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Professor Ermias Kebreab UC Davis
Professor Ermias Kebreab. Image credit: UC Davis

CRISPR: A gamechanger for livestock methane reduction? ‘It’s high-risk, high-reward,’ says UC Davis professor

June 26, 2024

From feed supplements to animal breeding to vaccines, multiple approaches are being explored to cut methane emissions from belching ruminants. But if you can edit the genes of the microbes responsible for the problem with a one-time treatment, says Professor Ermias Kebreab, you could change the game.

“It’s high-risk, high reward, but if it works, you won’t have to do anything else.”

A potent greenhouse gasmethane is generated by manure as it decomposes. It is also burped out by ruminants, who produce it in a stomach compartment called the rumen. Here, microbes break down complex carbs and produce gases that are converted into methane by another set of microbes (methanogens).

Dr. Kebreab, a professor at the University of California Davis who has conducted extensive research on livestock methane reduction, is one of a team of academics working on a $70 million initiative backed by the TED Audacious Project.

Led by Dr. Jill Banfield and Dr. Jennifer Doudna at UC Berkeley—pioneers in metagenomics and genome editing respectively—the seven-year ‘Engineering the Microbiome with CRISPR to Improve our Climate and Health’ project aims to develop “precision microbiome editing” to address two challenges associated with microbes: childhood asthma and livestock methane emissions.

AgFunderNews (AFN) caught up with Prof. Kebreab (EK) to discuss the livestock methane component of the study, and other approaches to dealing with cow burps.

Professor Ermias Kebreab, UC Davis
Professor Ermias Kebreab, associate dean of global engagement, UC Davis College of Agricultural & Environmental Sciences, is working with colleagues at UC Berkeley to understand the genomes of methane-producing microbes. Image credit: UC Davis

AFN: In a nutshell, what is the CRISPR project looking at?

EK: Our research on Asparagopsis [red seaweed used as a feed supplement to inhibit methane production via interfering with enzymes microbes need to make methane] shows that the decrease in methane wasn’t caused by a decline in the methanogen populations [microbes that make methane] but by downregulation of genes responsible for methane production, which identified a mechanism we could potentially target [in the CRISPR project].

In the cow’s rumen, bacteria first break down the cellulose and other material in cattle feed and produce hydrogen and carbon dioxide, which methanogens then use, producing methane as a byproduct. If you can identify the genes in these microbes that are responsible for methanogenesis, it may be possible to edit them out, so that they would otherwise function and still use hydrogen as a source of energy but won’t produce methane.

AFN: How might it work in practice?

EK: CRISPR is a pretty new tool when it comes to microbes as opposed to plants and animals. The idea is to find a carrier that will take this CRISPR Cas system to specific microbes and then edit them.

We also have to figure out how to package it so we can give it to calves [via an oral supplement] before the rumen is fully developed, so we’d be effectively reprogramming the rumen. It’s a high-risk and high-reward project, and definitely one of the most exciting approaches [to enteric methane reduction], as if it works, you won’t have to do anything else.

Our editing system could target several of the microbes that make up the cow’s microbiome [communities of microbes in the cow gut], so the first step will be bringing the microbes into the lab, and characterizing model versions of the microbiomes essential to methane production. The next step is to develop the tools so we can deliver editing tools into the target organisms individually.

AFN: How well do we understand the microbiome of cows? Will you need to edit several different kinds of microbes for this to work?

EK: We have started some research starting from calves all the way to adult animals, and we are taking samples every month and trying to understand the development of the microbiome throughout their lives and trying to identify the microbes that are important and needed to make the rumen stable.

Then we need to understand what happens to the animal if you inhibit methanogenesis, so we have experiments going on to try to understand that, as we want to have a functional microbiome. We don’t want to impact microbes that help maintain this microbiome.

AFN: Do you already have some insight from your trials with seaweed supplementation into what happens in the rumen when methanogenesis is inhibited?

