Effects of Alternative Dietary Substrates on Competition between Human Colonic Bacteria in an Anaerobic Fermentor System

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Abstract
Duplicate anaerobic fermentor systems were used to examine changes in a community of human fecal bacteria supplied with different carbohydrate energy sources. A panel of group-specific fluorescent in situ hybridization probes targeting 16S rRNA sequences revealed that the fermentors supported growth of a greater proportion ofBacteroidesand a lower proportion of gram-positive anaerobes related toFaecalibacterium prausnitzii,Ruminococcus flavefaciens-Ruminococcus bromii,Eubacterium rectale-Clostridium coccoides, andEubacterium cylindroidesthan the proportions in the starting fecal inoculum. Nevertheless, certain substrates, such as dahlia inulin, caused a pronounced increase in the number of bacteria related toR. flavefaciens-R. bromiiandE. cylindroides.The ability of three strictly anaerobic, gram-positive bacteria to compete with the complete human fecal flora was tested in the same experiment by using selective plating to enumerate the introduced strains. TheRoseburia-related strain A2-183Fwas able to grow on all substrates despite the fact that it was unable to utilize complex carbohydrates in pure culture, and it was assumed that this organism survived by cross-feeding. In contrast,Roseburia intestinalisL1-82RandEubacteriumsp. strain A2-194Rsurvived less well despite the fact that they were able to utilize polysaccharides in pure culture, except that A2-194Rwas stimulated 100-fold by inulin. These results suggest that many low-G+C-content gram-positive obligate anaerobes may be selected against during in vitro incubation, although several groups were stimulated by inulin. Thus, considerable caution is necessary when workers attempt to predict the in vivo effects of probiotics and prebiotics from their effects in vitro.

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