Metagenome of SHIME inoculated with apple pomace fermented with cold-adapted yeast

The prebiotic effect of fermented apple pomace and biological activity of cold-adopted yeast used for fermentation were assessed in the Simulator of the Human Intestinal Microbial Ecosystem (SHIME). It is a system that enables the simulation and maintenance of the human gastrointestinal microbial diversity in vitro. In this system, the pH, residence time, and temperature are controlled by a software. The SHIME is composed by five vessels simulating the stomach, the duodenum (or small intestine), and the ascending, transverse, and descending colon. The system is kept free of oxygen, by providing the input of nitrogen. During the experiment, samples were collected from the ascending colon, from research (fermented apple pomace) and control (model medium) conditions in three phases: T1 - the first week of the main phase of the experiment (supplementation of fermented apple pomace in research line and supplementation of non-fermented apple pomace in the control line); T2 - the second week of the main phase of the experiment; T5 - the last day of the main phase of the experiment before the silencing phase. Metegnome DNA was isolated from the samples and submitted for sequencing (WGS approach).