© Natural Resources Institute Finland© Natural Resources Institute Finland1 11.1.2016

Ilma Tapio and

RuminOmics consortium

Natural Resources Institute Finland (Luke)

ilma.tapio@luke.fi

RuminOmics final conference

Paris, France

7th of December, 2015

Field-scale study of rumen function,

efficiency and emissions in dairy cows

‘The 1000 cow study’

Rumen microbiome

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• Introduction

• Overview of the results

• Concluding remarks

Content of the presentation

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Holstein Friesian

UK

NUDC 243

Park 164

Nordic Red

SwedenFinland

Minkio 100 Robacksdalen 100

Italy

Bianchini 185

Gandolfi 48

Franciosi 176

Maize silage Grass silage

South-North gradient

Sampling design

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Rumen sampling by stomach tubing

Samples immediately frozen in liquid N2 or dry ice

Samples freeze-dried and DNA extracted using protocol (Yu and Morisson 2004)

Amplicon library preparation: bacteria-archaea(16S), ciliates (18S), fungi (ITS1)

Metabarcoding sequencing (Illumina)

Sequencing data analysis (OBITools, R)

Rumen sampling design

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3-Low 2-Medium 1-High

Country Farm6.6-15.6

methane g/kg DMI

15.6-22.4 methane g/kg DMI

22.4-39.4 methane g/kg DMI

UK NUDC 48 147 49

Park 47 77 39

Italy Franciosi 16 98 62

Bianchini 132 50 2

Gandolfi 5 39 4

Finland Minkio 0 40 60

Sweden Robacksdalen 5 54 37

Sampling design

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3-Low 2-Medium 1-High

Country Farm6.6-15.6

methane g/kg DMI

15.6-22.4 methane g/kg DMI

22.4-39.4 methane g/kg DMI

UK NUDC 48 147 49

Park 47 77 39

Italy Franciosi 16 98 62

Bianchini 132 50 2

Gandolfi 5 39 4

Finland Minkio 0 40 60

Sweden Robacksdalen 5 54 37

Sampling design

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Bacteria by farmBacteria methane g/kg DMI

high (1), medium (2), low (3)

Rumen bacteria

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Rumen bacteria

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Archaea by farmArchaea methane g/kg DMI

high (1), medium (2), low (3)

Rumen archaea

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Rumen archaea

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Fungi by farmFungi methane g/kg DMI

high (1), medium (2), low (3)

Rumen anaerobic fungi

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Rumen anaerobic fungi

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Ciliate by farmCiliate methane g/kg DMI

high (1), medium (2), low (3)

Rumen ciliate protozoa

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Rumen ciliate protozoa

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• Strong farm subdivision

• No clear microbial community composition correlation with methane output in the total set

• Within farm analysis needed

Concluding remarks

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Thank you!

RuminOmis consortium

Miika Tapio for help with R