The gut microbiota is tantamount to an internal organ in itself, but one which is prone to adaptation and alteration, with far-reaching effects throughout the human body. This capability to impinge on other faculties in the body as remote as the liver, for example, is undoubtedly due to its ability to produce an array of metabolic compounds with bioactive properties that are transported throughout the body via the circulatory system. Such bioactive compounds have now become a major focus associated with potential probiotic strains. For example, the production of conjugated linoleic acid (CLA) by a metabolically active Bifidobacterium strain in the mammalian gut has recently been shown to be associated with alterations in fatty acid composition of other regions in the body, including the liver and adipose tissue. Another important aspect of probiotic functionality is the ability to colonize and persist within the highly complex and often inhospitable ecosystem which is our large intestine. Bacteriocin production, which historically has often been touted as a possible probiotic mechanism, has recently been associated with dominance of producing strains within the gastrointestinal tract (GIT). Indeed, many of these antimicrobial peptides have demonstrated potent antimicrobial activity in vivo against human pathogens. This review explores the significance of CLA and antimicrobial peptides, namely bacteriocins, as markers of probiotic functionality for the intestinal gut microbiota. (C) 2009 Elsevier Ltd. All rights reserved.