rumen microbiome ecology and function - gen2phen · rumen microbiome ecology and function r. john...
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Rumen microbiome Ecology and function
R. John Wallace Rowett Institute of Nutrition and Health, University of Aberdeen, UK
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Rowett picture
“The Institute aims to conduct research at the forefront of nutrition: to define how nutrition can prevent disease, improve health, and enhance the quality of food
production in agriculture”
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The rumen
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CA TTLE AND SHEEP
Stomach (Abomasum)
Rumen
Reticulum
Omasum
Jejunum
Ileum
Colon
Caecum
PIG
Stomach
Jejunum
Ileum
Caecum
Colon
Gut anatomy
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The three domains of life
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Rumen ciliate protozoa
100 µm
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Enchelyodon sp.
Amylovorax dehorityi Bitricha tasmaniensis
Amylovorax dogieli Dasytricha ruminantium U57769 Dasytricha ruminantium (France)
Dasytricha ruminantium U27814 Epidinium caudatum Ophryoscolex purkynjei
RS65 Polyplastron multivesiculatum U27815 Polyplastron multivesiculatum (Poland) RS53
Polyplastron multivesiculatum U57767 Polyplastron multivesiculatum (France) Diplodinium dentatum
Ostracodinium dentatum (Poland) Enoploplastron triloricatum (Slovakia) Eudiplodinium maggii (France)
Eudiplodinium maggii (Poland) Eudiplodinium maggii RS61, RS99
Diploplastron affine (Poland) RS59
RS70 RS88, RS33 RS7
RS87 RS24
RS74 RS17
RS100, RS95 RS28 RS2
RS75 RS31 RS57
RS86 RS90
RS94 RS67, RS1
RS58, RS18, RS16, RS3 Entodinium nanellum (Slovakia)
RS14 RS89, RS97, RS63, RS13 RS105 Entodinium furca monolobum (Slovakia)
RS26 RS30 RS85
RS77 RS73
RS12 RS4 RS79 Entodinium bursa (Slovakia) RS71 RS64
Entodinium caudatum
Entodinium caudatum (UK) RS62
RS82, RS32, RS69, RS66, RS22 RS9 Entodinium caudatum (Slovakia)
RS92
RS93 Entodinium D?( France) RS5, RS107
Isotricha intestinalis Isotricha intestinalis (Poland) Isotricha prostoma (Slovskia) Isotricha prostoma (Poland) Isotricha prostoma (France)
RS19
100
100
73
97 100
100 91 92
100
100 96
94
94
100
77
95
85
69
79
Didinium nasutum
Unexpected protozoal diversity
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Fungal picture
Rumen anaerobic fungi
50 µm
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Fungal picture
© R.J. Wallace 2004
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Fungal life cycle
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Rowett picture
1 µm
Rumen bacteria
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Proteobacteria M ethanomicrobium mobile (M59142)
0.1
82 .7
88 .3
Proteobacter ia (OTUs 1-3)
Cytophaga-Flexibacter-Bactero ides Group (OTUs 6-78)
Low G+C Gram Positive Bacteria (OTUs 80-174)
Fibrobacter Group (OTU 175)High G+C Gram Positive Bacteria (OTUs 176 &177)Chlamydiales -Verrucimicrobia Group (OTUs 1 78 & 179)Spirochaetes (180)
Phylum? (OT U 4)
Phylum? (OTU 5)
Phylum? (OTU 79)
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8
Figure 9
High bacterial diversity
Cytophaga-Flexibacter-Bacte [CFB]
Proteobacteria
Low G+C Gram positive
High G+C Gram positive, Fib Spirochaetes, etc
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Rumen methanogenic archaea
1 µm
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Fermentation
H2 + CO2
CH4
Protozoa, fungi, bacteria Archaea
Methane production in ruminants
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109 - 1010 BACTERIA
Up to 106 PROTOZOA
?? ANAEROBIC FUNGI
108 ARCHAEA
per g digesta
FOOD
UNDIGESTED FOOD +
MICROORGANISMS
ACETATE
VFA PROPIONATE
BUTYRATE METHANE
Metabolism in
the rumen
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Hot topics in rumen microbiology
• Metagenomics • Methane
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Technological advances: 454 sequencing
The latest pyrosequencing platform by 454 Life Sciences (now owned by Roche Diagnostics), can generate 400 million nucleotide data in a 10 hour run with a single machine.
