The gut virome is a complex part of the gut ecosystem, and although it is implicated in many disease states, it’s not yet known to what extent the gut virome impacts everyday human health. Gut virome colonization begins at birth, becoming temporally stable over a 30-month period. The virome is highly specific to an individual and is modulated by varying factors such as age, gender, diet, antibiotic use, and disease state. The gut virome is primarily comprised of bacteriophages, predominantly crAssphage and other tailed phages (Caudovirales). Even after two decades, 40-90% of sequences in the gut virome remain unclassified and uncharacterized, the so-called “viral dark matter”. We have developed new mini-bioreactors to culture faecal microbiota and to monitor changes in the gut virome over time. We maintained faecal bacteria in our mini-bioreactors for 12 days, and used these bioreactors to develop new protocols for the extraction of viral DNA from faecal matter for sequencing. The mini-bioreactors allow us to simultaneously compare temporal changes in the virome in response to changes in the pH, and will allow us to investigate the effect of diet, antibiotics, and other external influences directly on gut viruses. We have developed a new method to investigate the gut virome and shed more light on the viral dark matter.