“Different biotechnologies are now available in the market and transferable to production animals to study the microbiome. The 16S rRNA gene sequencing is a common method used to analyse microbiome profile and diversity in intestinal segments of animals. Metabolomics is also used to evaluate the effect of metabolites on gut integrity, and to understand how shifting the microbiome can affect the production of these metabolites.”

For many decades, nutritionists have focused on quantifying energy and nutrient requirements to provide animals with ideal nutrient profiles at different production stages. Although these requirements are well-defined and consistently adjusted to new genetics, they are theoretical, and have been determined under specific growing conditions, given specific diet types.

Beyond the definition of nutrient requirements, stressors interfere with animal behaviour and typically impair feed intake, which in turn affects performance. It is now well acknowledged that maintaining good gut health is key to minimising the impact of these stressors on animal performance. Kogut and Arsenault (2016) defined gut health as the “absence/ prevention/avoidance of disease so that the animal is able to perform its physiological functions in order to withstand exogenous and endogenous stressors”. This definition is in line with the World Health Organization, who defined gut health in humans as a state of well-being with the “absence of gastrointestinal complaints”. In other words, supporting gut health in animals is about finding strategies which make the animal more robust and resilient for the maintenance of homeostasis.

Gut Health For Improved Robustness

Both robustness and resilience come into play as animals are raised in a constrained environment caused by ambient conditions (e.g., ventilation, temperature); ingredient quality (e.g., antinutritional factors, digestibility); feed quality (e.g., pellet durability, particle size); social stressors (e.g., stocking density, social interactions), and sanitary conditions (e.g., litter, parent stock) etc. These stressors tend to pull the animals out of homeostasis, and the ability to recover quickly becomes important to minimise the impact on overall herd performance and production cost.

Along with steps to rationalise antibiotic use in the livestock industry, there has been a paradigm shift in the importance of the interaction between nutrition and health. Many efforts have been made to understand the importance of the gut microbiome in supporting animals’ health and performance.

Stimulating good gut health with a proper functionality of the microbiome reduces the risk of dysbiosis and, eventually, inflammation. While acute inflammation is part of the normal recovery process and allows the body to fight infection locally, chronic inflammation may result in a systemic response, increase energy expenditure and impair performance or result in mortality.

Although there is no ideal microbiome profile, which maximises gut health, we know that gut barrier function relies on a gut microbiome which promotes homeostasis. Commensal bacteria supply the gut with beneficial metabolites which enable gut acidification, mucus production, increase the energy supply to the epithelial cells, and support the immune system.

We believe that looking into the functionality of the microbiome response to different production conditions can provide insights for producers and nutritionists to adapt management and feeding strategies. This, in turn, can increase robustness of animal populations by stimulating the integrity of the biome and potentially prevent the overgrowth of opportunistic pathogens, as well as chronic inflammation.

Gut Health for Animal Producers

Different biotechnologies are now available in the market and transferable to production animals to study the microbiome. The 16S rRNA gene sequencing is a common method used to analyse microbiome profile and diversity in intestinal segments of animals. Metabolomics is also used to evaluate the effect of metabolites on gut integrity, and to understand how shifting the microbiome can affect the production of these metabolites.

At AB Vista, we have been testing biotechnologies and assay methods which can be transposed in commercial settings to help select nutritional strategies that support gut integrity. From sample collection to results analysis and interpretation, we have developed practical solutions which can provide enough information for in-field decision making.

Sampling Type and Method

As a start, we have tested different sampling methods and have come to select BioFreeze vials (by Alimetrics Diagnostics) as a convenient and reliable method to be used in both research and commercial settings. While cecal content collection is commonly performed in broiler chickens, this method raises welfare issues and cannot be transposed commercially to other species such as sows, piglets, broiler breeders, turkeys, etc.

The sampling of fresh faeces and fresh poultry cecal content and cecal droppings has been made practically transposable in commercial barns as BioFreeze vials prevent any reaction from occurring in the sampled material, and without the need for the material to be kept in a freezer or on dry ice until it is analysed. We have now defined standard sampling protocols in commercial settings, making it possible to determine the optimal number of samples to be collected to ensure the measurements are representative of the herd and that the power of detection is strong enough to support data analysis.

Evaluating Microbiome Function

In poultry, the ceca is the major site of bacterial fermentation. Short chain fatty acids (SCFA) are metabolites produced by fibre-degrading bacteria. In addition to providing an energy source to the epithelial cells, SCFA play other roles -such as intestinal acidification, which prevents pathogen invasion and colonisation. Each of these metabolites has a functional role for the host, and understanding their metabolism can contribute towards understanding the animal response better.

The SCFA in the ceca of healthy birds are expected to exceed 100 mmol/kg passed 2 weeks of age. While acetate typically makes 70% of the SCFA, propionate and butyrate represent approximately 25% of the SCFA, and the remainder is composed of short-chain fatty acids, valerate and lactate.

Lactate is a SCFA highly present in the upper gut. However, lactate accumulation in the ceca may provide a good indicator of dysbiosis. Our database has shown lactate levels to be below 1 mmol/kg in healthy birds, when it can reach more than 30 mmol/kg in birds subjected to dysbiosis.

Butyrate is a metabolite of butyrate-producing bacteria, mainly represented by Clostridiales. Butyrate is an important metabolite that stimulates gut integrity by providing an energy source directly available to the epithelial cells. In commercial settings, we have measured that butyrate concentration in the ceca mainly correlated with Ruminococcaceae and Lachnospiraceae presence, which negatively correlated with lactate level (AB Vista, internal data).

Branched chain fatty acids (BCFA) are a specific group of SCFA, mainly composed of 2-methylbutyric acid, isobutyric acid and isovaleric acid. BCFA are not desired in the ceca as they are a sign of protein fermentation, associated with an excess of dietary protein or poor protein digestibility. Protein fermentation eventually leads to putrefaction and opportunistic pathogen overgrowth. Our measurements determined that BCFA concentration in the cecal content of healthy broilers and layers tends to remain at low levels, typically below 3 mmol/kg.


With gut health a major area of focus for the animal production industry, there are a lot of practical questions still to be answered to provide producers with an optimal tool for monitoring and evaluating gut integrity.

AB Vista’s objective – through our ongoing work in this area – is to provide producers with gut health indicators that supplement traditional performance data for a better understanding of animal responses to different nutritional strategies.