The Microbiome and Methane · You are mostly not human and Cows are mostly not cows . Can we use...
Transcript of The Microbiome and Methane · You are mostly not human and Cows are mostly not cows . Can we use...
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The Microbiome
and Methane
Elizabeth Ross / October 2013 Department of Environment and Primary Industries Victoria
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You are mostly not human
and
Cows are mostly not cows
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Can we use the rumen metagenome
(DNA from the microbiome
community) to predict methane
emission levels from ruminants?
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Methods
–Illumina sequencing
–Low depth profiling
–All species
- not just methanogens
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Contig 1 Contig 2 Contig 3 ...
Cow A 1 0 32
Cow B 47 10 1086
Cow C 6 23 892
....
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Methods
–Association study?
–BLUP – metagenomic predictions
–Many small effects
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Methods
–Predict ‘unknowns’
–Correlate prediction with real
phenotypes
–r is accuracy ( ≤ 0 is no prediction )
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Methods –2 Reference populations
• GMC M + P
• FT M + P
–2 Validation populations
• FCE 1 M only
• FCE 2 M only
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-0.6 -0.1 0.4 0.9
Accuracy (r)
Validation N=16
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-0.6 -0.1 0.4 0.9
Accuracy (r)
FT
GMC
Accuracy
N=15
N=31
Validation N=16
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Methane emission variation in
dairy cattle can be predicted
using microbiome profiles.
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What’s next?
Beef data
Different references
Repeatability between years
Sex effects
Faeces based predictions
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Consider this:
Sample storage
Prep cost (time and $$$)
Re-analyse data
Best phenotype
Collaboration and communication
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Acknowledgements
– Ben Hayes
– Ben Cocks
– Peter Moate
– Leah Marett
– La Trobe University
– The Gardiner Foundation
– Dairy Futures CRC
– DEPI
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Elizabeth Ross
www.dairyfuturescrc.com.au