Interplay between the host immune system and GI tract microflora has developed over millions of years of evolution. The immune system has both innate and adaptive mechanisms and can generate humoral and cell-mediated responses. The gastrointestinal tract is the largest contact area between microbes and the vertebrate body. The main function of the immune system is to protect the body against attacks by pathogenic bacteria, and it is now widely acknowledged that the intestinal microflora has profound importance for the immunological status of animals and human beings, with implications on health and well-being. Initial colonisation by microbes affects the immune system permanently. At later stages of life, certain microorganisms (probiotics) or other immunomodulatory compounds can be used to direct immune responses away from inflammatory pathways, which are often more destructive for the host than the actual microbial challenge.

Alimetrics is able to measure relevant immunological parameters: distribution of immune cells, concentrations of signal molecules (cytokines, interferons) and magnitude of humoral response (different immunoglobulins) from plasma, digesta and tissue samples using immunohistochemistry and techniques based on flow cytometry, PCR and ELISA. Examples of these techniques are described in more detail in sections Immunoglobulin analysis, Immunohistochemistry and Immune cell typing and sorting.