Upload
others
View
0
Download
0
Embed Size (px)
Citation preview
© Natural Resources Institute Finland© Natural Resources Institute Finland1 11.1.2016
Ilma Tapio and
RuminOmics consortium
Natural Resources Institute Finland (Luke)
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
© Natural Resources Institute Finland© Natural Resources Institute Finland2 11.1.2016
• Introduction
• Overview of the results
• Concluding remarks
Content of the presentation
© Natural Resources Institute Finland© Natural Resources Institute Finland3 11.1.2016
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
© Natural Resources Institute Finland
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
© Natural Resources Institute Finland5 11.1.2016
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
© Natural Resources Institute Finland6 11.1.2016
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
© Natural Resources Institute Finland7 11.1.2016
Bacteria by farmBacteria methane g/kg DMI
high (1), medium (2), low (3)
Rumen bacteria
© Natural Resources Institute Finland8 11.1.2016
Rumen bacteria
© Natural Resources Institute Finland9 11.1.2016
Archaea by farmArchaea methane g/kg DMI
high (1), medium (2), low (3)
Rumen archaea
© Natural Resources Institute Finland10 11.1.2016
Rumen archaea
© Natural Resources Institute Finland11 11.1.2016
Fungi by farmFungi methane g/kg DMI
high (1), medium (2), low (3)
Rumen anaerobic fungi
© Natural Resources Institute Finland12 11.1.2016
Rumen anaerobic fungi
© Natural Resources Institute Finland13 11.1.2016
Ciliate by farmCiliate methane g/kg DMI
high (1), medium (2), low (3)
Rumen ciliate protozoa
© Natural Resources Institute Finland14 11.1.2016
Rumen ciliate protozoa
© Natural Resources Institute Finland© Natural Resources Institute Finland15 11.1.2016
• Strong farm subdivision
• No clear microbial community composition correlation with methane output in the total set
• Within farm analysis needed
Concluding remarks
© Natural Resources Institute Finland
Thank you!
RuminOmis consortium
Miika Tapio for help with R