Strengths and weaknesses in techniques employed to measure the effects of dietary modulation on intestinal microbiota composition and function.

In this paper, intestinal microbial habitats in monogastric animals are discussed, with special reference to the intestinal segments of poultry. Physicochemical conditions in different segments vary and determine the selection of microbes that have nutritional and thermodynamic possibilities to thrive in the habitat. Understanding basic microbial ecology is a prerequisite for the knowledge-based development of microbiota modulating feed additives and ingredients. A prevalent research approach involves analysing intestinal parameters and calculating correlations between analytical data, animal health, and performance. However, this method cannot establish causal relationships or capture the dynamics of microbial metabolite production and their uptake by the intestinal brush border. An alternative or complementary approach is to use an ex vivo method, where the fresh, fully functional, authentic microbial community of the target intestinal segment is studied in the laboratory. For this approach to produce unbiased data, extremely careful handling of the oxygen-sensitive bacteria and precise replication of the physicochemical conditions of the target intestinal environment are critical. With such an ex vivo model, the effect of feed additives on the rate of metabolite production by the native microbiota can be accurately evaluated. All research approaches have their pitfalls, the details of which are discussed. Small methodological details can have a major impact on the reliability of the results. The most reliable approaches are unfortunately labour-intensive, and a successful outcome requires the use of multiple approaches in parallel. Although no research approach is perfect, combining multiple methods allows a comprehensive understanding to emerge gradually.