ISSUE FOCUS FEED & ADDITIVE MAGAZINE February 2026 77 STIMULATING MICROBIOME FUNCTION IN THE LOWER GUT Most microbial activity occurs in the lower intestine, where the majority of bacterial populations are located. Managing upper gut integrity is key to stimulate optimal microbiome function in the distal part, as excess or undigested nutrients will reach the lower intestine and become substrates for undesirable bacterial fermentation. Limiting starch flow to the lower intestine and maximising absorption by the animal helps control saccharolytic bacteria populations and reduces the risk of excessive lactic acid accumulation. Such accumulation may promote pathogen overgrowth and create more aerobic conditions, which are detrimental to key bacterial families such as butyric-acid-producing Lachnospiraceae. Similarly, the presence of amino acids in the lower intestine stimulates putrefaction, resulting from protein fermentation and the release of branchedchain fatty acids and toxic metabolites such as indole, skatole, phenol, and cresol. The microbiome plays multiple roles, many of which remain poorly understood. Microbial activity not only results in the production of metabolites that nourish the host, but also stimulates multiple host metabolic pathways and influences inter-bacterial communication (quorum sensing), which directly impacts bacterial family presence and activity. Although this may have sounded counterintuitive in the past, it is now well established that adding fermentable fibre to the diet is an effective strategy to feed the microbiome and, in turn, reinforce gut and immune function. In addition to carbohydrates, bacteria also require nitrogen. While there is a growing understanding of the types of carbohydrates that benefit key bacterial families (e.g., xylo-oligosaccharides feeding Bifidobacterium), bacterial protein requirements in monogastrics remain poorly quantified. Although an ideal microbiota has yet to be defined, quantifying bacterial family populations represents a valuable starting point to link microbial presence with key metabolites, such as short-chain fatty acids (SCFA), which may influence immune response, metabolism, and behaviour. In addition, studies have demonstrated how the gut–brain axis can influence animal behaviour, and how the gut–lung axis may play a role in respiratory diseases, as well as in the stimulation of inflammatory or anti-inflammatory responses. One of the main challenges is managing this high level of complexity, particularly under commercial production conditions. Translating biological responses into practical, actionable insights for decision-making therefore requires measurable and reliable indicators of gut function. One approach is to focus on microbiome activity rather than microbial composition alone. Short-chain fatty acids are key metabolites that reflect microbial fermentation activity in the gut. These biomarkers can be quantified to provide valu-
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