Gut barrier integrity plays a fundamental role in maintaining overall health by coordinating mucosal immune response and regulating the selective permeability of the intestinal epithelium. This barrier system controls the passage of nutrients while preventing the translocation of pathogens, antigens, and toxins into systemic circulation1. Chronic disruption of this interface, associated with increased intestinal permeability, commonly referred to as "leaky gut", is now identified not only as a consequence but also as a driver of chronic inflammatory states and a range of extra-intestinal pathologies2.
For instance, compromised gut barrier function has been shown to be a key component of autoimmune and metabolic disorders such as inflammatory bowel disease (IBD), juvenile idiopathic arthritis (JIA), and type 1 diabetes (T1D). This highlights the gut barrier state as a key biomarker, but also as a therapeutic target to prevent the initiation of pathophysiological processes as early as possible and to prevent the progression of acute inflammation to a chronic state3,4,5,6.
In this context, the neonatal period represents a unique and highly sensitive window of development during which the establishment and maturation of the gut-microbiota interface profoundly influence lifelong intestinal and systemic health7. At this early stage, the intestinal epithelium and immune system display heightened sensitivity to both endogenous and exogenous factors, undergoing rapid growth and differentiation while simultaneously adapting to microbial colonization and dietary changes. Disruptions impairing gut barrier integrity during this critical developmental window may play a pivotal role in the onset of a wide spectrum of acute and chronic disorders later in life. These conditions include immune-mediated diseases such as food allergy, and more severe chronic illnesses, such as IBD, JIA, and T1D7,8,9. These diseases underscore how pathophysiological processes often originate early, as the primary onset generally occurs between childhood and early adulthood10,11. Therefore, understanding the mechanisms that govern gut barrier function in neonates is essential for developing preventive and therapeutic strategies aimed at reducing the burden of many chronic diseases.
Given this context, there is a pressing need for reliable, physiologically relevant tools to study gut barrier integrity, chronic disease mechanisms, and inflammation specifically within the neonatal setting. Such tools must allow the replication of experimental assays already proven in the adult context without sacrificing precision and efficacy. Additionally, it is becoming increasingly urgent to investigate both short- and long-term effects of many molecular candidates of interest, which are expected to have beneficial or harmful effects on gut homeostasis in the neonatal context. Among the tools available, oral gavage administration in neonatal mouse pups represents a more than reliable method of delivering molecules of interest at a defined developmental stage. It allows for controlled investigations into the effects of various bioactive compounds, drugs, or microbial metabolites on gut maturation and barrier function.
The first part of this article describes a method for gavage of mouse pups as early as Day Of Life (DOL) 6, allowing the study of interventions before, during and after the massive expansion of the gut microbiota species numbers induced by food diversification. Thus, this technique enables longitudinal analyses of treatment effects on intestinal health as pups grow and develop.
In the second part of this article and complementing this approach, ex vivo assessment of colonic epithelial barrier function using Ussing chambers provides a sensitive and quantitative measure of permeability characteristics. Evaluation of both paracellular and transcellular permeability in colon biopsies from neonatal mice (e.g., DOL 10 pups) allows for precise determination of the impact of several key candidates on epithelial barrier integrity and function. Paracellular transport is an essentially passive mechanism occurring through the intercellular space of the epithelial layer. It allows for the passage of small solutes driven by electrochemical and osmotic gradients from the lumen to the basolateral side. This mechanism is mainly regulated by proteins of the tight junction family, such as claudins and occludin. Transcellular transport, in contrast, is an active mechanism, allowing for the absorption of bigger solutes and occurring through the epithelial cells via specific channels, carriers, and pumps.
Fluorescein isothiocyanate (FITC)-dextran (4 kDa) predominantly undergoes paracellular transport due to its size, whereas horseradish peroxidase (HRP; 44 kDa) is selectively conveyed to the basolateral side via transcellular routes. Quantification of these non-endogenous markers thus enables distinct assessment of paracellular and transcellular permeability, respectively. The Ussing chamber assay with FITC and HRP preserves tissue architecture and allows real-time measurement of respectively paracellular and transcellular permeability of any segment of the intestinal tract. This combination of neonatal gavage and Ussing chamber analysis offers a powerful strategy to study how specific molecules impact gut barrier function both immediately and over longer timeframes, informing strategies to mitigate inflammation and prevent chronic disease from the earliest stages of life.
In summary, this protocol describes two complementary experimental procedures allowing for: (1) administration of molecules of interest in the early neonatal period to mouse pups (step 1); (2) assessment of both para and transcellular permeability in intestinal tract segments from neonatal to weaning pups using Ussing chambers (steps 2-6).