Reducing ammonia in poultry production with CRISPR-Cas

Some of the most environmentally damaging gases produced in agriculture, such as ammonia and methane, are produced by the microbes that live within farmed animals. Current strategies for reducing emissions are dependent on careful management of diet and litter/manure with little focus paid to the root cause of the problem: the populations of microbes that fuel gas production. With new tools we are able to precisely remove or control specific microbes within a given environment, without compromising the “good” microbes that are so important for gut health and productivity.

Robert Habgood
Head of Research
FOLIUM Science

Ammonia (NH3) emissions represent severe challenges to the natural environment, agricultural productivity, and to human health. Ammonia is produced by enzymes that reside in microbes living within farmed animals. At FOLIUM Science, we are developing innovative environmental solutions using our CRISPR-Cas technology platform, Guided Biotics®, that precisely modulate these microbial populations with the aim of improving nutrient use efficiency and reducing the environmental footprint of food production.

Ammonia is a highly irritating gas that detrimentally affects the health and welfare of animals, their caretakers, and the surrounding environment. Apart from creating a foul odour, it causes irritation to the eyes, lungs and skin and increases the chances of certain diseases developing in the birds and their handlers. The UK government has committed to achieving a 16% reduction in ammonia emissions – from 2005 levels – by 2030, although reports suggest that a 50% reduction would prevent at least 3,000 premature deaths/year (The Guardian). Agriculture is the predominant source (88%) of the UK’s ammonia emissions (DEFRA) with a large proportion of this arising from animal housing and poultry production. Ammonia emissions can result in deposition of nitrogen in sensitive environments and in areas of intensive poultry production, such as the Wye Valley, this is having a profound impact on biodiversity.

European directives (Council Directive 2007/43/EC) stipulate that ammonia levels should be maintained below 20 ppm in poultry houses, but it is very common for levels to exceed 30-70 ppm in intensive poultry production. High ammonia emissions (>25 ppm) cause a range of problems to producers including reduced productivity, feed intake and feed conversion ratios. When ammonia comes into contact with moisture it forms corrosive ammonium, which can damage the lining of the birds’ respiratory tract. This can prevent mucus from being cleared effectively from the airways and means bacteria are more likely to become trapped in the lungs, which increases the birds’ susceptibility to infection. Corrosive ammonium in the litter can also result in hock burn and skin burns, a sign of poor welfare on farms, which is present on up to a third of birds available in UK supermarkets (BBC). The consumer is now increasingly aware of the environmental impact and welfare of farmed animals and therefore innovative solutions to control ammonia production are needed.

Unused nitrogen excreted from the bird is converted into ammonia under favorable conditions by a process involving microbes. Currently, management strategies to reduce ammonia emissions in livestock housing include limiting dietary protein (and hence, waste nitrogen), optimizing stocking density, providing sufficient ventilation and scrubbing, and careful litter and manure management. These practices are heavily focused on removing or limiting unused nitrogen, providing environmental conditions that are less conducive to ammonia formation, or quick removal of the ammonia once it has formed. They do not deal directly with the root cause of the problem: the microbes that produce ammonia in the first place.

Microbial enzymes called ureases are responsible for the last step in the formation of ammonia and are produced by bacteria residing in the manure and litter. These enzymes represent a promising target for ammonia management strategies. Chemical urease inhibitors that inactivate urease enzymes exist and are used for fertilizer stabilization but have not been widely adopted in poultry production. Although these chemicals have a low acute toxicity, they pose several health hazards to workers and there is a growing desire to transition from harsh chemistries to sustainable, biological solutions. FOLIUM Science has therefore developed a biological solution that precisely inhibits the formation of urease enzymes that is compatible with current management approaches and could be employed in a holistic management strategy to reduce ammonia.

Guided Biotics® are based on FOLIUM Science’s own CRISPR-Cas technology and allow precise control over the expression of specific enzymes within any population of microbes (a microbiome). FOLIUM Science has shown a conserved genus of bacteria with high ammonia-producing activity was consistently present in chicken manure and litter samples from farms across the UK. FOLIUM Science’s ammonia reducing product is a friendly probiotic bacterium that delivers Guided Biotics® technology to ammonia-producing bacteria normally found in the poultry house environment to reduce the expression of urease genes, and thus reduces the formation of ammonia. FOLIUM Science has demonstrated the utility of this approach in one of the most prevalent urease-producing bacteria found in poultry (Figure 1A). Up to an 80% reduction in the rate of ammonia generation was found under laboratory conditions. The Guided Biotics® technology shows significant reduction in ammonification in models that represent the chicken caecal microbiomes (Figure 1B). FOLIUM Science is now moving to test the technology on-farm.

Figure 1. FOLIUM Science’s Guided Biotics® are capable of reducing ammonia production by major urease-producing poultry microbes. (A) Ammonia production (pink colouration) is reduced in microbiological tests. (B) Chicken caecal microbiomes treated with Guided Biotic® in the lab display reduced urease enzyme activity. *p-value of <0.05 (t-test). Error bars represent ±SEM of biological triplicates.

FOLIUM Science is repurposing/redesigning the same technology to target the bacteria that produce urease enzymes in swine and cattle production, and in slurry storage. The ultimate goal is to not only reduce the formation of ammonia but to improve the efficiency of nitrogen use within the animal by enhancing the gut microbiome and its metabolic activities. The technology could also be used to tackle other microbial enzymes that result in methane production in cattle, or nitrification and denitrification that result in nitrous oxide production by fertilized soils.

About Robert Habgood
Robert Habgood is a microbiologist and former University of Oxford researcher who has been building FOLIUM Science’s Guided Biotics® technology platform and shaping its R&D pipeline for the past 4 years. FOLIUM Science is a UK-based biotechnology company that provides innovative solutions to sustainably transform the agri-food space by precisely modulating microbiomes. This includes specifically removing disease-causing bacteria, reducing greenhouse gas emissions, improving nutrient utilization and even providing rapid diagnostics.