Investigating the role of intestinal microbial populations significantly relies on the assumption of stability. Therefore, the microbial community composition of the simulator of the human intestinal microbial ecosystem was qualitatively, quantitatively and functionally characterised during reactor start-up to evaluate its capacity to produce a stable bacterial community, representative for the human intestinal tract. Using moving window correlation, a stability criterion was introduced to analyse the stability over time of the PCR-DGGE, plate counts, short chain fatty acids and ammonium results. A community was regarded stable when minimum 80% correlation was measured over at least one cell residence time. Species composition stability was reached after about 2 weeks, while it took some 3 weeks to reach functional stability. The combination of PCR-DGGE with moving window correlation proved to be an efficient approach to quantitatively evaluate the stability of the in vitro cultured intestinal microbial community.

Little is known about the chronic effect of herbicides on the soil microbial community, with most studies focusing on acute impacts. In this study, we investigated the effect of 20 years of atrazine and metolachlor application on the community structure, abundance and function of bacterial groups in the bulk soil of a maize monoculture. Group-specific PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) of 16S rRNA genes was used to characterize the composition of the microbial community. Primers specific for the entire bacterial group, as well as for the Acidobacterium group, the actinomycetes, the ammonium oxidizers, and the Type I and II methanotrophs were used in the PCR-DGGE analysis. Cluster analysis of the DGGE patterns obtained with the different primer sets differentiated between the herbicide-treated and the non-treated control soil. In particular the methanotrophic community differed, with three bands (phylotypes) being absent (or showing a lower intensity) in the DGGE patterns of the herbicide-treated soils compared to the patterns of the control soil. The differences in the methanotrophic community structure were not reflected in the methane oxidation capacity, which was similar for the two treatments. The prevalence of methanotrophs as evaluated with real-time PCR analysis also did not differ between the herbicide-treated and non-treated soil. Our results indicate that the long-term use of the herbicides atrazine and metolachlor resulted in an altered soil community structure, in particular for the methanotrophic bacteria. These observed changes did not cause a decreased community function (methane oxidation), probably because the total abundance of the methanotrophs in the soil system was preserved.

A bacteriophage, designated UZ1 and showing lytic activity against a clinically important strain (BE1) of Enterobacter aerogenes was isolated from hospital sewage. The stability and lytic activity against this strain under simulated gastro-intestinal conditions was evaluated. After addition of bacteriophage UZ1 to a liquid feed at gastric pH 2, the phage was immediately inactivated and could not be recovered. However, by use of an antacid to neutralize stomach acidity, no significant changes in phage titer were observed after 2 h incubation at 37°C. After supplementing pancreatic juice and further incubation for 4 h, the phage titer remained stable. The persistence of UZ1 in a mixed microbial ecosystem that was representative for the large intestine was monitored using an in vitro simulation of the human intestinal microbial ecosystem. A pulse administration of bacteriophage UZ1 at a concentration of 10 5 plaque-forming units (PFU)/ml to reactor 3 (which simulates the ascending colon) showed that, in the absence of the host, bacteriophage UZ1 persisted for 13 days in the simulated colon, while the theoretical washout was calculated at 16 days. To assess its lytic activity in an intestinal microbial ecosystem, a green fluorescent protein (gfp)-labeled E. aerogenes BE1 strain was constructed and gfp-specific primers were designed in order to quantify the host strain using real-time PCR. It was observed that bacteriophage UZ1 was able to replicate and showed lytic activity against E. aerogenes BE1/gfp in an intestinal microbial ecosystem. Indeed, after 17 h a 2 log unit reduction of E. aerogenes BE1/gfp was measured as compared with the assay without bacteriophage UZ1, while the phage titer increased by 2 log units at an initial multiplicity of infection of 0.07 PFU/colonyforming unit. This is the first report of an in vitro model to study bacteriophage activity in the complex intestinal microbial community.

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