Aquaculture for all

Can the Biomark X9 revolutionise aquatic pathogen testing?

Atlantic Salmon Genomics Health +6 more

A machine that is capable of screening for multiple pathogens, with exceptional speed, is about to be launched on the global aquaculture market.

A person holding a pipette in a laboratory.
Standard Biotools' Biomark X9 allows users to perform realtime PCR on 96 genes simultaneously

© Standard BioTools

The Biomark X9 high-throughput genomics system offers cost-effective, high-throughput and automated solutions for PCR and next-generation sequencing (NGS) workflows in aquaculture laboratories – be they on-farm, or within research institutions.

Developed by Standard BioTools (previously known as Fluidigm), the Biomark X9 has the potential to significantly upgrade the level of biosecurity on fish and shrimp farms of all scales – offering early warning of any impending health threats as well as rapid diagnosis of any pathogens present in the water or in the animals themselves.

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According to Phillip Kilgas, product manager for the system, although the X9 was developed for the human health sector, the company sees aquaculture as one of the most promising avenues to diversify into – due to the variety of farmed species, the variety of pathogens that they are exposed to, and the open (relatively non-biosecure) nature of many aquaculture systems.

“The Biomark X9 is better suited to aquaculture than to other livestock sectors, such as cattle or poultry, as our technology fits better – cattle and poultry only have a few pathogens, and a few samples at a time, to deal with, so a more traditional PCR approach fits well for them. On the other hand aquaculture involves large numbers of animals in each farm, and a wide range of diseases – which makes it a good fit for our technology,” he explains.

According to Kilgas, the Biomark X9 combines a number of functions that previously required numerous devices to achieve.

“Our R&D team figured out a way to consolidate these into one instrument and put different applications onto a single platform. For example the Biomark X9 can do real time PCR and NGS library prep all in one system – it’s the first instrument on the market that’s able to handle both these applications and this will give researchers and farmers access to the ever growing number of genomic applications that can be performed in the aquaculture space,” he notes.

The Biomark X9 was launched at the end of 2022, initially with a focus on PCR, with NGS capabilities being added more recently.

“We’ve already had a lot of success in the public health sector, in dealing with novel diseases and breakouts,” notes Kilgas. “And I think the same will apply to aquaculture, because of the range of pathogens that effect the industry.”

A person looking at a computer screen in a lab.
The old version of the Biomark was considerably larger

The latest model is much more portable, and has even been deployed on research vessels. © Standard BioTools

Remarkably, despite the increase in functions, the machines are becoming more portable.

“We’re consolidating the design down so it’s a much smaller, benchtop platform,” Kilgas explains.

And although the machines are primarily designed to be used in onshore laboratories, they have also been successfully trialled in more testing conditions.

“One customer has installed one on a boat, where it has been used to monitor salmon runs in Alaska during the fishing season, to hep understand their migration patterns. However, it’s a unique use case and we had to do a very specific engineering feat, which is not necessarily scalable,” Kilgas reveals.

Despite the complexity of the machine, operating it is straightforward, according to Kilgas.

“It’s pretty much plug-and-play. Operating the Biomark X9 is similar to doing conventional PCR, but because we use nanolitre volumes, and combining multiple assays into one plate, it makes it much faster and easier to perform multiple experiments in one go.”

And he believes that it has many advantages over more established testing devices.

“It’s an improvement from a few angles: you can do simultaneous detection which means you can test multiple samples for multiple pathogens at the same time. We also reduce the use of plastics by 100x – a single one of our plates is needed, where 100 plates would be needed in conventional PCR testing. That also equates to less time and less labour needed to do the testing,” says Kilgas.

Another key advantage is the machine’s flexibility

“Generally, people are locked into the targets they are trying to detect. But if there’s a sudden outbreak of a new pathogen they just need to add one assay to our technology to detect it,” he observes.

Target customers

In terms of sales, Kilgas sees government bodies, private labs and academic institutes as the main target markets, especially in Europe and Asia, but sees the reach expanding over time – thanks in part to the impressive reduction in the size of the machine, which makes it much more portable and adaptable.

“While of course there is a capital investment cost related to acquiring the machine, the low price per datapoint (due to assay miniaturisation) and the reduction in turnaround time to get your results, makes our technology feasible to be implemented in a multitude of different laboratories – ranging from farms, to contract research organisations, to fisheries,” he explains.

Uses in aquaculture so far have included studies into the link between gene expression and growth, stress and welfare in channel catfish, studies into the link between gene expression and the impact of whitespot syndrome virus (WSSV) on vannamei shrimp, and studies into the link between gene expression and immune response, welfare and epidemiology in Atlantic salmon (links open as a PDF document).

A person's hand removing samples from a machine.
The new Biomark X9 in operation

Early aquaculture adopters include the Scottish Fish Immunology Research Centre at the University of Aberdeen © Standard Biotools

Users of the system include Prof Sam Martin, director of the Scottish Fish Immunology Research Centre at the University of Aberdeen, who has been impressed by the speed and capacity of the system.

As he explains: “It allows us to do realtime PCR on 96 genes – potentially from 96 different animals – at the same time. The advantage is that we’re able to really increase the number of different individuals and replicates that we’re looking at, with a good number of markers that we know will tell us the health status of the fish.

“We’ve had a number of projects examining molecular basis of complex gill disease and AGD. Our work previously used deep sequencing – a very expensive and time-consuming form of RNA sequencing that costs about £150 per fish.

“We’ve linked our analysis of Atlantic salmon gills and linked this closely with our histopathology work to find a set of genes that are indicators of fish health. Now what we will be able to do is to take fish from a farm and let the farmers know the health status of that fish using a whole repertoire of fish health biomarkers which we’ve already characterised as being indicative of fish health status. Other new project involve examining antiviral signatures to help understand protection following vaccination.

“Instead of doing expensive RNA sequencing on five fish or taking lots of fish and just doing one or two genes, we can take a lot of fish and do a lot of genes at the same time – we can do several months worth of real time PCRs in a day.”

Meanwhile both the Canadian Department of Fisheries and Alaska Fish and Game have used it for work on wild fish stocks.

Future developments

Looking ahead Kilgas believes that, as the Biomark X9 develops, so will the ways it can be used.

“As farmers get better at understanding the technology and the local pathogens, they will be able to move from a reactive to a proactive state. Since we can easily adapt our assays for any type of experiment If they have an inkling that a pathogen might be there we can add the assay for it for very little additional cost, to allow the farmers to do routine testing for it,” he explains.

He also believes that the X9 could help to improve the sustainability of the aquaculture sector, and adds that the machine could be made more sensitive, to allow for higher level detection of pathogens.

“This technology is for everyone in the aquaculture community interested in disease management, feeding strategy and general animal welfare and who wants to improve the aforementioned using new high-throughput and easy to use genomic tools to do so. We’re looking forward to talking to customers about their needs and pain points so we can continue to develop the technology,” Kilgas reflects.

To find out more…

You can find out more about how the Biomark X9 can solve a range of aquaculture problems here or email

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