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Animal nutrition and microbiome: study design & sample collection

Why are microbiome studies so important in feed industry nowadays? For innovators in the feed industry, developing products that enhance animal health and performance is a key focus. Whether it's a functional ingredient, a diet formulation, or a probiotic additive, your goal is to position products on the market with a demonstrated effect on animal health and performance. Feed or animal trials are a powerful means to demonstrate these effects. Once you've identified a positive effect on animal health or performance, delving into the gut microbiome can provide valuable additional insights. The composition of the gut microbiome directly influences gut health, which in turn affects animal health. By conducting a microbiome study, you can gain a deeper understanding of your product's mechanisms and use the findings for strategic product marketing to gain a competitive edge.

Why perform a microbiome study?
Study setup for microbiome studies
Sample collection tubes and containers


Let's explore the process of setting up a microbiome study. A key tip is that there's no need to conduct a separate animal trial specifically for a microbiome study. You can utilize the same study setup as for your product testing. Collect the samples you wish to analyze for the microbiome and store them for later use. However, there are specific considerations for microbiome studies, such as the number of samples per group/treatment and timepoint. It is recommended to have at least five samples, but ideally aim for around 10 samples per treatment and timepoint. This is crucial for robust data analysis in microbiome studies, as having more samples enhances the reliability of the statistical outcomes. Additionally, when working with animals in different pens, it's helpful to consider the following scenario. For instance, if you have a control group and a treatment group, each consisting of five pens with six animals in each pen, you should ensure that you select one animal from each pen in both groups. This means taking five animals from the control group, with each animal originating from a different pen, and doing the same for the treatment group. By following this method, you will have five animals in each group.

Proper sample collection is a critical aspect of microbiome studies, as it can significantly impact the outcome. When collecting samples, remember to wear gloves and protective clothing, and use sterile containers for sample collection. It's advisable to avoid using plastic bags and opt for appropriate containers instead. Once you have collected your samples, ensure that they are stored at the correct temperatures. During sample collection, it is crucial to keep the samples at refrigeration temperatures, typically around 4°C, to minimize microbial growth and maintain the original composition of the microbiome. If a refrigerator is not available, a box filled with ice or ice packs can be used to keep the samples cold. After collection, the samples should be stored at freezing conditions. For short-term storage, such as a few weeks, -20°C is suitable, while for longer-term storage, several months, it is recommended to store at -70 to -80°C. These temperature guidelines have been validated by various scientific studies, emphasizing the importance of immediately freezing samples at -70 or -80°C if possible to preserve the microbiome composition and to avoid freeze-thaw cycles. It is essential to keep the samples frozen until they are processed in the lab to maintain sample integrity.
Sample collection examples for different animal species
Different types of samples are required depending on the animal being studied. For large production animals or companion animals (dog, cat, horse...), fecal samples are typically used for gut microbiome studies. It is crucial to collect fresh samples directly from the animal and not from the floor. This is to avoid contamination and to ensure the microbiome composition remains intact. For poultry, sample collection is often done from the caecum or ileum. Fish or shrimp samples are taken directly from the gut. 
With this information, you should be able to think about the planning of your microbiome studies.
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