microbiomes and fermentation Flashcards
Anton van Leewenhoek
Used his early microscopes to study
his own faeces and his dental plaque
in the 1670s
Microbiome
- The ‘last organ’….to be identified
- An organ that is not an organ, but a
community…or ecosystem - A regulated, interactive community of
microbes in dynamic balance with the
host - Virtually all open surfaces, but
especially skin and GIT
Microbiome is critical for
digestion
While host mucus protects against invasion
in parts of the GIT, the microbiome itself
protects
against potentially pathogenic
bacteria
General microbial molecules, contain microbe specific patterns, These microbial molecules target pattern recognition receptors in intestinal ____ cells
Paneth
General microbial molecules, contain microbe specific patterns, These microbial molecules target pattern recognition receptors in intestinal Paneth cells
These in turn induce secretion of _______ by Paneth cells
antimicrobial molecules
when are paneth cells synthesized after birth
Paneth cells synthesized after weeks
to months of birth
Microbial surface molecules are taken up by host across
gut lining
Composition of microbiome is important in ____ immune balance
systemic
Microbiome protects against pathogens; Some bacteria in microbiome induce _____
immunoglobulins
how do microbiota prevent extreme
immune responses- ie allergic responses
provide feedback “information”
how does microbiome maintain integrity of gut lining
- Bacteroides thetaiotaomicron is said to help maintain desmosomes through production of a molecule (small proline-rich protein 2A)
- Lactobacillus species can impair apoptosis (programmed cell death) of lining
cells - Other bacteria promote proliferation of GIT epithelium
In mammals- foetal GIT is
sterile; no microbiome
colonized soon after birth
how is microbiome colonized
- vaginal delivery- early GIT microbiome features microbes of reproductive tract
- Caesarean delivery- early GIT microbiome features microbes of skin
- Subsequent diversification of microbiome dependent on feed- milk vs artificial, feed
and other factors - Microbes ingested with:
- feed
- from environment
- Faeces
- Respired- (esp rumen microbiome; eruction of cattle disperses microbiome into air)
do microbes inhabit the fetus
no
but rapidly enter post-birth infants
Composition of microbiome is highly host-_____
specific
Composition of micorbiome influenced primarily by
phylogeny: Related species have more related GIT microbiomes
Relationships of species had more or less influence than diet or geographic locations for similarity of microbiomes
more
What factors regulate the microbiome?
- Age of host
- Diet of host
- Antibiotics
- Disease state
- Disruption
- Toxins
- Parasites
- Cancer
- Metabolic disease
which of the forestomachs have higher number of organisms
Numerical density of organisms highest in the rumen and reticulum, lowers through the
omasum abomasum and SI, increases in hind-gut. Some fermentation occurs in hind gut
rumen wall organisms
bacteria, archaea, ciliata, anaerobic fungi
bacteriophage/ arachaephage
axenic environment
no bacteria
Milk feeding bypasses the rumen through
oesophageal groove
early development of rumen microbiome; colonizers are
aerobic bacteria
Early development of microbiome
- Colonizers are aerobic bacteria
- These are supplanted by anaerobes- anaerobic digestion is conducive to fermentation
- By 1-2 weeks, cellulose digesting bacteria and fungi appear
- After two weeks, the ciliates appear
- Appearance of ciliates is disrupted by feed conditions (artificial milk is detrimental to
ciliates- probably indirectly) - At weaning diversity of species of all groups drops, but microbiome diversity increases with age (and probably diversification of diet) and husbandry.
