Detection and Identification of Probiotic Microorganisms and Other Beneficial Organisms from the Human GI Tract

Most probiotics are similar to the microorganisms naturally found in the human gastrointestinal tract, and are mainly from the genera of Lactobacillus or Bifidobacterium. Conventionally, these microorganisms have been found to be fastidious, acid-tolerant, and strictly fermentative, producing lactic and acetic acids as the major end products of sugar fermentation. Exceptions from this general description have been found to occur. In addition, interaction between probiotic microorganisms or their derivatives with the gut microbiota is now a focal point of probiotics research. This requires the characterization and enumeration of all microorganisms colonizing the gut. Molecular microbiological analysis has increased the understanding of the diversity and phylogeny of beneficial strains and their functions. Modern techniques, including genotyping methods, become increasingly important for species identification and for the differentiation of probiotic strains. The precise classification and identification of probiotic strains give a strong indication of their typical habitat and origin, safety and technical applicability, and provides possibilities for monitoring and product quality. This chapter provides an overview of probiotic strain characterization, gut metagenomics, and the analytical methods (FISH, PCR, RAPD, DGGE, repPCR, PFGE, RFLP, microarray, high throughput sequencing) required for their study.