Little is known about how colonic transit time relates to human colonic metabolism and its importance for host health, although a firm stool consistency, a proxy for a long colonic transit time, has recently been positively associated with gut microbial richness. Here, we show that colonic transit time in humans, assessed using radio-opaque markers, is associated with overall gut microbial composition, diversity and metabolism. We find that a long colonic transit time associates with high microbial richness and is accompanied by a shift in colonic metabolism from carbohydrate fermentation to protein catabolism as reflected by higher urinary levels of potentially deleterious protein-derived metabolites. Additionally, shorter colonic transit time correlates with metabolites possibly reflecting increased renewal of the colonic mucosa. Together, this suggests that a high gut microbial richness does not per se imply a healthy gut microbial ecosystem and points at colonic transit time as a highly important factor to consider in microbiome and metabolomics studies.
The transfer of the R1drd19 plasmid between isogenic strains of Escherichia coli BJ4 in batch cultures of laboratory media and intestinal extracts was compared. Using an estimate of plasmid transfer rate that is independent of cell density, of donor :recipient ratios and of mating time, it was found that transfer occurs at a much lower rate in intestinal extracts than in laboratory media. Furthermore, the results suggest that the majority of intestinal plasmid transfer takes place in the viscous mucus layer covering the epithelial cells. Investigation of plasmid transfer in different flow systems harbouring a dynamic, continuously growing population of constant size showed that transfer kinetics were strongly influenced by bacterial biofilm formation. When donor and recipient populations were subjected to continuous mixing, as in a chemostat, transfer continued to occur at a constant rate. When donor and recipient populations retained fixed spatial locations, as in a biofilm, transfer occurred very rapidly in the initial phase, after which no further transfer was detected. From in vivo studies of plasmid transfer in the intestine of streptomycin-treated mice, results were obtained which were similar to those obtained in the biofilm, but differed markedly from those obtained in the chemostat. In spite of peristaltic movements in the gut, and of apparently even distribution of E. coli as single cells in the intestinal mucus, the intestinal environment displays transfer kinetics different from those expected of a mixed, liquid culture, but quite similar to those of a biofilm.
Growth rates of Escherichia coli BJ4 colonizing the large intestine of streptomycin-treated mice were estimated by quantitative hybridization with rRNA target probes and by epifluorescence microscopy. The ribosomal contents in bacteria isolated from the cecal mucus, cecal contents, and feces were measured and correlated with the ribosomal contents of bacteria growing in vitro at defined rates. The data suggest that E. coli BJ4 grows at an overall high rate in the intestine. However, when taking into account the total intestinal volume and numbers of bacteria present in cecal mucus, cecal contents, and feces, we suggest that E. coli BJ4 in the intestine consists of two populations, one in the mucus which has an apparent generation time of 40 to 80 min and one in the luminal contents which is static.The animal intestinal tract harbors a vast number of bacteria representing a complex ecosystem in which the microorganisms are present without overgrowing the host but also without being flushed out by the host's intestinal activities, e.g., peristaltic movements and fluid flow. At least 400 to 500 different bacterial species are thought to be present at any time in the healthy human intestinal tract, and up to 10 12 bacteria are found per g of feces (3, 9). One question of interest is whether the intestinal flora grows as a homogeneous population at a low rate or as a heterogeneous population containing fast, slow, and nongrowing organisms.Accurate calculations of the rates of bacterial proliferation in the intestine have so far been represented only by average estimates at the level of populations. For example, the growth rate of Escherichia coli has been estimated in vivo, i.e., in the mouse intestine, by radioisotope techniques (8), by dilution by growth of a nonreplicating genetic marker (17,25), and simply by counting the number of viable cells (12,14). With these techniques, generation times from 30 min to 40 h have been estimated for E. coli (12,14,16,36). Also, continuous-flow cultures have been developed to mimic bacterial interactions in the gut and estimate overall growth rates (13, 27). These systems, however, do not reflect the physiological conditions in the gut, where entrapping of the bacteria in the mucus gel plays an important role. Furthermore, bacterial cell morphology, protein profiles, and growth physiology have been found to be distinct during growth in the intestine when compared with growth in laboratory media (22,33).We have previously found that in test tubes E. coli BJ4 is rod shaped, appears as large cells, and has a great potential for fast growth; however, soon after colonization of mice, E. coli BJ4 differentiates into a coccoid morphology, the so-called small variant, which grow more slowly than the rod-shaped E. coli cells in aerated test tubes (22). Here, we continue our investigation of the growth physiology of E. coli BJ4 present in its natural environment, the large intestine. Bacterial growth rates can be estimated from the cellular RNA and/or DNA contents, since the cellular RNA...
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