Test 2: microbiome Flashcards
great plate count anomaly
what you can culture is different from what you can count under microscope
important features of 16s rRNA
functionally constant
ubiquitous across all prokaryotic life
abundant in the cell
different parts change at different rates
secondary structure
how does 16S marker gene profiling work
culture independent
PCR that has primer to peak and valley (amblicon)
peaks are conserved
valleys (variable regions)
shotgun metagenomics
break bacterial genomes and sequence what is left
who and what they might be doing- what genes are there
16S vs metagenomics
16s only requires a small amount of bacteria because
undergoes PCR- replication
An OTU is the unit of measurement for microbiome diversity, that —
groups related (97% identical) sequences together as a single taxonomic unit
operational taxonomic unit
used for 16S to try to organize sequences
high alpha diversity
count of different taxa in a sample
beta diversity
compare two different areas and what grows there
low beta diversity
two samples have a lot in common
high beta diversity
two samples have nothing in common
low alpha diversity
there are few different type of things in a specific site
pathobiont
pathogen that is always there but can become oppurtunist
canine chronic enteropathy cause
chronic persistent or recurrent GI- vomiting and diarrhea and weight loss
diagnosed by exclusion- rule our everything else it has to be this
5 ways to diagnosis canine chronic enteropathy
- chronic symptoms
- histopath shows mucosal inflammation
- exclusion of other diseases
- does not respond to antibiotics or dietary therapies
- response to anti-inflammatory or immunocuppressive agents
boxer dog colitis used to be called
small intestinal bacterial overgrowth
antibiotics and diet change helped CCE dogs more then diet alone
no
helped at first, but antibiotics caused resurg in “bad” pathogens
what are secondary bile acids
bile acids are made by the liver and stores in gallbladder. when you eat fatty meal released, most resorbed
some make it to large intestine and microbiome will help convert primary to secondary bile acids (DCA, LCA)
bai operon cause
primary to secondary bile acids
LCA, DCA
transfaunation
take rumen and give to other animal to stimulate growth
—- is negatively associated with C. diff
C. scindens → bile acid producing clostridia that limits the expansion of pathogenic C. diff
what bacteria in fortiflora
enterococcus faecium
— can be used to treat mastitis
lactococcus lactis
(lactic acid bacterium will inhibit gram + mastitis pathogens)
probiotics for bovine mastitis are cultured, freeze dried that then rehydrated in
polysorbate/liquid paraffin
