Role, relevance, and possibilities of in vitro fermentation models in human dietary, and gut‐microbial studies

Abstract

Dietary studies play a crucial role in determining the health‐benefiting effects of most food substances, including prebiotics, probiotics, functional foods, and bioactive compounds. Such studies involve gastrointestinal digestion and colonic fermentation of dietary substances. In colonic fermentation, any digested food is further metabolized in the gut by the residing colonic microbiota, causing a shift in the gut microenvironment and production of various metabolites, such as short‐chain fatty acids. These diet‐induced shifts in the microbial community and metabolite production, which can be assessed through in vitro fermentation models using a donor's fecal microbiota, are well known to impact the health of the host. Although in vivo or animal experiments are the gold standard in dietary studies, recent advancements using different in vitro systems, like artificial colon (ARCOL), mini bioreactor array (MBRA), TNO in vitro model of the colon (TIM), Simulator of the Human Intestinal Microbial Ecosystem (SHIME), M‐SHIME, Copenhagen MiniGut, and Dynamic Gastrointestinal Simulator, make it easy to study the dietary impact in terms of the gut microbiota and metabolites. Such a continuous in vitro system can have multiple compartments corresponding to different parts of the colon, that is, proximal, transverse, and distal colon, making the findings physiologically more significant. Furthermore, postfermentation samples can be analyzed using metagenomic, metabolomic, quantitative‐polymerase chain reaction, and flow‐cytometry approaches. Moreover, studies have shown that in vitro results are in accordance with the in vivo findings, supporting their relevance in dietary studies and giving confidence that shifts in metabolites are only due to microbes. This review meticulously describes the recent advancements in various fermentation models and their relevance in dietary studies.

The use of an in vitro fecal fermentation model to uncover the beneficial role of omega-3 and punicic acid in gut microbiota alterations induced by a Western diet

“…Indeed, batch systems are the simplest, most versatile, and most accessible approach, and are very useful for testing different biotic and abiotic conditions on microbiota activity. [104][105][106] They are particularly helpful to study the impact of a given diet on the human gut microbiota. 104,105 Thus, it allows the understanding of how the microbial community is changed over time, how a compound is digested, which metabolic pathways are triggered, and the quantity and type of microbial products produced.…”

New Horizons in Probiotics: Unraveling the Potential of Edible Microbial Polysaccharides through In Vitro Digestion Models

“…Gastrointestinal dynamic simulation effectively models food digestion, which is preferred for studying fluid dynamics and digestion rates. In vitro human gastrointestinal simulation systems replicate physiological functions, providing a simple, convenient, safe, and ethical alternative for research that is widely applied in assessing food safety, gastrointestinal metabolic dynamics, and nutritional substance bioavailability [ 25 , 26 ]. Currently, in vitro intestinal digestion models are broadly categorized into static single-chamber, dynamic single-chamber, dynamic double-chamber, and dynamic multi-chamber models [ 25 ].…”

Mathematical modeling of fluid dynamics in in vitro gut fermentation systems: A new tool to improve the interpretation of microbial metabolism

“…Nonetheless, fecal microbiota is considered the closest proxy for colonic microbiota, even if it blurs the differences between luminal and mucosal intestinal ecosystems or colonic regions 5 . Several in vitro mono‐ and multi‐compartmented dynamic gut fermentation systems have been developed over the last 20 years to simulate the in vivo conditions 6–10 . The Polyfermentor Intestinal Model (PolyFermS) and the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®) emerged as robust and validated alternatives to study the human gut microbiome in a host‐uncoupled fashion 11,12 .…”

“…5 Several in vitro mono-and multi-compartmented dynamic gut fermentation systems have been developed over the last 20 years to simulate the in vivo conditions. [6][7][8][9][10] The Polyfermentor Intestinal Model (PolyFermS) and the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®) emerged as robust and validated alternatives to study the human gut microbiome in a host-uncoupled fashion. 11,12 Gut fermentation systems rely on long-term cultivation of fecal microbiota (2 weeks minimum) under specific physicochemical conditions reproducing human colonic environment.…”