ciliates are ___ of biomass in rumens
50%
If you remove protozoa from
bovine rumen:
* increase microbial amino acid supply by ____
* Decrease methane production by ____
30%
11%
Ciliates produce _____ through metabolism
hydrogen
Some _____ colonise the ciliates
(endosymbiosis) to use the hydrogen ions
prokaryotes
These prokaryotes can from their
‘protected’ environments produce
metabolic byproducts
hindgut fermenters site of fermentation
Caecum and colon
kangaroos are _____ fermenters
foregut
koalas are ____ fermenters
hind gut
Metabolic action of microbiome required to
convert feed components into usable
sources of energy
fermentation: Microbiome provides enzymes for hydrolysis of large molecules, similar to
glandular digestion but…
- Much slower than glandular digestion
- Substrates altered to a much greater degree
The cell walls of plant cells contain the
polysaccharide
cellulose
do vertebrates have cellulases
NO
Vertebrates do not have cellulases and few animals are efficient at breaking down cellulose
how do animals break down cellulose
animals have established a partnership with symbiotic fermentative microbes (bacteria, single-celled eukaryotes, and fungi) that can break cellulose
what do microbes and animals get out of the relationship
The microbes get a nice environment and
plenty of food, the animal gets the microbes’ energy-rich waste products (plus some microbe flesh served on the side)
Microbiome (bacteria predominantly) digest _____% of the digestible dry matter
70-80%
why do animals Require gradual transition from one type of diet to another
so microbial populations can adjust
Chewing and rumination increase the _____ available for microbial fermentation
surface area
Saliva produced contains ____ and _____ ions these buffer the Volatile Fatty Acids* being produced
bicarbonate and phosphate
Plant cell walls, containing cellulose, are important substrates for _____
fermentative digestion
pH of rumen usually between
6 and 7
however may be lower in grain-fed animals
_____ are the main substrate that provides VFAs (as a byproduct of microbe metabolism),
Carbohydrates
do microbes need protein for growth
yes
steps of Carbohydrate Fermentation producing Volatile Fatty Acids
In lumen of forestomach
* CHO in Plant fibres, starch, complex sugars
* Extracellular Digestion (mostly)
*Simple sugars
in cells
* Simple Sugars absorbed by microbial cells
* Endocellular glycolysis
* Pyruvate and H+ and ATP and NADH
–> VFAs
____ is converted into acetate (acetic acid), propionate (propionic acid), butyrate (butyric acid), but also generates H+ and gases (CO2 + CH4). Gases much be removed.
Pyruvate
Plant matter is ___% CHO (carbs)
75
_____ CHOs (such as simple sugars) are digested 100x faster than storage CHOs (such as starch), which are still 5x faster than the structural CHOs (such as cellulose)
Soluble
_____ CHOs are digested by bacteria, producing a large proportion of acetate
Structural
Bacteria that digest starchy foods (eg cereal grains) are generally insensitive to
acidity and produce mainly proprionic acid
If cow eats high fibre diet →increased ____
High starch diet → increased _____
acetate
propionate
Papillae are important – provide
surface area
VFAs are absorbed across the stratified squamous epith. of the gut → major source of
energy for herbivores
70% of VFA absorbed from
rumen-reticulum
Absorption increases at ____ pH
lower
do undissociated or dissociated acids (HAc) diffuse more readily
what about at pH of rumen:
undissociated
at pH or rumen dissociated form dominates
how are VFAs absorbed
Carbonic anhydrase in cell produced carbonate and hydrogen ion
These are secreted.
Carbonate is used for buffering in lumen of rumen H+
lowers pH in pericellular region
- H+ associates with Ac- to form disassociated form of the VFA, which is absorbed
fermentation of proteins results in ____ of a large portion of amino acid
deamination
Microbial protein digested in _____- digestion of dead bacteria
abomasum and SI
are ruminants able to recycle N
yes
Ruminants able to recycle N from
- From NH3 absorbed from deamination of protein in rumen
- From deamination of endogenous protein in liver
favourable conditions in rumen to optimize fermentation
- Supply substrate
- T° 37°C- raised temps affect microbiome
- Osmolality ~300 mosm (isosmotic with blood
for absorption) - Negative oxidation-reduction potential (requires anaerobic conditions)
- Indigestible waste removed- large objects
- Rate of removal of microbes = regeneration of most favourable microbes-
- VFAs must be buffered or removed
Two basic patterns occur for reticulorumen motility
- Primary or mixing contractions: Occur every 1 to 3 minutes
- Secondary or eructation contractions: Occur every other primary contraction
primary contractions
- Occur every 1 to 3 minutes
- Results in circular movement of ingesta in dorsal and ventral sacs that moves denser material over cranial pillar towards reticulo-omasal orifice
secondary contractions
- Occur every other primary contraction
- When occur do so immediately following 1° contractions
- Results in gas entering oesophagus and being
eructated
Primary contractions (mixing) steps/ which direction each sac is moving
- biphasic contraction of reticulum, virtually obliterating lumen of reticulum
- caudal-moving peristaltic contraction of dorsal sac
- caudal-moving peristaltic contraction of ventral sac
- cranial-moving contraction of dorsal sac
- cranial-moving contraction of ventral sac
secondary contractions (mixing) steps/ which direction each sac is moving
- cranial-moving wave starting in dorsal blind sac, forces gas cap cranially
- cranial sac relaxes and cranial pillar elevates so liquid ingesta moves away from cardia
- gas enters oesophagus and is eructated
control of reticulorumen motility: control center is in
brainstem
vagus nerve has afferent and efferent fibers
Distinct zones or phases of rumen ingesta, top to bottom
- Gas cap
- Solid zone with intertwined forage (rumen mat), floats on slurry as lots of air trapped in between
- Slurry zone
- Liquid zone
Rumen digestion; initial mastication reduced particle size to
1-2cm
Particles need to be ____ long to pass thru reticulo-omasal orifice
2 to 3 mm
Food intake and rate of particle passage from the rumen influenced by:
- Digestibility of feed – how quickly can rumen process feed
- Physical characteristics of feed
Chopping poorly digestible forages increases rate of passage thru rumen (increasing food intake) but decreases digestibility, why
fermentation time is reduced
H2O moves thru rumen at much ____ rate than particulate matter
faster
ingesta for remastication comes from ___ zone in dorsal reticulum, hence partially fermented
slurry
during reticular contractions; ingesta moves into
omasum
as omasal orifice closes, canal ____ forcing ingesta into leaves of omasum
Body and leaves contract intermittently, forcing ingesta into _____
contracts
abomasum
what phase does Anticipation of suckling invokes central stimulation
cephalic phase
when young are suckling, Fluid in pharynx stimulates afferent fibres that reinforces
cephalic phase
adults don’t suckle, so what stimulates afferent fibres that reinforces
cephalic phase
antidiuretic hormone (ADH)
when severely dehdryated rumen drinks gastric groove
When a severely dehydrated ruminant drinks, the groove is closed, so that water goes to animal, not rumen.
