Agriculture and environment
Case stories
How to collect the samples, from where, how many?
Like in any project, with microbiome analyses planning is key to good results. At Biomcare we have a lot of experience with planning microbiome projects and have seen the results of many projects where lacking experience in microbiome analyses resulted in project designs that could not give conclusive results.
Here is an example of good project planning: A customer engaged in product development for farming a specific crop wanted to analyse fungi taxa in the soil of their test fields to control for the role of the fungi on the outcome measures when studying the effect of the product on plan health and yield.
We decided an amplicon ITS method with >100.000 reads/ sample was a good sequencing strategy, but also noted we did not have enough data to select the best sampling method: How deep should the samples be taken and how far from the plant? So, a pilot study was setup where samples were collected at different depths and distances.
This gave us a detailed understanding of the variation in fungi around these specific crops and in this type of soil, and it allowed us to validate that our sequencing approach gave the desired information. It costed some time and money, indeed. But now going into the big project with many 100 samples, we were confident the results would give solid insight.
We are happy to be engaged from early phases of a new project so don’t hesitate to contact us early on.
Setting up a new RAS ?
Bacteria affect the living conditions and even the taste of fish and it is important to know how system settings affect the bacteria and how the populations can be controlled, especially in recirculating aquaculture systems (RAS).
System settings such as oxygen levels and temperature affect the bacteria in the systems, and therefore are not only important for the fish directly. Different measures can be implemented to control the populations, such as adding beneficial cultures or purging, but how often to add? What to add? what is the cost benefit? Better to purg? How often?
There are many questions and when wanting to find the answers you need a method to measure the bacterial populations and how the changes affect these. At Biomcare we offer such methods, based on sequencing solutions.
Monitoring for bacteria causing off-flavor in fish
Water quality and bacteria populations is of great importance in aquaculture. Bacteria affect the living conditions and even the taste of fish. Therefore, it is important to be able to control, monitor and evaluate the bacterial population in productions, especially in recirculating aquaculture systems (RAS).
NGS platforms can be used to monitor the bacterial species in the system, and when implemented correctly, allow the company to monitor the stability and fluctuations in the bacterial populations, to detect when changes start to occur and when new species are introduced or spike in abundance in the system, potentially warming up to become a problem.
Every facility is however unique in terms of location, setup, size etc. It is therefore important to start with a discussing and planning phase and often, a pilot study to access open questions and identify the baseline population in the different sample types. We help to access the system and identify the samples to be collected, the frequency of sampling, the sequencing method to be used etc, to implement NGS for bacteria monitoring.
NGS Service for Microbiota and Health Monitoring in Animal Model Facilities
Our Next-Generation Sequencing (NGS) service, utilizing metagenomic shotgun sequencing, offers a comprehensive solution for microbiota and health monitoring in animal model facilities. This approach is based on the findings of a 2021 study by Scavizzi et al., which demonstrated the efficiency and accuracy of metagenomic sequencing for microbiome assessment and pathogen detection in murine colonies.
Unlike traditional health monitoring methods, which rely on multiple tests and the use of sentinel animals, NGS metagenomics can analyze the entire microbiome and detect bacterial, viral, fungal, and parasitic pathogens in a single test. This method not only improves pathogen detection but also enhances ethical compliance by reducing the need for sentinel animals, in line with the 3R (Replacement, Reduction, Refinement) guidelines.
Our service provides high-resolution data on microbiota composition, enabling early detection of pathogens that could affect both animal health and the integrity of scientific results. By offering a more inclusive “microbiota surveillance,” we help researchers maintain specific pathogen-free (SPF) conditions, improve animal welfare, and ensure the reproducibility of experimental outcomes. This service streamlines monitoring processes, reduces costs, and enhances the reliability of preclinical research in animal model facilities.
