Microbiome & Fermentation Flashcards
The microbiome is located
Virtually on all open surfaces, especially the skin and GIT
The microbiome is a dynamic community that is (3)
-host specific
-site specific
-individual specific
5 ways the microbiome is critical for digestion
-fermentation
-synthesis of vitamins K and B12
-conversion of some amino acids into simple sugars, VFAs, etc
-breakdown of polyphenols into active molecules
-removal/deactivation of drugs/xenobiotics
Microbial molecules target
Pattern recognition receptors in intestinal Paneth Cells
intestinal Paneth cells are synthesized
After weeks to months post-birth
Paneth cells induce secretion of
Antimicrobial molecules
Microbial molecules include (6)
-peptidoglycan
-LPS
-lipid A
-flagella
-bacterial RNA/DNA
-fungal cell wall beta-glucans
Microbial surface molecules are taken up by the host
Across the gut lining
Microbiota provides
Feedback information to prevent extreme immune responses (ie. allergic reactions)
Some bacteria in the microbiome will induce
Immunoglobulins
Composition of microbiome is important in ___ immune balance
Systemic
3 major functions of the GIT microbiome
-protection
-structure
-metabolic
Bacteroides thetaiotaomicron is said to help maintain
Desmosomes through production of a molecule
Lactobacillus species can impair ____ of lining cells
Apoptosis (programmed cell death)
Meconium
First faeces occurring within 40 hours of birth
In mammals, the foetal GIT is
Sterile
During vaginal delivery, early GIT microbiome will feature
Microbes of the reproductive tract
Diversification of microbiome is dependent on
Feed
4 ways microbes can be ingested
-feed
-from environment
-faeces
-respired (especially rumens)
In a caesarean delivery, early GIT microbiome features
Microbes of the skin
True or False: microbes inhabit the foetus
False. Microbes enter rapidly post-birth in infants
Composition of microbiome is highly ____ and influenced primarily by ___
Host-specific; phylogeny
Related species have a more
Related GIT microbiome
Which two species have evolved to have a shared microbiome? Why?
-humans and dogs
-domestication and close association
Different regions of the mouth will have
Different microbial community structures
5 factors that regulate the microbiome
-age of host
-diet of host
-antibiotics
-disease state
-disruption (toxins, parasites, cancer, metabolic disease)
Neoplasia is
A new (abnormal) growth of cells/tissues
In one study, it was found diseased dogs had
A grater diversity of certain bacteria species
In ruminants, the numerical density of organisms is highest in ____ lowers in ____ and increases in ____
Highest in the rumen and reticulum; lower through the omasum, abomasum, and small intestines; increases in the hind-gut
The most numerous microbial group in the rumen are
Bacteria
Archae are the rumen’s
Methanogens
5 types of microbial groups in the rumen wall
-bacteria
-archaea
-Ciliata (single cell eukaryotes)
-anaerobic fungi
-bacteriophage/archaeaphage
Which microbial group is the regulator of microbial populations in the rumen
Bacteriophage/archaeaphage
In the rumen, the early microbiome of calves reflects
The dam’s reproductive tract
The oesophageal groove is used to
Allow milk to bypass the rumen
Fermentation activity is induced by (2)
-solid food
-ruminal papillae
Development of the rumen microbiome (5)
- Colonizers are Aerobic bacteria
- Aerobic bacteria are replaced by Anaerobes
- By 1-2 weeks of age, cellulose digesting bacteria and fungi appear
- After 2 weeks of age, ciliates appear
- At weaning, diversity of all groups drops
Microbiome diversity of the rumen will increase with (3)
-age
-diversification of diet
-husbandry
Ciliates of the rumen (2)
-apex predators
-50% of biomass
If you removed Protozoa from the bovine rumen (2)
-increase microbial amino acid supply by 30%
-decrease methane production by 11%
Metabolic byproduct of the rumen is
Methane
Ciliates predate on
Bacteria and archeans
Ciliates produce ___ through ___
Hydrogen ions; metabolism
2 sites of fermentation
-forestomachs
-hindgut fermenters
Forestomachs (2)
-highly developed in ruminants
-non-glandular region in horses and rats
The cardiac gland region in foregut fermenters
Does NOT produce HCl or pepsinogen
Which parasite is present in large numbers in a healthy kangaroo gut
Nematodes
Hindgut fermenters (3)
-fermentation occurs in caecum and colon
-variation in anatomy but functionally similar to ruminants
-examples: horse, rabbit, koala, some ruminants
Koalas and kangaroos are
Hind gut fermenters
A koala’s hindgut microbiome is (2)
-low diversity
-highly specialized
Metabolic action of microbiome is required to
Convert feed components into usable sources of energy
Microbiome provides enzymes for
Hydrolysis of large molecules
Compared to glandular digestion, fermentation is (2)
-much slower
-substrates are altered to a greater degree
The cell walls of plant cells contain
The polysaccharide cellulose
Vertebrates lack ___, which means they are inefficient at breaking down ___
Cellulases; cellulose
Animals have established a partnership with _____ that can break down cellulose
Symbiotic fermentation microbes
3 types of symbiotic fermentative microbes
-bacteria
-single celled eukaryotes
-fungi
The microbiome digests ____% of digestible dry matter
70-80%
Microbe species are categorized according to
The type of substrate they ferment
Chewing and ruminantion help to
Increase the surface area available microbial fermentation
