MiGut: a scalable in vitro platform for simulating the human gut microbiome – development, validation, and simulation of antibiotic induced dysbiosis

Abstract

In vitro models of the human colon have been used extensively in developing understanding of the human gut microbiome and how internal and external factors affect the residing bacterial populations. Such models can be highly predictive of in vivo effects of antibiotics, and indeed more so than animal models. The complexity required by current in vitro models to closely mimic the physiology of the colon poses practical limits on their scalability. MiGut allows considerable expansion of model runs, increasing the capacity to test reproducibility or parameters under investigation. The MiGut platform has been assessed against a well-studied triple-stage chemostat model in a demanding nine-week study, with exposure to multiple antibiotics inducing a state of dysbiosis in the microbiome. A good correlation is found, both between individual MiGut models and against the triple-stage chemostat. Together with high-throughput molecular techniques for sample analysis, it is now conceivable that tens of in vitro models could be run simultaneously, allowing complex microbiome-xenobiotic interactions to be explored in far greater detail. MiGut is a unique platform whereby multiple colonic models can be run simultaneously with minimal added resource and complexity to support our understanding of the cause-effect relationships that govern the gut microbiome. This model system expands the capacity to generate clinically relevant data that can optimize interventions which target the gut microbiome directly or indirectly.

PETR: A novel peristaltic mixed tubular bioreactor simulating human colonic conditions

“…These include physiological temperatures (Pearson et al, 2012), anaerobic conditions (Zheng et al, 2015), and peristaltic mixing (Sarna, 2010), as well as varying conditions across the different colon parts, for example, in terms of nutrient availability and fermentation activity (Macfarlane et al, 1992) or increasing pH in distal direction (Cummings et al, 1987), and especially the absorption of water (Sandle, 1998) and fermentation products (McNeil, 1984). Besides the trend of miniaturizing gut-mimicking systems (Davis Birch et al, 2023;Jin et al, 2022;Makivuokko et al, 2005;Robinson et al, 2014;Wiese et al, 2018), the bioreactor was intentionally developed as a comparatively large system with dimensions comparable to the adult human colon (Kararli, 1995). This ensures differences and gradients over the length and the ability to collect sufficient sample volume without disturbing the running system.…”

“…These vessels are typically stirred magnetically (Barroso et al, 2015a;Cinquin et al, 2006;Macfarlane et al, 1998;Molly et al, 1993) or with conventional agitators (Blanquet-Diot et al, 2012;Feria-Gervasio et al, 2011;Feria-Gervasio et al, 2014;Haindl et al, 2021). In miniaturized reactors, mixing was also conducted with nitrogen sparging (Davis Birch et al, 2023;Jin et al, 2022). Other in vitro systems also incorporate simulation of intestinal peristalsis.…”

“…To prevent overregulation due to this time delay and to prevent damage of the membrane because of locally low or high pH values, the pH control was programmed with a rather slow supply and acid and base had relatively low concentrations. Therefore, initial gradient formation takes some time, but this is neglectable regarding typical cultivation times of several days or even weeks (Davis Birch et al, 2023;Cinquin et al, 2006;McDonald et al, 2013;Molly et al, 1993) as shown in Table 1. Once the gradient was generated, acid and base were added almost linearly to maintain the set points.…”

“…Some systems also used heat mats (Davis Birch et al, 2023), temperature-controlled incubation chambers (Makivuokko et al, 2005;Robinson et al, 2014;Wiese et al, 2018), or performed temperature control via surrounding dialysis liquid (Probert & Gibson, 2004;Spratt et al, 2005) or pressurized water used for peristaltic mixing (Minekus et al, 1999).…”