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VETS1003 > microbiomes and fermentation > Flashcards

microbiomes and fermentation Flashcards

1
Q

Anton van Leewenhoek

A

Used his early microscopes to study
his own faeces and his dental plaque
in the 1670s

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2
Q

Microbiome

A
  • 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
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3
Q

Microbiome is critical for

A

digestion

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4
Q

While host mucus protects against invasion
in parts of the GIT, the microbiome itself
protects

A

against potentially pathogenic
bacteria

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5
Q

General microbial molecules, contain microbe specific patterns, These microbial molecules target pattern recognition receptors in intestinal ____ cells

A

Paneth

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6
Q

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

A

antimicrobial molecules

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7
Q

when are paneth cells synthesized after birth

A

Paneth cells synthesized after weeks
to months of birth

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8
Q

Microbial surface molecules are taken up by host across

A

gut lining

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9
Q

Composition of microbiome is important in ____ immune balance

A

systemic

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10
Q

Microbiome protects against pathogens; Some bacteria in microbiome induce _____

A

immunoglobulins

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11
Q

how do microbiota prevent extreme
immune responses- ie allergic responses

A

provide feedback “information”

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12
Q

how does microbiome maintain integrity of gut lining

A
  • 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
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13
Q

In mammals- foetal GIT is

A

sterile; no microbiome

colonized soon after birth

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14
Q

how is microbiome colonized

A
  • 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)
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15
Q

do microbes inhabit the fetus

A

no
but rapidly enter post-birth infants

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16
Q

Composition of microbiome is highly host-_____

A

specific

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17
Q

Composition of micorbiome influenced primarily by

A

phylogeny: Related species have more related GIT microbiomes

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18
Q

Relationships of species had more or less influence than diet or geographic locations for similarity of microbiomes

A

more

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19
Q

What factors regulate the microbiome?

A
  • Age of host
  • Diet of host
  • Antibiotics
  • Disease state
  • Disruption
    • Toxins
    • Parasites
    • Cancer
    • Metabolic disease
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20
Q

which of the forestomachs have higher number of organisms

A

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

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21
Q

rumen wall organisms

A

bacteria, archaea, ciliata, anaerobic fungi
bacteriophage/ arachaephage

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22
Q

axenic environment

A

no bacteria

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23
Q

Milk feeding bypasses the rumen through

A

oesophageal groove

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24
Q

early development of rumen microbiome; colonizers are

A

aerobic bacteria

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25
Q

Early development of microbiome

A
  • 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.
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26
Q

ciliates are ___ of biomass in rumens

A

50%

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27
Q

If you remove protozoa from
bovine rumen:
* increase microbial amino acid supply by ____
* Decrease methane production by ____

A

30%
11%

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28
Q

Ciliates produce _____ through metabolism

A

hydrogen

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29
Q

Some _____ colonise the ciliates
(endosymbiosis) to use the hydrogen ions

A

prokaryotes

These prokaryotes can from their
‘protected’ environments produce
metabolic byproducts

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30
Q

hindgut fermenters site of fermentation

A

Caecum and colon

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31
Q

kangaroos are _____ fermenters

A

foregut

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32
Q

koalas are ____ fermenters

A

hind gut

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33
Q

Metabolic action of microbiome required to

A

convert feed components into usable
sources of energy

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34
Q

fermentation: Microbiome provides enzymes for hydrolysis of large molecules, similar to
glandular digestion but…

A
  1. Much slower than glandular digestion
  2. Substrates altered to a much greater degree
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35
Q

The cell walls of plant cells contain the
polysaccharide

A

cellulose

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36
Q

do vertebrates have cellulases

A

NO
Vertebrates do not have cellulases and few animals are efficient at breaking down cellulose

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37
Q

how do animals break down cellulose

A

animals have established a partnership with symbiotic fermentative microbes (bacteria, single-celled eukaryotes, and fungi) that can break cellulose

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38
Q

what do microbes and animals get out of the relationship

A

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)

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39
Q

Microbiome (bacteria predominantly) digest _____% of the digestible dry matter

A

70-80%

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40
Q

why do animals Require gradual transition from one type of diet to another

A

so microbial populations can adjust

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41
Q

Chewing and rumination increase the _____ available for microbial fermentation

A

surface area

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42
Q

Saliva produced contains ____ and _____ ions these buffer the Volatile Fatty Acids* being produced

