A Review of Gastrointestinal Microbiology with Special Emphasis on Molecular Microbial Ecology Approaches

Abstract

All animals, including humans, are adapted to life in a microbial world. Large populations of micro-organisms inhabit the gastrointestinal tract of all animals and form a closely integrated ecological unit with the host. This complex, mixed, microbial culture can be considered the most metabolically adaptable and rapidly renewable organ of the body, which plays a vital role in the normal nutritional, physiological, immunological and protective functions of the host animal. Bacteria have traditionally been classified mainly on the basis of phenotypic proper-ties. Despite the vast amount of knowledge generated for ruminal and other intestinal ecosystems using traditional techniques, the basic requisites for ecological studies, namely, enumeration and identification of all community members, have limitations. The two major problems faced by microbial ecologists are bias introduced by culture-based enumeration and characterization techniques, and the lack of a phylogenetically-based classification scheme. Modem molecular ecology techniques based on sequence comparisons of nucleic acids (DNA or RNA) can be used to provide molecular characterization while at the same time providing a classification scheme that predicts natural evolutionary relationships. These molecular methods provide results that are independent of growth conditions and media used. Also, using these techniques, bacteria can be classified and identified before they can be grown in pure culture. These nucleic acid-based techniques will enable gut microbiologists to answer the most difficult question in microbial ecology: namely, describing the exact role or function a specific bacterium plays in its natural environment and its quantitative contribution to the whole. However, rather than replacing the classical culture-based system, the new molecular-based techniques can be used in combination with the classical approach to improve cultivation, speciation and evaluation of diversity. The study of microbial ecology in gut ecosystems involves investigation of the organisms present (abundance and diversity), their activity (usually determined in vitro, but in vivo activity or expression of activity is really required), and their relationship with each other and the host animal (synergistic and competitive interactions). This entails the study and measurement of many types of interactions, both beneficial and competitive.