whens when ADH is secreted
ADH promotes
water conservation: Secreted when dehydrated- promotes water conservation
When a severely dehydrated ruminant drinks, the groove is closed, so that water goes to animal, not rumen.
in horses Fermentation may be aided by
prior gastric action (soaking, acid)
in horses; Although there is absorption anteriorly, substantial amounts of sugars and starches are not absorbed in SI
This material passes
to caecum
in horse Proteins are absorbed in ____ however a small amount escapes
digestion and reaches the caecum and colon
SI
where is urea recycled in horse
Urea is recycled into caecum and colon, as with rumen of
complex stomach
how long does it take in horse for Soluble ingesta to reach caecum
2 hours
Caecal and ascending colon contents in horse
- high H2O content
- slurry-like consistency
caecum contractions in horse
basic low-amplitude contractions that mix
contents and maintains an homogenous state
in horse: Every 3 to 4 minutes there occurs a strong contraction where body and apex of colon shorten and constrict, lifting ingesta to base and thru
caecocolic orifice
horse ; pelvic flexure is a ‘pacemaker’ why
→ pelvic flexure contracts to only allow small particles to pass into dorsal colon
* → retropulsion in left ventral colon
* → ventral colon stores food (allowing fermentation)
horse ; impactions tend to occur at _____ as this is the primary site of
flow restriction
pelvic flexure
horse caecum and colon mixing
Retropulsive (towards mouth) and propulsive peristalsis
horse caecum and colon contractions
- segmental contractions
- brings VFAs into close contact with
epithelium
equine fermentation; unlike ruminants cannot use ___ to buffer VFAs
saliva
in horse, unlike rumen, large intestine of horse has ____ epthelium
glandular
secretes large volumes of electrolytes (Na+, Cl-)
H2O and HCO3-
* H2O needs to be reabsorbed
* reabsorbed with VFAs
in horse Considerable absorption of H2O, Na+, and phosphate occurs in
descending colon
Large water and electrolyte fluxes make horses particularly vulnerable to
colonic disease
Functional differences between foreand hindgut fermenters
Foregut
* Direct availability of microbial protein
and nutrients (essential FAs, vitamins)
* Detoxification
* Rumination allows particle reduction
* Limited availability of dietary glucose
Hindgut
* No direct availability of microbial
protein and nutrients (essential FAs,
vitamins).
* Reliance on coprophagy and
caecotrophy in some species.
* Availability of dietary glucose
caecotrophy
pass food through intestine twice. Ingest soft pellets from anus, heldin stomach and nutrients absorbed. Rabbits can distinguish between faecal balls from LI vs caecum and eat caecal ones
Microbes responsible for fermentation include
bacteria, fungi and protozoa, creating complex ecosystem
VFAs produced under _____ conditions, important energy
substrate for host
anaerobic
Fermentation results in _____ of large portion of aa’s,
nonprotein N sources can also be utilised by microbes
deamination
Microbial protein can be utilised by ruminants from microbes passing into
abomasum and SI
_____ maintains environment favourable to
fermentation pattern that benefits host
Reticulorumen
cattle; Motility is such that it combines with gravity to selectively retain actively fermenting material while allowing unfermentable
residue to pass to ____
omasum
Reticulorumen motility controlled by ____ and affected by _____
CNS via vagus n.
intraluminal conditions
VFAs produced during fermentation represent ___% of energy requirements and are absorbed directly thru mucosa
60-80
Equine hindgut fermentation essentially ___ as for the rumen
same
horse; Motility patterns retain fermenting material in
ascending colon