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Technological advances: Illumina sequencing
Nature 9 Sept 2010
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Science 28 Jan 2011
Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen
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Science 28 Jan 2011
Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen
The paucity of enzymes that efficiently deconstruct plant polysaccharides represents a major bottleneck for industrial-scale conversion of cellulosic biomass into biofuels. Cow rumen microbes specialize in degradation of cellulosic plant material, but most members of this complex community resist cultivation. To characterize biomass-degrading genes and genomes, we sequenced and analyzed 268 gigabases of metagenomic DNA from microbes adherent to plant fiber incubated in cow rumen. From these data, we identified 27,755 putative carbohydrate-active genes and expressed 90 candidate proteins, of which 57% were enzymatically active against cellulosic substrates. We also assembled 15 uncultured microbial genomes, which were validated by complementary methods including single-cell genome sequencing. These data sets provide a substantially expanded catalog of genes and genomes participating in the deconstruction of cellulosic biomass.
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Fig. 2 (A) Sequence identity of 90 candidate sequences assembled from the switchgrass-associated rumen microbiome and tested for carbohydrate-degrading activity to known
carbohydrate-active enzymes.
M Hess et al. Science 2011;331:463-467
Published by AAAS
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Fig. 3 Carbohydrolytic potential of candidate carbohydrate-active enzymes on glycosidic substrates of different complexity.
M Hess et al. Science 2011;331:463-467
Published by AAAS
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Science 28 Jan 2011
Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen
Genome Bin Genome Size (Mb) Phylogenetic Order Estimated Complete-ness AFa 2.87 Spirochaetales 92.98% AMa 2.21 Spirochaetales 91.23% AIa 2.53 Clostridiales 90.10% AGa 3.08 Bacteroidales 89.77% AN 2.02 Clostridiales 78.50% AJ 2.24 Bacteroidales 75.96% AC2a 2.07 Bacteroidales 75.96% AWa 2.02 Clostridiales 75.77% AH 2.52 Bacteroidales 75.45% AQ 1.91 Bacteroidales 71.36% AS1a 1.75 Clostridiales 70.99% APb 2.41 Clostridiales 64.85% BOa 1.67 Clostridiales 64.16% ADa 2.99 Myxococcales 62.13% ATa 1.87 Clostridiales 60.41%
Genome Bin APb 55 Scaffolds 2.41 Mb
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Hot topics in rumen microbiology
• Metagenomics – The Hungate 1000 project
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Methane, ruminants and the environment
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Greenhouse gases: CO2
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Methane as a greenhouse gas
CH4 has a global warming potential (“radiative forcing”) 25 times that of CO2 Methane contributes approximately 18% to the overall global warming effect
US Environmental Protection Agency, 2000
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Methane as a greenhouse gas
Dlugokencky et al., 2003
t½ of CH4 in atmosphere is 12 years
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70% of global methane formation is due to man's activities
Sources of atmospheric methane
US Environmental Protection Agency, 2001
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Therefore, 20% of global methane formation is due to ruminants
Sources of atmospheric methane
US Environmental Protection Agency, 2001
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And so 20% of the 18% = 3.6% of the total radiative forcing is caused by ruminants
Sources of atmospheric methane
US Environmental Protection Agency, 2001
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Ruminants, cars and methane 164 g CO2/km at 19,000 km/year
= 164 × 19000 g CO2/year = 3 × 106 g CO2/year
=
500 L CH4/day = 365 × 500 L/year = 2 × 105 L/year = 2 × 16/22 × 105 g/year = 1.5 × 105 g/year ≅ 25 × 1.5 × 105 g CO2/year ≅ 3 × 106 g CO2/year
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Ruminants, cars and methane =
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Ruminants, cars and methane =