Saliva produced contains ___ and ___ which help to ____
Bicarbonate and phosphate ions; buffer VFAs being produced
Higher digestibility of feed will increase
VFA production
The main substrate that provides VFAs are
Carbohydrate
pH of rumen is usually between
6-7
The pH in grain-fed animals may be
Lower than 6-7
Pyruvate is converted into (3)
-acetate
-propionate
-butyrate
Carbohydrate fermentation produces
Volatile Fatty Acids
Plant matter is approximately
75% CHO
Simple sugars are digested ____ than starch
100x faster
soluble CHOs includes
Simple sugars
Storage CHOs include
Starch
Starch is digested ____ than cellulose
5x faster
structural CHOs includ
Cellulose
Structural CHOs are digested by ____, producing a large proportion of ____
Bacteria; acetate
A high fibre diet will result in
Increased acetate
A high starch diet will
Increase propionate production
Amount of VFAs produced depends on
Feed
VFAs are absorbed
Across the stratified squamous epithelium
70% of VFA is absorbed from
Rumen-reticulum
Papillae are important for providing
Surface area for absorption
Absorption of VFA increases at a
Lower pH
Undissociated acids will diffuse
More readily than dissociated forms
Carbonate is used for
Buffering in lumen of rumen
H+ lowers
pH in pericellular region
Carbonic anhydrase in the cell produces
-carbonate
-hydrogen ions
Fermentation of proteins results in (3)
-deanimation of a large portion of amino acid
-formation of VFAs
-ammonia (NH3)
Ruminal microbes can synthesize microbial protein from
Non-protein N sources (ie. ammonia, nitrate, and urea)
Ruminants are able to recycle
Nitrogen
In the liver, freed nitrogen is converted to
Urea
What do ruminants do with urea they have produced? (2)
-recycle to rumen via blood or saliva to convert to microbial protein
-excreted by kidneys
Two basic patterns of reticulorumen motility
-primary or mixing contractions
-secondary or eructation contractions
Primary (mixing) contractions occur
Every 1-3 minutes
Secondary (eructation) contractions occurs
Every other primary contraction
5 steps to primary (mixing) contractions
- Biphasic contraction of reticulum
- Caudal-moving peristaltic contraction of dorsal sac
- Caudal-moving peristaltic contraction of ventral sac
- Cranial-moving peristaltic contraction of dorsal sac
- Cranial-moving peristaltic contraction of ventral sac
3 steps to Secondary (eructation) contractions
- Cranial-moving wave starting in dorsal blind sac which forces gas cap cranially
- Cranial sac relaxes and cranial pillar elevates so liquid ingests moves away from cardiac
- Gas enters oesophagus and is eructated
Control of reticulorumen motility (2)
-control centre in brain stem
-vagus nerve (afferent and efferent fibres)
4 distinct zones/phases of rumen ingest a
- Gas Cap (removed via eructation)
- Solid Zone with Intertwined Forage (rumen mat)
- Slurry Zone (remastication)
- Liquid zone (where small particles sink to be passed through reticulo-orrifice)
The Solid Zone sits on top of the
Slurry Zone
Initial mastication in rumen digestion reduces particle size to
1-2 cm
Particles need to be ___ long to pass through the reticulo-omasal orifice
2-3 mm
Food intake and rate of particle passage from the rumen is influenced by (2)
-digestibility of feed (ie. how quickly the rumen can process the feed)
-physical characteristics of feed
___ moves through the rumen at a faster rate than particulate matter
H2O
Chopping poorly digestible forages will ____ the rate of passage through the rumen, but ____ digestibility
Increase; decreases
Ingests for remastication comes from the ___ zone in the ____
Slurry zone; dorsal reticulum
Ingests moves into the omasum during _____
Reticular contractions
Closure of the gastric groove (4)
-reflex action
-efferent fibres running from brain stem via vagus nerve
-in adults, stimulated by antidiuretic hormone (ADH)
-in calves, anticipation of suckling invokes central stimulation (Cephalic Phase)
Antidiuretic hormone (ADH) is secreted during ____ to promote ____
Dehydration; water conservation
In hindgut fermenters, sugars are starches are
NOT absorbed in the small intestine
___ is absorbed in the small intestine of hindgut fermenters
Proteins
In hindgut fermenters, urea is
Recycled into the caecum and colon
In hindgut fermenters, soluble ingests reaches the caecum in
~2 hours
Caecum and ascending colon in hindgut fermenters have (2)
-high H2O content
-slurry-like consistency
Retropulsive means
Towards the mouth
In horses, every 3-4 minutes there occurs a
Strong contraction where the body and apex shorten and constrict, lifting ingests to the base and through the caecocolic orifice
Retropulsive and propulsive peristalsis in horses help to
Prolong fermentation and absorption
Segmental contractions bring
VFAs into close contact with the epithelium
What part of the horse stores food for fermentation
Ventral colon
Primary site of flow restriction in horses GIT is the
Pelvic flexure
The pelvic flexure in horses
Contracts to only allow small particles to pass into dorsal colon with Retropulsive in left ventral colon
Unlike ruminants, horses cannot
Utilize saliva to buffer VFAs
Unlike the rumen, the horse’s large intestine
Has glandular epithelium that secretes large volumes of electrolytes
Absorption of water, sodium, and phosphate in horses occurs in the
Descending colon
Some species of hindgut fermenters rely on
Coprophagy and caecotrophy (allows food to pass through intestines twice)