A

bicarbonate and phosphate

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43
Q

Plant cell walls, containing cellulose, are important substrates for _____

A

fermentative digestion

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44
Q

pH of rumen usually between

A

6 and 7

however may be lower in grain-fed animals

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45
Q

_____ are the main substrate that provides VFAs (as a byproduct of microbe metabolism),

A

Carbohydrates

46
Q

do microbes need protein for growth

A

yes

47
Q

steps of Carbohydrate Fermentation producing Volatile Fatty Acids

A

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

48
Q

____ is converted into acetate (acetic acid), propionate (propionic acid), butyrate (butyric acid), but also generates H+ and gases (CO2 + CH4). Gases much be removed.

A

Pyruvate

49
Q

Plant matter is ___% CHO (carbs)

A

75

50
Q

_____ 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)

A

Soluble

51
Q

_____ CHOs are digested by bacteria, producing a large proportion of acetate

A

Structural

52
Q

Bacteria that digest starchy foods (eg cereal grains) are generally insensitive to

A

acidity and produce mainly proprionic acid

53
Q

If cow eats high fibre diet →increased ____
High starch diet → increased _____

A

acetate
propionate

54
Q

Papillae are important – provide

A

surface area

55
Q

VFAs are absorbed across the stratified squamous epith. of the gut → major source of

A

energy for herbivores

56
Q

70% of VFA absorbed from

A

rumen-reticulum

57
Q

Absorption increases at ____ pH

A

lower

58
Q

do undissociated or dissociated acids (HAc) diffuse more readily

what about at pH of rumen:

A

undissociated

at pH or rumen dissociated form dominates

59
Q

how are VFAs absorbed

A

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

60
Q

fermentation of proteins results in ____ of a large portion of amino acid

A

deamination

61
Q

Microbial protein digested in _____- digestion of dead bacteria

A

abomasum and SI

62
Q

are ruminants able to recycle N

A

yes

63
Q

Ruminants able to recycle N from

A
  • From NH3 absorbed from deamination of protein in rumen
  • From deamination of endogenous protein in liver
64
Q

favourable conditions in rumen to optimize fermentation

A
  1. Supply substrate
  2. T° 37°C- raised temps affect microbiome
  3. Osmolality ~300 mosm (isosmotic with blood
    for absorption)
  4. Negative oxidation-reduction potential (requires anaerobic conditions)
  5. Indigestible waste removed- large objects
  6. Rate of removal of microbes = regeneration of most favourable microbes-
  7. VFAs must be buffered or removed
65
Q

Two basic patterns occur for reticulorumen motility

A
  • Primary or mixing contractions: Occur every 1 to 3 minutes
  • Secondary or eructation contractions: Occur every other primary contraction
66
Q

primary contractions

A
  • 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
67
Q

secondary contractions

A
  • Occur every other primary contraction
  • When occur do so immediately following 1° contractions
  • Results in gas entering oesophagus and being
    eructated
68
Q

Primary contractions (mixing) steps/ which direction each sac is moving

A
  1. biphasic contraction of reticulum, virtually obliterating lumen of reticulum
  2. caudal-moving peristaltic contraction of dorsal sac
  3. caudal-moving peristaltic contraction of ventral sac
  4. cranial-moving contraction of dorsal sac
  5. cranial-moving contraction of ventral sac
69
Q

secondary contractions (mixing) steps/ which direction each sac is moving

A
  1. cranial-moving wave starting in dorsal blind sac, forces gas cap cranially
  2. cranial sac relaxes and cranial pillar elevates so liquid ingesta moves away from cardia
  3. gas enters oesophagus and is eructated
70
Q

control of reticulorumen motility: control center is in

A

brainstem
vagus nerve has afferent and efferent fibers

71
Q

Distinct zones or phases of rumen ingesta, top to bottom

A
  1. Gas cap
  2. Solid zone with intertwined forage (rumen mat), floats on slurry as lots of air trapped in between
  3. Slurry zone
  4. Liquid zone
72
Q

Rumen digestion; initial mastication reduced particle size to

A

1-2cm

73
Q

Particles need to be ____ long to pass thru reticulo-omasal orifice

A

2 to 3 mm

74
Q

Food intake and rate of particle passage from the rumen influenced by:

A
  1. Digestibility of feed – how quickly can rumen process feed
  2. Physical characteristics of feed
75
Q