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The New Zealand response
Carbon tax As part of the Climate Change Policy Package, released in 2002, the government will be introducing a carbon tax in New Zealand from April 1, 2007. Hon. Pete Hodgson, Convener of the Ministerial Group on Climate Change, has announced that the carbon tax will be set at $15 per tonne of CO2 and has released a consultation paper on the implementation of the tax. Now New Zealand leads the Global Research Alliance
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Methane production in ruminants
95% 5%
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Other important topics in rumen microbiology
• Protein metabolism • Fatty acid metabolism • Rumen dysfunction • Feed additives
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Protein metabolism in the rumen
Protein
Peptides
Amino acids
Ammonia
Ammonia
Undegraded food protein +
Microbial protein
Food protein
Microbial protein
B C
A
Urea
INEFFICIENCES
Loss of N Microbial protein breakdown Amino acid imbalance
B
C
A
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Protein metabolism in the rumen
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Proteolytic ruminal microorganisms
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Proteinase zymograms from ruminal fluid
Protease in rumen fluid supernatants
• Falconer & Wallace (1998)
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Zymogram of proteolytic activity in the rumen of sheep
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Properties of rumen proteinases
• Mainly cysteine proteinases • Cell surface-associated • Low activity • Activity increases 3-fold or more in animals
receiving fresh forage
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Microbial protein turnover
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Fig. 8. Chemical classes of saponins
Steroid
O
O H
O
O
3
22
25 26 27
Steroidal alkaloid
N H
O H
O
O
3
22
2 26
Triterpene O H
3
28
Chemical classes of saponins
R R
R
R = sugars
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Multipurpose trees Fuel Shelter Fertilisation Water retention Protein supplement Rumen manipulating agent
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0
5
10
15
20
25
30
35
0 1 2 3Incubation time (h)
Deg
rada
tion
of S
. rum
inan
tium
(%)
Influence of Sesbania sesban on the bacteriolytic activity of ruminal protozoa
Control
1 g/l
10 g/l
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0
5
10
15
20
25
0 7 14 21 28 35 42
Days of experiment
Num
ber
of p
roto
zoa
(x10
5 /ml)
Influence of Sesbania sesban on protozoal numbers in the sheep rumen
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Fig. 8. Chemical classes of saponins
Steroid
O
O H
O
O
3
22
25 26 27
Steroidal alkaloid
N H
O H
O
O
3
22
2 26
Triterpene O H
3
28
Chemical classes of saponins
R R
R
R = sugars
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Effect of addition of Enterolobium cyclocarpum N
umbe
r of p
roto
zoa
(105 /m
l)
Days of experiment
J J
J
J
J
J J J
J
J J
J J J
J
1 3 5 7 8 9 10 0
5
10
15
20
25 Enterolobium cyclocarpum addition
1 1 12 13 14 16 18 20 21
on protozoal numbers in sheep
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Rumen epithelium
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Effects of flavomycin in sheep
• Gut tissue turnover >40% of total body protein synthesis; <5% of body weight
• Flavomycin causes 20% decrease in gut protein turnover in sheep
• Flavomycin produced a 20% increase in LWG (MacRae et al. 1999)
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Influence of flavomycin on gut tissue turnover in sheep
CONTR +FLAVOMY SE ProbabilRumen 13.9 10.1 1.8 0.075Abomasum 16.6 15.1 3.2 NSDuodenum 48.0 36.7 4.1 0.027Jejunum 42.8 38.3 3.7 NSIleum 36.5 34.7 2.3 NSCaecum 20.2 17.9 2.0 NSLarge 24.5 26.4 5.0 NSLiver 15.5 18.0 3.0 NS
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Influence of flavomycin on ruminal bacteria
Gram -ve Species Strain MIC50 (mg/ml) Fusobacterium necrophorum A54, A12 0.25 Fibrobacter succinogenes S85 0.5 Ruminobacter amylophilus WP109 4 Veillonella parvula L59 4 Prevotella albensis M384 8 Megasphaera elsdenii J1 32 Prevotella bryantii B14 32 Anaerovibrio lipolytica 5S >64 Mitsuokella multiacidus 46/5 >64 Prevotella brevis GA33 >64 Prevotella ruminicola 23 >64 Selenomonas ruminantium HD4 >64 Selenomonas ruminantium Z108 >64
