Designs and methodologies to recreate in vitro human gut microbiota models

TLDR

The human gut microbiota, a metabolic organ essential to host physiology, comprises diverse microbes whose imbalances are linked to disease, and in vitro models are widely used to study its fermentation, composition, and host interactions. This review aims to outline the essential components for building reproducible, accurate in vitro gut microbiota cultures and to evaluate devices used for fermentation and host–microbe interaction studies. The review discusses bioreactors and microfluidic devices that culture gut microbes in dynamic conditions, with or without eukaryotic cells, to study fermentation and host–microbe interactions. A graphic abstract summarizes the review.

Abstract

Abstract The human gut microbiota is widely considered to be a metabolic organ hidden within our bodies, playing a crucial role in the host’s physiology. Several factors affect its composition, so a wide variety of microbes residing in the gut are present in the world population. Individual excessive imbalances in microbial composition are often associated with human disorders and pathologies, and new investigative strategies to gain insight into these pathologies and define pharmaceutical therapies for their treatment are needed. In vitro models of the human gut microbiota are commonly used to study microbial fermentation patterns, community composition, and host-microbe interactions. Bioreactors and microfluidic devices have been designed to culture microorganisms from the human gut microbiota in a dynamic environment in the presence or absence of eukaryotic cells to interact with. In this review, we will describe the overall elements required to create a functioning, reproducible, and accurate in vitro culture of the human gut microbiota. In addition, we will analyze some of the devices currently used to study fermentation processes and relationships between the human gut microbiota and host eukaryotic cells. Graphic abstract