Development of a single-stage bioreactor for the study of the ascending colon microbial ecology

Introduction: Understanding the intricate interactions occurring within the gut microbiome and unravelling its impact on human health is a challenging task. Invasive strategies, such as endoscopy and nasoenteric probes that allow direct sampling of the gut environment, face practical and ethical limitations. Bioreactors are in vitro models used to overcome some of these limitations, which have contributed to our understanding of gut microbial ecology by providing controlled environments that mimic some of the features of the gastrointestinal tract. Objectives: the aim of this work is to develop a single-stage bioreactor for the simulation of selected conditions of the ascending colon. Methods: All the experiments were performed in a Bio-Book Compact bioreactor. The conditions selected for the system were: temperature, 37 °C; pH, 6.8; hydraulic retention time, 12 h; and a working volume of 250 mL. A fresh stool sample from a 30-year-old healthy donor was used as inoculum, and a culture medium mimicking the nutrients available in the colon was used as feedstock. Anaerobic conditions were first established by purging the culture vessel with high-purity Argon during inoculation, and after this step, the microbial community sustained the anaerobic environment. The cultivation was run for a total of 9 days. 16s rRNA amplicon sequencing was used to characterize the microbial communities growing in the bioreactor, and proton nuclear magnetic resonance (1H NMR) experiments were performed for metabolic profiling.