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Protein metabolism in the rumen
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Biphasic Breakdown of Peptides
Dipeptidyl peptidase
Rapidly degraded peptides • Ala or other neutral AA at N-terminus • Neutral or basic peptides
Slowly degraded peptides • Gly or Pro at N-terminus or
(n-1) residue • Acidic AA residues • Blocked N-terminus
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NH2-CR-CO-[NH-CO-CR]N-COOH
N-terminal blocking of peptides
NH-CR-CO-[NH-CO-CR]N-COOH CH3-CO-
Acetic anhydride
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15N recovery determinedat the ileum
15N-peptides injectedinto jejunumRumen Caecum &
colon
Nutritive value of N-terminally blocked peptides
>97% absorption of acetylated peptides
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Proteolytic ruminal microorganisms
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Properties of ammonia production
Organism Ammoniaproduction
rate (nmol/mgprotein/min)
Monensinsensitivity
Growth onpeptides
Mixed rumenbacteria
30 Partly +
Megasphaeraelsdenii
19 No -
Selenomonasruminantium
15 No -
Prevotellaruminicola
14 No -
Peptostreptococcusanaerobius
346 Yes +
Clostridiumsticklandii
367 Yes +
Clostridiumaminophilum
318 Yes +
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Properties of ammonia production
Organism Ammoniaproduction
rate (nmol/mgprotein/min)
Monensinsensitivity
Growth onpeptides
Mixed rumenbacteria
30 +
Megasphaeraelsdenii
19 No -
Selenomonasruminantium
15 No -
Prevotellaruminicola
14 No -
Peptostreptococcusanaerobius
346 Yes +
Clostridiumsticklandii
367 Yes +
Clostridiumaminophilum
318 Yes +
Hyper-Ammonia-Producing bacteria
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• Health implications • Biochemistry of lipases and biohydrogenation • Microbial ecology • Why does biohydrogenation occur? • Plant extracts as modifiers • Conclusions
Biohydrogenation of fatty acids in the rumen
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LA
LNA
Saturated fatty acids
BIOHYDROGENATION
unsaturated saturated
LA
LNA C18:2 c9 c12
C18:3 c9 c12 c15
Health implications of biohydrogenation in the rumen
LNA – linolenic acid LA – linoleic acid
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Fatty acid composition of feed and ruminal digesta
(% total fatty acids)
Shorland et al. (1955) Nature 175:1129-1130
Fatty acid Clover pasture Ruminal digesta
C16:0 8.9 16.9
C16:1 7.9 1.8
C18:0 2.8 48.5
C18:1 9.5 19.4
C18:2 8.1 2.9
C18:3 58.9 3.3
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CLA Stimulates Immune Response
Helps Prevent Heart Disease
Helps Prevent Cancer
Health implications of biohydrogenation in the rumen
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cis-9, cis-12 linoleic acid
cis-9, trans-11 linoleic acid
trans-10, cis-12 linoleic acid
Conjugated linoleic acids (CLA)
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CLA in foods
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CLA and cancer
Incidence of carcinogen-induced mammary tumours in mice (%)
01020304050607080
0 5 10 15CLA in diet (g/kg)
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CLA and atherosclerosis
Severity of cholesterol-induced aortic lesions in rabbits (on a scale 0-4)
Kritchevsky (2000)
0
0.5
1
1.5
2
2.5
0 1 5CLA in diet (g/kg)
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CLA and body composition
Influence of dietary CLA (5 g/kg for 32 d) on body fat composition in mice (%)
Park et al. (1997)
02468
101214161820
Protein Fat
ControlCLA
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CLA and immune modulation
• Enhanced immune function: – Lymphocyte proliferation in pigs (Chew et al., 1997a)
• CLA suppress inflammatory bowel disease • Protection from metabolic effects of infection:
– Chicks fed CLA resisted growth suppression by LPS injection (Chew et al., 1997b)
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CLA in foods
To provide 10 g of CLA/day requires 3.6 kg cheese
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How can we increase our intake of CLA?
