01.11.2019 - 12:16 pm
Our aim is to improve sustainable food solutions, by improving our understanding of the relationship between animals and their associated gut microorganisms. To do this, HoloFood has brought together industry and research expertise from across Europe, and each of our work packages – the deliverables and targets set out for HoloFood – are built on each other, like a pyramid. Thus, one of the first tasks achieved this year was the setup and collection of an enormous number (over 1500 animals and over 30.000 samples) of samples from our two animal systems: salmon and chicken. This remarkably valuable dataset will form the basis of not only all future HoloFood activities, but we hope many future studies.
Ongoing chicken sampling setup
Just running these experiments alone was no small feat.
For the poultry, many chickens have to be selected, housed and kept in specific ways, segregated and fed the probiotic or prebiotic or control (neither additive) diets, monitored continuously and sampled across many time points. Up to 15 people were required at each sampling event, so that measurements could be taken for each chicken, and then allow the different teams from the consortium to collect over 25 samples per animal for downstream measurements and analysis. Timing was very crucial because any delay can skew the results, and any deviation had to be properly recorded.
Salmon tanks for the HoloFood experiments
The salmon experiments were set up differently; with salmon grown in controlled environments and selected at the same age for each experiment. Again, these setups required considerable organisation to allow for constant monitoring and acclimation of the salmon, feeding them the right combination of diet (seaweed or blue mussel or control) and sampling each fish in a timely and accurate manner. Each fish was measured, and 11 unique biological samples per animal were again distributed between partners.
Collecting the samples and metadata for experiments of this scale is a huge undertaking. Sampling protocols, discussions, streamlining and efficiency are all taken into account, not only as this will help all partners of HoloFood work towards the Holo-omic solution but also the data collected and generated will eventually be deposited in public repositories – so future generations of researchers and industries can return to the unique multi ‘omics HoloFood dataset for reference, use in other studies or as a model of how to conduct holo-omic analysis.
The stakes are high, and the first months proved our great teamwork among partners, regardless of an industry or academic background.
Aside from working hard on these experiments, HoloFood hit the ground running with our first kick off meeting held in the first month of the project, and our first experiments starting in week two of our first month. Naturally, hiring the right people was one of our first priorities, and new positions are still being advertised by the consortium. Since then we have had a number of satellite meetings, and a successful first steering board meeting in September. Moreover, the first months of any action involves the delivery of much needed ethics reports; a website and twitter channel launched, both that need to be updated frequently, and an internal intranet to help partners optimise their collaboration. HoloFood also completed its first training course, hosted and organised by partner EMBL-EBI over the summer - to a very oversubscribed class. Team members have also attended conferences around the world, and even had a chance to represent HoloFood at the Research and Innovation Days in Brussels in September as part of one of the WOW exhibits.
With two months to go before the completion of our first year, we are looking forward to the generation of the first set of our samples into genomic data – that is starting to process the samples and extract the DNA and RNA they contain. For a project of this scale, this requires streamlining and optimisation of the laboratory processing pipeline, a task that is currently ongoing at full steam in Copenhagen. Partners who are working on measuring key performance indicators are also busy on generating these for the 1000s of samples collected. All this information will then be integrated into our HoloFood database, so that the researchers will be able to start processing the information, and ultimately further our understating of how this will be streamlined. In this regard, our partners in EMBL-EBI have started preparing for datasets to be introduced into their systems and generate the appropriate setup to make sure data analysis will be as smooth as possible once generated. Moreover, we have started preparation for our industry aimed workshops and stakeholder survey.
Overall, with our one year anniversary coming up in, HoloFood’s team members are happy to have not only completed the challenging sampling regime that is the basis for our future cutting edge research, but excited to see what the next years’ results will show!