This paper introduces a new type of system to simulate conditions in the large intestine. This system combines removal of metabolites and water with peristaltic mixing to obtain and handle physiological concentrations of microorganisms, dry matter and microbial metabolites. The system has been designed to be complementary to the dynamic multi-compartmental system that simulates conditions in the stomach and small intestine described by Minekus et al. [Minekus M, Marteau P, Havenaar R, Huis in't Veld JHJ (1995) ATLA 23:197-209]. High densities of microorganisms, comparable to those found in the colon in vivo, were achieved by absorption of water and dialysis of metabolites through hollow-fibre membranes inside the reactor compartments. The dense chyme was mixed and transported by peristaltic movements. The potential of the system as a tool to study fermentation was demonstrated in experiments with pectin, fructo-oligosaccharide, lactulose and lactitol as substrates. Parameters such as total acid production and short-chain fatty acid (SCFA) patterns were determined with time to characterize the fermentation. The stability of the microflora in the system was tested after inoculation with fresh fecal samples and after inoculation with a microflora that was maintained in a fermenter. Both approaches resulted in total anaerobic bacterial counts higher than 10(10) colony-forming units/ml with physiological levels of Bifidobacterium, Lactobacillus, Enterobacteriaceae and Clostridium. The dry matter content was approximately 10%, while the total SCFA concentration was maintained at physiological concentrations with similar molar ratios for acetic acid, propionic acid and butyric acid as measured in vivo.

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The Bacteria and Archaea from the meromictic Lake Pavin were analyzed in samples collected along a vertical profile in the anoxic monimolimnion and were compared to those in samples from the oxic mixolimnion. Nine targeted 16S rRNA oligonucleotide probes were used to assess the distribution of Bacteria and Archaea and to investigate the in situ occurrence of sulfate-reducing bacteria and methane-producing Archaea involved in the terminal steps of the anaerobic degradation of organic material. The diversity of the complex microbial communities was assessed from the 16S rRNA polymorphisms present in terminal restriction fragment (TRF) depth patterns. The densities of the microbial community increased in the anoxic layer, and Archaea detected with probe ARCH915 represented the largest microbial group in the water column, with a mean Archaea/ Eubacteria ratio of 1.5. Terminal restriction fragment length polymorphism (TRFLP) analysis revealed an elevated archaeal and bacterial phylotype richness in anoxic bottom-water samples. The structure of the Archaea community remained rather homogeneous, while TRFLP patterns for the eubacterial community revealed a heterogeneous distribution of eubacterial TRFs.Permanent anoxic basins are of great interest to microbial ecologists, and during the last decade several papers have been published on microbial assemblages from different marine anoxic basins (e.g., see references 42 and 36). Among permanent anoxic aquatic systems, meromictic lakes are unusual and provide a special opportunity for research in aquatic biology for several reasons, e.g., the high physical stability of the water masses, clearly separated compartments, a relatively constant vertical stratification of bacterial populations, a compact and stable transition zone between the oxic mixolimnion and the anoxic monimolimnion, and in many cases the presence of a dense microbial community at the redox transition zone (6). These small and well-defined ecosystems can be useful for studying anaerobic microbial community structure and diversity and providing information on global carbon cycling and biogeochemical processes. Although molecular characterizations of microbial communities from Lake Saelenvannet (31, 41), Lake Cadagno (6), Mono Lake (18), and Mariager Fjord (34, 40) have been reported, the microbial populations and communities living in anaerobic zones of meromictic lakes remain largely unexplored.This paper focuses on the in situ distribution, abundance, and diversity of the Bacteria and Archaea communities in the anoxic zone of Lake Pavin, which has the advantage of being in a steady state (28). We have conducted culture-independent studies of the anoxic water column of Lake Pavin and of samples collected from the oxic zone to provide comparative information. Terminal restriction fragment length polymorphism (TRFLP) and fluorescent in situ hybridization analyses were performed on samples from between 50-and 90-m depths to characterize the microbial assemblages using 16S rRNA genes. Because previous geochemic...