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Aims
• Aims To increase the CLA
content of meat and milk To increase PUFAs in
meat and milk To increase MUFAs in
meat and milk
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Lipase
Bacterial lipases in the rumen
• Lipases hydrolysing triacylglycerol (TAG) : Anaerovibrio lipolytica
• Lipases hydrolysing phospho- and galactolipids : Butyrivibrio spp.
• Lipolysis essential for fatty acid biohydrogenation to occur
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Rumen Animal tissues
C C C C C
C C C C C
2H
vaccenic acid
C C C C C
9 12 C C C C C
C C C C C
2H
C C C C C
2H
linoleic acid
vaccenic acid (VA)
stearic acid
cis cis
cis cis trans trans
trans trans
cis-9, trans-11 CLA
cis-9, trans-11 CLA
CLA is an intermediate in the biohydrogenation of linoleic acid
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Ruminal microorganisms
50 µm
0.5 µm
100 µm
Ciliate protozoa 106 per g digesta
Anaerobic fungi 103 per g digesta
50 µm
Bacteria 1010 per g digesta
Methanogenic archaea 108 per g digesta
0.5 µm
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Role of protozoa in ruminal fatty acid metabolism
0.0
0.5
1.0
1.5
2.0
2.5
3.0
3.5
0 2 5
Time after feeding (h)
cis9
, tra
ns11
C18
:2 (u
g/m
g pr
otei
n)
ProtozoaBacteria
0.0
1.0
2.0
3.0
4.0
5.0
6.0
7.0
0 2 5
Time after feeding (h)
tran
s11
C18
:1 (u
g/m
g pr
otei
n)ProtozoaBacteria
From Devillard et al. (2006) Br. J. Nutr. 96, 697-704
0
2
4
6
8
10
12
14
Isotric
ha pr
ostom
a
Entodin
ium na
nnelum
Entodin
ium fu
rca m
onolo
bum
Anoplo
dinium
dentic
ulatum
Entodin
ium ca
udatu
m
Epidinium
ecau
datum ca
udatu
m
Ophryo
scole
x caud
atus
Diplop
lastro
n affin
e
Fatty
aci
ds (g
/100
g to
tal f
atty
aci
ds)
C18:1 t11Total CLA
CLA VA
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C C C C C
9 12 C C C C C
C C C C C
2H
C C C C C
2H
linoleic acid
conjugated linoleic acid
vaccenic acid
stearic acid
-10
0
10
20
30
40
50
60
70
0 5 10 15 20 25
Time (h)
µg
fatt
y ac
ids/
mg
prot
ein
CLA and VA formation from LA
VA, bacteria VA, total CLA, total
CLA, bacteria
VA, protozoa CLA, protozoa
Role of protozoa in ruminal fatty acid metabolism
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1 2 3 4 5 6 8 7 9 10 11
Role of protozoa: incubations with [14C]stearic acid
C18:0
C18:1
Protozoa Bacteria
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Protozoal fatty acid metabolism
C C C C C
C C C C C
2H
trans-11-vaccenic acid
C C C C C
9 12 C C C C C
C C C C C
2H
C C C C C
2H
linoleic acid
trans-11-vaccenic acid
stearic acid
cis cis
cis cis trans trans
trans trans
cis-9, trans-11 CLA
cis-9, trans-11 CLA
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• Contain high concentrations of PUFA, including CLA and VA
