Sheep breeders could have a faster and more flexible way to identify low-methane animals, after researchers in New Zealand showed that the microbes living in a sheep’s rumen can reliably predict methane output, and could be used directly in breeding programmes.
In a large-scale study published in the journal Springer Nature, scientists at the AgResearch analysed rumen microbiome data from more than 4,500 lambs across multiple flocks, breeds and years.
The team discovered that microbial ‘fingerprints’ were strongly linked to methane emissions measured using portable accumulation chambers (PAC). Importantly, those microbial signals were heritable and genetically aligned with sheep methane outputs, meaning they can be used to rank animals for selection.
Reducing methane through breeding is seen as one of the most durable ways to cut livestock emissions without sacrificing productivity. But genetic progress depends on measuring enough animals to identify low-methane genetics; something that remains limited by the cost, availability and the time it takes to process animals using methane measurement equipment.
PAC units are currently the main on-farm tool used to measure methane in sheep. While they’re effective, a single PAC trailer can typically measure fewer than 100 animals per day, and access is often constrained by logistics and seasonal demand.
Overcoming data bottlenecks
The researchers tested whether rumen microbiome data could help overcome that bottleneck. Each sheep has a unique mix of microbes in its rumen that drives how feed is fermented and how much methane is produced. By sequencing DNA from a rumen fluid sample, the team generated a rumen metagenome community (RMC) profile — effectively a microbial fingerprint for each animal.
Using this approach proved to be a clearer way of ranking sheep for methane than relying on the animal’s DNA alone. Methane levels predicted from rumen microbes more closely matched PAC measurements than predictions based only on an animal’s genetics.
When methane output was compared with measurements taken in PACs, predictions based on rumen microbes were about twice as accurate as genomic predictions. They also showed a strong genetic link (0.75) with methane measured using portable chambers, proving that the two measures were closely aligned.
Importantly for breeding, the study showed that differences in microbial profiles were partly controlled by the animal’s genetics and could therefore respond to selection.
That genetic link means rumen microbiome data can be used as a proxy for methane measurements when ranking animals, and could be incorporated into breeding programs, the researchers said.
Speedier sampling
From a practical perspective, the cost of generating a rumen microbiome profile is similar to a PAC measurement, at about NZ$60 (GBP£26/USD$35) per animal. However, sampling can be carried out much faster – a small team can collect rumen samples from 250–300 sheep per day, compared with fewer than 100 animals using a PAC trailer.
Scaling microbiome sampling also relies on people rather than specialised infrastructure, making it easier to increase throughput. This could allow more animals to be assessed within the same breeding window, helping breeders identify low-methane genetics earlier.
The study also found that rumen microbiome-based methane rankings were consistent across flocks and years, supporting their use beyond experimental settings.
“The methane traits generated from the RMC profiles are predictive of an animal’s methane emissions relative to an overall flock and are genetically correlated with PAC methane traits,”the authors said.
Despite the potential, the researchers said there are still limitations. Rumen microbiome profiles are influenced by factors such as diet, age and sampling time, meaning animals need to be compared within similar groups to maintain reliable rankings. Integrating microbiome data into national genetic evaluations will also require further development.
Even so, the researchers said the findings suggest rumen microbiome profiling could significantly expand the number of animals that can be ranked for methane genetics.
Want to read more stories like this? Sign up to our newsletter for bi-weekly updates on sustainable farming and agtech innovation.
