The Microbiome

and Methane

Elizabeth Ross / October 2013 Department of Environment and Primary Industries Victoria

You are mostly not human

and

Cows are mostly not cows

Can we use the rumen metagenome

(DNA from the microbiome

community) to predict methane

emission levels from ruminants?

Methods

–Illumina sequencing

–Low depth profiling

–All species

- not just methanogens

Contig 1 Contig 2 Contig 3 ...

Cow A 1 0 32

Cow B 47 10 1086

Cow C 6 23 892

....

Methods

–Association study?

–BLUP – metagenomic predictions

–Many small effects

Methods

–Predict ‘unknowns’

–Correlate prediction with real

phenotypes

–r is accuracy ( ≤ 0 is no prediction )

Methods –2 Reference populations

• GMC M + P

• FT M + P

–2 Validation populations

• FCE 1 M only

• FCE 2 M only

-0.6 -0.1 0.4 0.9

Accuracy (r)

Validation N=16

-0.6 -0.1 0.4 0.9

Accuracy (r)

FT

GMC

Accuracy

N=15

N=31

Validation N=16

Methane emission variation in

dairy cattle can be predicted

using microbiome profiles.

What’s next?

Beef data

Different references

Repeatability between years

Sex effects

Faeces based predictions

Consider this:

Sample storage

Prep cost (time and $$$)

Re-analyse data

Best phenotype

Collaboration and communication

Acknowledgements

– Ben Hayes

– Ben Cocks

– Peter Moate

– Leah Marett

– La Trobe University

– The Gardiner Foundation

– Dairy Futures CRC

– DEPI

Elizabeth Ross

www.dairyfuturescrc.com.au