• Carry out neither biohydrogenation nor desaturation
• Ingested bacteria carry out biohydrogenation. Other observations at least partly due to ingestion of chloroplasts
Microbial ecology: role of protozoa
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Role of anaerobic fungi in fatty acid metabolism
Anaerobic fungi produce cis-9,trans-11-18:2 from LA
Nam & Garnsworthy (2007). J. Appl. Microbiol. 3, 55-56
OUR DATA Neocallimastix frontalis produced 25 µg/ml CLA from 50 µg/ml LA in 96 h
Maia et al. (2007) Ant. v. Leeuw. 91, 303-314
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Microbial ecology: role of bacteria
>350 bacterial species
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PrevotellaJK668JK669G222JK205SU6C-proteoH17c SANCDO 2435JK724X2D62UC142Bu43NCDO 2432NCDO 2434NCDO 222210295JK611NCDO 2398JK612Mz9Mz3JK614JK609JK615WV1ATCC19171C211NCDO 2221JK662OB156LP1265JK618SH1JK663O110JK23/210296H17cNCDO 2223NCDO 2397Mz5B835NCDO 2249JL5JK626JK10/1JK86AR11SR8510316Mz7JK729S2/1010317D6/1JW11DSM9787Mz6Mz4JK170SH13Mz8pC-XS6A46pC-XS7NCDO 2399pC-XS2JK633JK730
100
74
95
78
99
97
79
9283
100
9480
77
99
98
82
92
89
Butyrivibrio proteoclasticus
Butyrivibrio hungatei
Butyrivibrio fibrisolvens and Pseudobutyrivibrio spp.
CLA, VA formed
from LA
Produce C18:0
Microbial ecology: role of bacteria
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Seven dairy trials: two in
Reading, five in MTT, Finland
Intake, milk production Rumen VFA, NH3, pH
Milk fatty acid composition
qPCR of bacterial population
LIPGENE
Microbial ecology, LIPGENE project results
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Seven dairy trials: two in
Reading, five in MTT, Finland
Intake, milk production Rumen VFA, NH3, pH
Milk fatty acid composition
qPCR of bacterial population
LIP GE
Microbial ecology, LIPGENE project results
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AtB
Bfi
Bhu
Cpr
Sbo
SA But
Pac
Ori
IFor
age
DM
ICon
c D
MIA
dded
Oil
ITot
al O
ilID
MIO
MIN IC
PIS
tarc
hIA
shIW
SCIN
DF
IAD
FIiN
DF
IpN
DF
IME
I12:
0I1
4:0
IC15
:0I1
6:0
I18:
0I1
8:2
n-6
I18:
3(n-
3)I1
8:4(
n-3)
I20:
0IC
20:1
c5IC
20:1
c8I2
2:0
I22:
5(n-
6)I2
2:5(
n-3)
I22:
6(n-
3)I2
4:0
Isat
urat
edIM
UFA
IPU
FAIT
otal
Rumen microbiology and dietary intake
C4:0C6:0C8:0C10:0C12:0C14:0C14:1_c9C15:0C16:0C16:1_totalC16:1_c9C17:0C18:0t_4t_5t_6_8t_9t_10t_11t_12t_13c_9t_15c_11c_12c_13t_16c15c16trans_18:1_totaC18:2C6t_8tt_6_c_8c_t_6_8C7t_9tC7t_9cC8t_10tC8t_10cTotal_CLAC18:3n_6C18:3n_3C18:3_totalC20:0C20:1C20:2Total_saturatesTotal_MUFATotal_PUFATotal_trans
Milk
com
p
Heatmap showing correlations between (vertically) components of milk composition and (horizontally) rumen microbiology and dietary intake