Molecular and biochemical approaches to determining what bacteria are doing in vivo

Conclusions

Although the results of experiments carried out to date have not given unambiguous answers to the question of which polysaccharides are being utilized byBacterioides in the colon, the results nonetheless encourage us to think that it may be possible to develop methods for answering this and related questions in the furture. Given the complexity of the in vivo environmental and the impossibility of knowing, much less controlling, all parameters, it will probably be necessary to use more than one approach to answering a particular question and assume that if anseers obtained by different approaches are consistent, they are probably correct. For example, the general conclusions from the experiments testing the performance of mutants in the germfree mouse model are in agreement with those arising from direct biochemical analysis of human feces. Also, results from these experiments with help to guide the design of more specific antibody probes because they indicate which polysaccharides are most likely to be important. A bootstrap type of approach in which each successive set of experiments produces information that makes possible a more specific type of probe may be the only approach that makes sense when dealing with metabolically versatile organisms in a highly complex ecosystem.