequences, giving a snapshot of the gene pool and functional potential of the microbiome.
Transcriptomics - analysis of mRNA to provide measure of gene expression
What arer SCFA and what do they do
Metabolite of bacterial b/d of indigestible dietary components
Utilised by colonocytes as energy source
maintain the epithelial barrier by strengthening tight junctions,
help to regulate intestinal motility,
stimulate the production of anti-inflammatory compounds
Role of biome in bile acid metabolism
Once primary bile acids enter the gastrointestinal tract, over 50 chemically distinct secondary bile acids are produced
Specifically, gut microbes utilise bile salt hydrolases to deconjugate primary host bile acids. Bile salt hydrolases (BSH) are highly conserved across the microbiome
One bacteria may not have all the enzymes to complete conversion so process may involve many organisms acting on different intermediates
2ry bile acids are anti-inflammatory, promote intestinal ight junctions, are reabsorbed and reused by liver and modulate glucose and insulin homoestasis
Failure to convert 1ry bile acids can result in secretory diarrhoea
Major metabolic functions of biome that are beneficial
SCFA production
Conversion of 1ry to 2ry bile acids
Tryptophan metabolism to indole metabolites
Synthesis of folate, vit K and biotin
What is dysbiosis and what are common causes
Any change to biome that adversely affects host health
- abnormal substrates (fatty foods, medications) –> alter metabolite composition and may cause secretory diarrhoea
- Loss of function (selective loss of spp) –> reduced SCFA and 2ry BA –> loss of anti-inflam effects
- increased total bacterial load –> excessive metabolite production
- increased adherent or invasive bacteria promoting an inflammatory immune response
Prebiotic definition
a non-digestible food ingredient that beneficially affects the host by selectively stimulating the growth and/or activity of 1 or a limited number of bacteria in the colon. Fermented by colonic bacteria, generating end-products such as SCFAs that provide essential nutrients for the enteric epithelium
Probiotic definition
Living organisms that impart benefits beyond those of inherent basic nutrition
Proposed MOA of probiotics
remodelling of microbial communities,
suppression of pathogens (increase defensins, IgA and mucins),
upregulation of antiinflammatory factors,
downregulation of proinflammatory factors from epithelial cells,
promotion of tolerance and preservation of intestinal barrier function.
JVIM review summary for evidence of probiotics in acute gastroenteritis
evidence is not sufficiently robust to determine the effectiveness of probiotics in reducing clinical signs
may reduce duration/severity
Often small studies with high risk of bias
JVIM 2019 prokolin trial - DB, PC study with 148 dogs. Prokolin had better clinical outcome, less interventions and faster recovery.
JVIM review summary for evidence of probiotics in CHRONIC GI dz
The evidence was primarily against an effect of probiotic supplementation on clinical variables and results indicated that dietary intervention is more important than probiotic supplementation,
but all of these studies included a very small or small number of dogs, significantly adversely affecting statistical of power
Diseases where altered GI biome has been demonstrated
EPI - increased functional gene expression and reduced alpha diversity before Tx
AHDS - reduced diversity, increased Providencia and C perfringens in one outbreak
Lymphoid neoplasia in dogs - Alpha diversity was significantly reduced in dogs with tumors. Dysbiosis index was higher
CIE/IBD
CKD - intestinal dysbiosis contributes to the production of uraemic toxins in humans. Reduced biome diversity and richness identified in cats with CKD and indoxyl sulfates are increased
Obesity
Probiotic use in prevention of ABx associated GI upset
Recent DB, PC prospective cross over trial reported that a synbiotic administration reduced the severity of hyporexia in dogs administered dual antibiotics
What is the dysbiosis index
measures the abundance of seven bacterial taxa and mathematically summarizes the results as a single number.
Reference intervals for healthy dogs have been established, meaning this index could be used to assess the intestinal microbiota in clinical patients
Reference ranges and different organisms designed for dogs with chronic enteropathy
Negative results are healthy, dysbiosis is >0, anything >2 is dysbiotic.
Limitations of Dysbiosis index
Only looking at small proportion of population and there are huge limitations
disease specific dysbiotic states may not be captured by this index since it is limited to evaluating only seven bacterial taxa. Further investigation and validation studies are required to determine if the canine DI is suited for all states of canine intestinal dysbiosis.
Dogs with acute diarrhoea have a normal DI, but that does not mean there isn’t a different dysbiosis as this was designed for CE
Clinical studies evaluating the diagnostic and therapeutic utility of the canine DI are required
