Dairy methane seminar 13.11.2017

1. © Natural Resources Institute Finland© Natural Resources Institute Finland
Ilma Tapio, PhD
Senior researcher
ilma.tapio@luke.fi
Functional role of rumen
microbiome linked to methane
production in dairy cows

2. © Natural Resources Institute Finland2 16.11.2017
Luke in Jokioinen
Minkiö barn 8 km

3. © Natural Resources Institute Finland3
ATP
H2
CO2
CH4
Bacteria, protozoa, fungi
ArchaeaVFA

4. © Natural Resources Institute Finland
Microbial fermentation patterns are not equivalent
in terms of H2 metabolism and methanogenesis
Carbohydrates
Fibre, Starch
PYRUVATE Acetyl-CoA
ACETATE BUTYRATE
H2 H2
H2 production
Oxaloacetate
H2
Malate
Fumarate
H2
Succinate
Acrylate
PROPIONATE
H2
H2
H2 utilization
CH4
CO2 + 4H2 = CH4 + 2H2O

5. © Natural Resources Institute Finland
Rumen microbiota analysis tools
5 16.11.2017
Microbiota
Metagenome
Metatranscriptome
What species are different?
What genes are different?
Which genes are expressed differently?

6. © Natural Resources Institute Finland
16S V2-V3 region Primer RMID2 Primer F
16S V2-V3 region Primer RMID3 Primer F
16S V2-V3 region Primer RMID4 Primer F
16S V2-V3 region Primer RMID1 Primer F
16S rRNA

7. © Natural Resources Institute Finland
Methane
0
5
10
15
20
25
30
LOW HIGH
Methane(g/kgDMI)
P = 0.004
0
0,5
1
1,5
2
2,5
3
3,5
4
LOW HIGH
Abundance(%)
Archaea
0
2
4
6
8
10
12
LOW HIGH
Abundance(%)
Succinovibrionaceae
P = 0.014
P = 0.002
Four highest and four lowest methane emitters
from 72 beef cattle

8. © Natural Resources Institute Finland
Tammar Wallaby - Herbivore - Foregut fermenter
Has high abundance of Succinovibrionaceae
Produces 20% of methane per DMI compared to cattle

9. © Natural Resources Institute Finland
Figure 2. Methanogenesis pathway
Leahy SC, Kelly WJ, Altermann E, Ronimus RS, Yeoman CJ, et al. (2010) The Genome Sequence of the Rumen Methanogen
Methanobrevibacter ruminantium Reveals New Possibilities for Controlling Ruminant Methane Emissions. PLOS ONE 5(1): e8926.
https://doi.org/10.1371/journal.pone.0008926
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0008926

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Further conclusions:
Differences in abundance of 22 microbial genes explained the variation
in methane emissions by 88%

11. © Natural Resources Institute Finland11 16.11.2017

12. © Natural Resources Institute Finland12 16.11.2017
Feed efficient cows:
Lower microbial diversity
Limited No of metabolic pathways – less diverse metabolites
Better energy utilization by the animal
Feed inefficient cows:
Higher microbial diversity
Higher No of metabolic pathways – more diverse use of resources
Not all metabolites are efficiently utilized by the animal

13. © Natural Resources Institute Finland
The measurement of CH4 yields in sheep.
Weibing Shi et al. Genome Res. 2014;24:1517-1525
© 2014 Shi et al.; Published by Cold Spring Harbor Laboratory Press

14. © Natural Resources Institute Finland
Comparisons of gene and transcript abundance for enzymes involved in methanogenesis
between high and low CH4 yield sheep.
Weibing Shi et al. Genome Res. 2014;24:1517-1525
© 2014 Shi et al.; Published by Cold Spring Harbor Laboratory Press

15. © Natural Resources Institute Finland15 16.11.2017

16. © Natural Resources Institute Finland16 16.11.2017
Chemogenomics targets
Methanogen vaccines

17. © Natural Resources Institute Finland
Needs for the future – collection of samples/data
from large herds in non-experimental settings

18. © Natural Resources Institute Finland

19. © Natural Resources Institute Finland19 16.11.2017

20. © Natural Resources Institute Finland16.11.201720
What are we dealing with?
Microbiome Pan-genome

21. © Natural Resources Institute Finland
Thank you!
Acknowledgements:
Green Technology, Luke;
Bio-based business and industry, Luke;
RuminOmics consortium