Chopping poorly digestible forages increases rate of passage thru rumen (increasing food intake) but decreases digestibility, why

A

fermentation time is reduced

76
Q

H2O moves thru rumen at much ____ rate than particulate matter

A

faster

77
Q

ingesta for remastication comes from ___ zone in dorsal reticulum, hence partially fermented

A

slurry

78
Q

during reticular contractions; ingesta moves into

A

omasum

79
Q

as omasal orifice closes, canal ____ forcing ingesta into leaves of omasum

Body and leaves contract intermittently, forcing ingesta into _____

A

contracts
abomasum

80
Q

what phase does Anticipation of suckling invokes central stimulation

A

cephalic phase

81
Q

when young are suckling, Fluid in pharynx stimulates afferent fibres that reinforces

A

cephalic phase

82
Q

adults don’t suckle, so what stimulates afferent fibres that reinforces
cephalic phase

A

antidiuretic hormone (ADH)

83
Q

when severely dehdryated rumen drinks gastric groove

A

When a severely dehydrated ruminant drinks, the groove is closed, so that water goes to animal, not rumen.

whens when ADH is secreted

84
Q

ADH promotes

A

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.

85
Q

in horses Fermentation may be aided by

A

prior gastric action (soaking, acid)

86
Q

in horses; Although there is absorption anteriorly, substantial amounts of sugars and starches are not absorbed in SI
This material passes

A

to caecum

87
Q

in horse Proteins are absorbed in ____ however a small amount escapes
digestion and reaches the caecum and colon

A

SI

88
Q

where is urea recycled in horse

A

Urea is recycled into caecum and colon, as with rumen of
complex stomach

89
Q

how long does it take in horse for Soluble ingesta to reach caecum

A

2 hours

90
Q

Caecal and ascending colon contents in horse

A
  • high H2O content
  • slurry-like consistency
91
Q

caecum contractions in horse

A

basic low-amplitude contractions that mix
contents and maintains an homogenous state

92
Q

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

A

caecocolic orifice

93
Q

horse ; pelvic flexure is a ‘pacemaker’ why

A

→ pelvic flexure contracts to only allow small particles to pass into dorsal colon
* → retropulsion in left ventral colon
* → ventral colon stores food (allowing fermentation)

94
Q

horse ; impactions tend to occur at _____ as this is the primary site of
flow restriction

A

pelvic flexure

95
Q

horse caecum and colon mixing

A

Retropulsive (towards mouth) and propulsive peristalsis

96
Q

horse caecum and colon contractions

A
  • segmental contractions
  • brings VFAs into close contact with
    epithelium
97
Q

equine fermentation; unlike ruminants cannot use ___ to buffer VFAs

A

saliva

98
Q

in horse, unlike rumen, large intestine of horse has ____ epthelium

A

glandular

secretes large volumes of electrolytes (Na+, Cl-)
H2O and HCO3-
* H2O needs to be reabsorbed
* reabsorbed with VFAs

99
Q

in horse Considerable absorption of H2O, Na+, and phosphate occurs in

A

descending colon

100
Q

Large water and electrolyte fluxes make horses particularly vulnerable to

A

colonic disease

101
Q

Functional differences between foreand hindgut fermenters

A

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

102
Q

caecotrophy

A

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

103
Q

Microbes responsible for fermentation include

A

bacteria, fungi and protozoa, creating complex ecosystem

104
Q

VFAs produced under _____ conditions, important energy
substrate for host

A

anaerobic

105
Q

Fermentation results in _____ of large portion of aa’s,
nonprotein N sources can also be utilised by microbes

A

deamination

106
Q

Microbial protein can be utilised by ruminants from microbes passing into

A

abomasum and SI

107
Q

_____ maintains environment favourable to
fermentation pattern that benefits host

A

Reticulorumen

108
Q

cattle; Motility is such that it combines with gravity to selectively retain actively fermenting material while allowing unfermentable
residue to pass to ____

A

omasum

109
Q

Reticulorumen motility controlled by ____ and affected by _____

A

CNS via vagus n.
intraluminal conditions

110
Q

VFAs produced during fermentation represent ___% of energy requirements and are absorbed directly thru mucosa

A

60-80

111
Q

Equine hindgut fermentation essentially ___ as for the rumen

A

same

112
Q

horse; Motility patterns retain fermenting material in

A

ascending colon

VETS1003 (23 decks)

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