Bacterial colonization plays an important role in the normal development, differentiation, function and regulation of intestinal mucosal immune system. Through mechanisms that are still not fully understood, the intestinal mucosal immune system generates effective protective immunity against pathogen invasion and at the same time it develops immune tolerance, preventing the development of disease conditions, such as IBD and food allergy. The regulatory role of the intestinal flora in the development and function of the intestinal mucosal immune system is well established. Recent work has suggested that colonization with probiotics in the gut may play an essential role in balancing the intestinal mucosal immune system, which may contribute to the induction and maintenance of immunological tolerance to other luminal antigens in the normal host or to the inhibition of the dysregulated responses induced by luminal antigens in diseased hosts. A better understanding of the cellular and molecular mechanisms controlling the development and regulation of intestinal mucosal epithelial system by intestinal bacteria (commensal and probiotics) and their regulatory role in various diseases will help establish new strategies to prevent and control these disease conditions.

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Gut is the site of active fermentation of non-digestible dietary components (dietary fibre and prebiotics) as well as bioconversion and absorption of plant-derived phenolics. These compounds have an important role in gut fermentation by influencing the composition of microflora and fermentation metabolites, and consequently by contributing to both local and systemic effects in humans. Possibilities to enhance viability and promote growth of probiotic bacteria by non-digestible food components have been a subject to extensive scientific interest in the last ten years. Gut bacteria are known to degrade and ferment dietary fibre, producing metabolites, especially short-chain fatty acids. They also mediate a number of important consequences through their further metabolism in the liver. Current research is at quick steps increasing our understanding about the interactions between gut microbes and bioactive dietary phenolics. Absorption and metabolism of phenolic compounds occurs along the digestive tract. Those compounds not absorbed or converted earlier enter the colon, and may be converted to metabolites concomitantly with carbohydrate fermentation. All the colonic metabolites can have effects on the epithelium at the site of conversion, and also affect the colonic flora locally. When absorbed the metabolites are found in plasma and urine and can have systemic health effects. The health effects of phenolic compounds have been studied extensively, but those of the metabolites are poorly known. As strong antimicrobial agents the phenolics might also have unpredictable effects on the composition of the intestinal flora.

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Identification of Bifidobacterium species are a difficult task because of phenotypic and genetic heterogeneities. Various DNA-based techniques to rapidly characterise Bifidobacterium species and to support the conventional biochemical and morphological classification methods have been described. Sequencing of the 16S rRNA gene and 16S to 23S internally transcribed spacer region and comparing with the sequences data present in GenBank are the most popular techniques in identifying Bifidobacterium species. Conserved sequences other than the 16S rRNA gene such as ldh, recA and hsp60 genes have become worthy tools for the elucidation of various taxonomic features such as genera, species and strains of Bifidobacterium. However, as an alternative to sequencing which is both time consuming and technically demanding, genus- or species-specific primers or probes were successfully designed to rapidly identify Bifidobacterium species. In this review, amplified ribosomal DNA restriction analysis (ARDRA) method derived from the 16S rRNA gene is also discussed because of it rapid, reproducible and easy to handle characteristics. Furthermore, randomly amplified polymorphic DNA (RAPD), Pulsed-Field Gel Electrophoresis (PFGE) and repetitive elements fingerprinting (Rep) were the popular methods to study the genetic diversity among Bifidobacterium species due to its versatility.

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The survival and growth rate of twenty eight isolates of bifidobacteria in bile were evaluated. Of 28 isolates, 25 were tolerance towards 2.0% concentration of bile while 14 isolates were tolerance towards 4.0% of bile after 12 hours of exposure. Six isolates of bifidobacteria with higher tolerance to 4.0% of bile were further evaluated for their ability to deconjugate different types of bile acids namely taurocholic acid (TC), glycocholic acid (GC), taurochenodeoxycholic acid (TCDC), glycochenodeoxycholic acid (GCDC), taurodeoxycholic acid (TDC), and glycodeoxycholic acid (GDC). Three Bifidobacterium pseudocatenulatum isolates (D22, F117, and G4) were found to have the similar deconjugation activity and were able to deconjugate 78.6-84.6% (TC), 98.9-99.9% (GC), 87.9-97.5% (TCDC), 91.1-100.0% (GCDC), 83.7-87.8% (TDC) and 96.5-99.0% (GDC).

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