EK: There’s only one long term study that was done in dairy that we have to go by, but we don’t really know from that the makeup of the microbiome. So we’re looking at studies now where we try feeding calves seaweed until three weeks after weaning and then we stop and see if there is any kind of reprogramming that we can do, just giving them this this additive at a very early age.

And then there’s another treatment within the study where we look at continuously providing seaweed supplements throughout the cows’ lives, and see what it does to them.

AFN: Can you share a bit more detail on who is doing what in the CRISPR project?

EK: We work with UC Berkeley and UC San Francisco, and our role at UC Davis is focused on the livestock part, while UC Berkeley is focused on the CRISPR tech itself, so at the moment we’re collecting samples [of microbes from cattle rumen and getting the DNA from the organisms] that we send to Berkeley.

Finally, if and when we have a system figured out we’ll do the animal trials [of the final product, likely an oral supplement that can be given to calves to edit microbes in their rumen] at UC Davis, where we have our own dairy farm.

AFN: What progress has been made so far?

EK: Over the past six months we’ve collected a lot of samples from a trial that is right now with five calves but we are aiming to get up to 24 by the end of the year. We’re taking samples every month from those calves and analyzing what’s happening [in the rumen].

Cow burps are a significant source of methane emissions
A potent greenhouse gas, methane is generated by manure as it decomposes, but is also burped out by ruminants, who produce it in a stomach compartment called the rumen. Here, microbes break down complex carbs and produce gases that are converted into methane by another set of microbes (methanogens). Image credit: UC Davis

AFN: Stepping back, where do you see the CRISPR approach fitting into the broader toolbox of interventions when it comes to enteric methane reduction?

EK: We have to come at this problem from multiple different directions. One approach is to breed animals that are inherently low methane emitters and that’s happening in New Zealand with sheep where they have sheep that are about 12-20% lower in methane [production]. That work is being done in cattle as well, where the natural variability in terms of emissions is about 30%, so that’s definitely one of the interesting tools in the toolbox, especially for grazing animals.

The drawback of this [selective breeding] approach is that it will take a long time.

AFN: Can we learn anything from animals that naturally emit less methane that might help inform other enteric methane reduction strategies?

EK: We don’t know a lot about why [some cows/sheep produce less methane than others], it could be that they are more efficient at feed conversion, or it’s something about the makeup of their microbiome, but we don’t really know too much about it. We need to find out exactly what makes an animal inherently lower methane emitting.

AFN: What is the potential of seaweed [Asparagopsis] as a feed additive for methane reduction?

EK: You can see huge reductions in emissions from seaweed but there’s still more work that needs to be done and which is being done to ensure it’s safe for animals and people, so we don’t have an issue in terms of the increased level of iodine and bromide.

It’s less of an issue in beef cattle because [these substances] don’t really accumulate in the cells, whereas in dairy, it could impact the milk, although you can grow seaweed with less iodine. With bromide it’s more challenging because you want bromoform [one of the key components in red seaweed that inhibits methane production], so how do you make sure you have enough bromoform but you don’t have bromide in the end product?

AFN: You’ve also done some recent research on grape pomace as a methane inhibitor?

EK: Grape pomace [a byproduct of wine production] contains some tannins and lipids which have been shown to reduce emissions, so we did an experiment looking at if we supplement with an appreciable amount of grape pomace, 10-15%, of an alfalfa-based diet for dairy cows, what impact would that have?

We saw about a 10-12% reduction in emissions, better feed efficiency, and a [positive] change in the fatty acid composition of the milk.

AFN: What in your view will drive update of feed additives or other tech to tackle enteric methane production?

EK: There has to be some sort of incentive so you’ll probably see more big players that buy a lot of milk generating [carbon] credits or accessing funds [that will help cover the cost of feed additives for farmers]. But I don’t see many farmers doing it themselves right now, whereas the multinational companies have already committed to reduce emissions.

A new video from the Innovative Genomics Institute below explains what the researchers are working on in more detail:

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