Non-invasive in situ monitoring of fish gut microbiota in aquaculture operations

Aquaculture is a key technology for achieving sustainable food security. However, the sustainability of aquaculture largely depends on the composition of the feed being used to grow the fish. While the traditional aqua-feeds include less sustainable protein sources such as fish and soy meals, insect-based alternatives hold promise due to their ability to efficiently convert organic waste substrates into protein and lipids, while producing low amounts of greenhouse gases. But they also contain wide-spectrum antimicrobial peptides, whose impact in fish gut microbiota is unclear.

A healthy microbiota is key for having a healthy fish, and monitoring it can therefore be a way to assess the impact of a certain diet and potentially the future health of the fish. However, gut microbiota is assessed by laborious and invasive processes such as stripping or authopsies, which prevents continuous monitorization in commercial operations. It is therefore desirable to find non-invasive ways of monitoring the status of microbiomes in aquaculture operations.

This pilot project will monitor the response of the gut microbiota to different insect-based experimental feeds and a control. We will validate the use of non-invasive sampling techniques that would allow to access the fish gut microbiome without interrupting normal commercial operations. We will also explore in situ sequencing and analysis protocols that would allow companies to continuously monitor the microbial status of their facilities, potentially leading to improved fish health, reduced disease outbreaks, and a more sustainable operation.

Partners involved

Main Applicant:

• Fernando Puente Sanchez, Department of Aquatic Sciences and Assessment, NJ-Faculty at SLU.

Co-applicants:

• Aleksandar Vidakovic, Department of Animal Nutrition and Management, VH-Faculty at SLU.
• Matthias Hötzinger, Department of Aquatic Sciences and Assessment, NJ-Faculty at SLU.