What will next generation livestock farms look like? Mick Watson examines scenarios and what we should do to get there.
Farmer Jane opened the gate and walked along the track that meandered along the side of her cattle barn. Chuckling to herself, she was old enough to remember how disease surveillance used to be done. It was so much easier now. Inside the barn, she approached the first of the ten cattle that had been randomly isolated, reached into her bag and took out the first of her SeqPensTM. Removing the protective lid, she briefly pressed the steel nib to the neck of the first animal then stood back to wait for the lights to change.
The painless microneedle pens would capture a tiny amount of blood and extract all of the DNA in the sample, whether from the cow, or the myriad parasites and pathogens that could infect her. The DNA would pass through an engineered nanopore that would determine the exact sequence in a matter of seconds.
The sequence data was uploaded immediately to Defra disease monitoring servers over the 5G wireless network, and each sequence screened against every known pathogen (and strain thereof), including foot-and-mouth disease, bluetongue and Schmallenberg virus. If nothing was found the pen would flash a green light; bad news produced a red light and recommendations would arrive by text, such as isolating the animals until a vet arrived.
Jane was yet to see a red light; this was mid-21st century disease surveillance and it had helped control most farm animal diseases throughout the UK.
Farmer John sat down in front of his PC and logged on to the GrowthMonitorTM website to check the past and predicted growth curves for his chicken flock. GrowthMonitor helped him design the perfect diet for his birds that would almost guarantee his broilers would achieve optimum weight.
Experiments carried out during the second great DNA sequencing revolution (2005-2015) had allowed scientists to link diet and the contents of the gut flora (the bacterial populations that live in the guts of animals and enable them to digest food) to growth, weight, meat quality and even taste.
GrowthMonitor worked through tiny nanopores in the floor of John’s chicken shed that extracted, amplified and sequenced segments of DNA directly from the waste produced by the chickens. These were uploaded to the GrowthMonitor servers and screened against databases of known bacteria so John could make sure his chickens had the optimum gut flora for growth; a specific diet would then be designed with additional pro- and pre-biotics to maintain it.
Of course, the technology had the added benefit of being able to screen for once-common pathogens such as Salmonella and Campylobacter. If detected at dangerous levels, next-generation antibiotics could be added to the chicken feed to maintain a healthy, well-fed flock that would achieve optimum weight in time to be sold.
Fact or fiction?
The stories of John and Jane are, so far, fiction. But how long will it be until it’s a reality?
Since 2007, the cost of DNA sequencing has been decreasing exponentially, with newer and faster technologies arriving every few years.
In 2012, the British company Oxford Nanopore Technologies presented a tiny DNA sequencer that would plug into the USB port of your computer and sequence DNA directly from blood using an engineered nanopore as described in the stories above. A year later, a British company in Cambridge, Base4, announced plans to develop a nanopore sequencer with Hitachi.
Although not yet on the market, these machines could revolutionise many areas of biology and medicine.
Right now, scientists throughout the world are using DNA sequencing technologies, such as the Illumina HiSeq system and LifeTech’s Ion Torrent, for pathogen surveillance and detection; others are sequencing the microbial gut contents of animals and linking the results to health, disease and obesity.
It’s clear that the technology to sequence DNA using nanopores is here now, and many think they will be commercially available in the next 12-24 months. If the cost of sequencing using the new nanopore devices becomes cheaper than traditional diagnostic tests, then we can begin to expect products such as the SeqPen to become available in the next five years, with more complex systems such as GrowthMonitor in the next 10 years.
The major predicted problem is how we will deal with the mountains of data – once it becomes possible to sequence everything so quickly and cheaply we will do exactly that. Specialist software will be needed and may end up costing more than the data generation.
In addition, once we start sequencing complex ecosystems such as farms, who knows what we may find? Bacteria and viruses will exist in these locations, undetectable with current technologies, which may never cause any problem for the farmer or animal. But once discovered, will farmers be put under pressure to remove them anyway?
It’s an exciting new world, but success will only be achieved through close collaboration between farmers and scientists, and with clear and concise information provided to engage with the public.
About Mick Watson
Mick Watson is a computational biologist and Director of ARK-Genomics, a DNA sequencing facility, at the University of Edinburgh, with research interests in bioinformatics, genomics and animal disease. In his spare time, he also writes short fiction. Read more of Mick Watson’s biological musings on his Opiniomics blog.