The ruminal microbiome and animal health

R. John Wallace

The ruminal microbiome and animal health

• Ruminal microbiota

• Ruminal function and dysfunction

• The ban of GPA and its consequences

• The microbiome and rumen function

• The microbiome and animal health: SARA

• Conclusions

The three domains of life

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

Fungal picture

Rumen anaerobic fungi

50 m

Rowett picture

1 m

Rumen bacteria

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 1: Phylogenetic tree of 16S rDNA rumen library sequence data.

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

~350 bacterial species

Narrow diversity

Bacteroidetes

Proteobacteria

Low G+C Gram positive

High G+C Gram positive, Fibrobacter,

Spirochaetes, etc

Rumen methanogenic

archaea

1 m

The ruminal virome

We undertook random pyrosequencing of

virus-enriched metagenomes (viromes)

isolated from bovine rumen fluid and

analysed the resulting data using

comparative metagenomics. A high level of

diversity was observed with up to 28 000

different viral genotypes obtained from

each environment.

Berg Miller et al. (2012) Environ Microbiol

14, 207

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

Digestive disorders: lactic acidosis spiral

Rapid ingestion of starch

Streptococcus bovis

takes over

OnlyLactobacillus can grow

Digestive disorders: subacute ruminal acidosis

• 5.1 < pH < 5.8

• No lactic acid

• VFA absorption compromised

• Inappetance, liver abscesses, laminitis

• Very common when high grain fed

• Difficult to detect except post mortem

Digestive disorders: bloat

The ruminal microbiome and animal health

• Ruminal microbiota

• Ruminal function and dysfunction

• The ban of GPA and its consequences

• The microbiome and rumen function

• The microbiome and animal health: SARA

• Conclusions

Regulations controlling use of antimicrobial growth promoters

Sweden Complete ban, 1986 European Union Complete ban, 2006 Australasia Case-by-case North America Case-by-case FAO/WHO Monitor, risk assessment

Concern: antibiotic resistance in animal gut bacteria will be transmitted to human pathogens, making therapy ineffective

Mode of action of monensin: energy metabolism

Cellulose, starch

Glucose

Pyruvate

Propionate Acetate Butyrate

Methane H2

Mode of action of monensin: protein breakdown

• Inhibits ‘hyper-ammonia producing’ bacteria (HAP)

• Adaptation in Prevotella spp. leading to slower

peptide uptake

Digestive disorders: lactic acidosis spiral

Rapid ingestion of starch

Streptococcus bovis

takes over

OnlyLactobacillus can grow

Alternatives to AGP

• Alternative feed additives

– Plant extracts

– Direct-fed microbials

– Bacteriocins

• Bacteriophages

• Immunization

– Methane

– Acidosis

• Genetic control of the microbiome

Essential oils Essential oils are steam-volatile or organic-solvent extracts of plants,

proven to have antimicrobial and insecticidal properties. They

comprise mainly cyclic hydrocarbons and their alcohol, aldehyde or

ester derivatives.

H

H

H

HO

O

HH

H

H

H

H

HH

Eugenol

H

H

HH

HH

H HH

HH

HHH

H

H

Limonene

Influence of essential oils on rumen fermentation

PROTEIN

OLIGOPEPTIDES

DIPEPTIDES

AMINO ACIDS

AMMONIA

COLONISATION

AMYLASE ACTIVITY

ATTACHMENT

R. amylophilus

HAP bacteria

Prevotella spp

O2

Oxygen ingested

with food

Oxygen diffusing

from blood

O2

Yeast

Protection of

ruminal microbes

Direct-fed microbials: yeast culture

Reducing methane emissions in sheep by immunization against rumen methanogens

Wright et al. (2004) Vaccine 22, 3976

25

205

170 169

136

191

172

147 151

189

0

50

100

150

200

250

Meth

an

e (

g/d

ay)

AA1 AA2 AA3 AA4 AA5 LIM6 LIM7 LIM8 LIM9

Sire

Significant differences among sires of 72 tested steers for methane emissions

The ruminal microbiome and animal health

• Ruminal microbiota

• Ruminal function and dysfunction

• The ban of GPA and its consequences

• The microbiome and rumen function

• The microbiome and animal health: SARA

• Conclusions

Science 28 Jan 2011

Metagenomic Discovery of Biomass-Degrading Genes and

Genomes from Cow Rumen

Bacterial communities in the rumen

Sub-acute ruminal acidosis

Denis Krause

1965-2011

High soluble LPS

Barrier function

compromised

E. coli biotypes

Khafipour E et al. Appl. Environ. Microbiol. 2009;75:7115-

7124

Changes in the microbiome in SARA

Khafipour E et al. Appl. Environ. Microbiol. 2009;75:7115-

7124

Changes in the microbiome in SARA: discriminant analysis

Khafipour et al. (2011) Journal of Dairy Science 94, I351 - 360

Changes in the microbiome in SARA: E. coli

Production/

health

Animal

genome

Ruminal

microbiome

The ruminal microbiome and animal health: conclusions/challenges