Background The human gut microbiome has an immense part in human health. Disruption of the
gut microbiome (or dysbiosis) is associated with various intestinal conditions, including
obesity, inflammatory bowel disease, and even cancer. Understanding the strong demand
for a platform to study human gut microbiome, we focus on the establishment of a novel
in vitro model for the human gut that could be implemented into clinical practice.
Aim The main goal of this study was to optimize sampling and culture conditions, including
the possible time between sample collection and culture and the choice of the medium,
to resemble physiological conditions in the gut.
Methods The stool collection procedure was performed using an anaerobic microbiome collection
kit GutAlive (MicroViable therapeutics, Spain). The stool samples were stored in four
GutAlive containers for less than 1 hour, 2, 24, and 48 hours after sampling. Stool
samples were prepared anaerobically and then cultured in a DASbox mini bioreactor
system (Eppendorf, Germany) for 5 days. Bryant and Burkey (BB), or continuous flow
fermentation (CFF) medium were tested as potential medium composition. Every 24 hours,
cell viability was evaluated, and samples were analyzed with a flow cytometry-based
microbial fingerprinting approach. pH, temperature, and dissolved oxygen were measured
continuously within the bioreactors.
Results Flow cytometry analysis revealed that sample storage in anaerobic microbiome collection
containers did not have strong influence on microbial community structure for up to
48 hours. According to the results, the BB medium caused a higher pH than the CFF
medium. It resulted in significantly higher cell viability and more stable pH values.
Conclusion In conclusion, samples from patients can be stored for up to two days in GutAlive
container without significant changes in the microbiome structure. BB medium is more
suitable to maintain the microbial structure and physiological pH of the distal colon.
