Validation of the Simulator of the Human Intestinal Microbial Ecosystem (SHIME) Reactor Using Microorganism-associated Activities

Abstract

The recently developed SHIME reactor (Simulator of the Human Intestinal Microbial Ecosystem) was validated by analysing a number of microorganism-associated activities. Data from the reactor were compared with values from the literature and results obtained from the analysis of faecal material of eight healthy persons. The fermentation patterns of four polysaccharides were studied. Arabinogalactan, xylan and pectin gave fermentation patterns in vitro indistinguishable from in vivo. Five different enzymatic activities were compared with in vivo experiments. All had activities which were of the order of those observed in vitro. The pro-drug sulphasalazine, whose active compound is released through microbial modification in the large intestine, was used as a reference compound. A fair correlation between in vivo and in vitro was found for the latter transformation. In addition the effect of Lactobacillus plantarum on the autochthonous microbial populations was investigated. Administration of L plantarum resulted in an in virro decrease in gram-negative anaerobic bacteria and total anaerobes. The same effect has been reported in vivo. The results obtained by the various validation experiments indicate that the reactor can be used to study the microbial communities of the gastrointestinal tract.

Variability of arsenic bioaccessibility and metabolism in soils by human gut microbiota using different in vitro methods combined with SHIME

“…After 3-4 weeks of adaptation, stable microbial communities were obtained in the respective colon compartments. The distal colon microbial fermentation activity (short chain fatty acid production and ammonium production) and community composition were investigated, and found to be consistent with those of previous SHIME runs and the in vivo situation (Molly et al, 1994;Yin et al, 2015b). For the dynamic SHIME, the feed solution contained (in grams/liter) arabinogalactan (1.0), pectin (2.0), xylan (1.0), starch (4.0), glucose (0.4), yeast extract (3.0), peptone (3.0), mucin (1.0), and cystein (0.5).…”

“…Feed solution was added three times per day to provide digested nutrition for the colon microorganisms. The temperature (37°C) and pH (5.6-5.9, 6.15-6.4, and 6.7-6.9 in the ascending colon, transverse colon and descending colon, respectively) (Molly et al, 1994) were controlled automatically. The SHIME reactors were continuously stirred and kept under anaerobic conditions by regularly flushing with nitrogen.…”

Optimization of a yeast estrogen screen and its applicability to study the release of estrogenic isoflavones from a soygerm powder.

“…This computer-controlled reactor was developed to simulate the bacterial communities found in certain parts of the intestines. Each of the six reactors contains the microbiota of a different part of the human gastrointestinal tract, in order of sequence (compartments 1-6): the stomach, the duodenum, the small intestine, and the ascending, transverse, and descending colon (18). A detailed scheme of the reactor setup is provided in Figure 2.…”

The Simulator of the Human Intestinal Microbial Ecosystem (SHIME®)

“…The fi rst validation paper of the conventional SHIME ® setup concerned a study from Molly et al ( 1994 ) where several microbe-associated characteristics were defi ned. The authors focused on fermentation profi les of pectin, xylan, arabinogalactan and starch and found these to be consistent with the results from incubations of the same products with fecal microbiota from human volunteers (Englyst et al 1987 ).…”