Food matrix and the microbiome: considerations for preclinical chronic disease studies

The role of the gut microbiome in health and disease has received considerable attention over the last decade. The gut microbiome is the most diverse and complex community of microorganisms in the body, consisting of more than a thousand bacterial species. The relationships between these bacteria and the host are generally commensal or symbiotic in nature. For instance, it is estimated that humans obtain approximately 10% of their daily energy intake from short-chain fatty acids (SCFAs) derived from microbial fermentation.

Alternatively, many studies have been performed examining the relationship between the gut microbiome and health, and it is now known that dysbiosis of the gut microbiome is associated with numerous diseases, including metabolic syndrome, inflammatory bowel syndrome, and colorectal cancer. Much of this pioneering work has been performed using preclinical models. Rodent models of human disease have been invaluable for mechanistic studies, in part because experimental variation can be tightly controlled among investigations.

The use of inbred rodent strains, standardized environments, and semipurified diets has helped reduce experimental variability and allowed for investigations from different laboratories to be compared and replicated. Moreover, gnotobiotic or antibiotic depletion protocols can be used along with microbiota transfer to investigate whether the gut microbiome is correlative or causative in disease models. An assumption in the use of animal models in biomedical and nutrition research is that the results will be of value to human well-being.

Yet, it is estimated that up to 80% of therapeutics fail in humans after being previously shown to be safe and (or) effective in rodents. Two possible explanations for this discordance were suggested by Ioannidis . The first may lie in fundamental physiological differences between the animal model and humans, both in healthy and in diseased conditions.

Basal rodent diets and fiber

The composition and metabolic activity of the gut microbiota influence many aspects of health. Consequently, there is interest in dietary strategies to improve health via modulating the microbiota. Mice are the most common model organisms used to study the microbiota, yet the translational relevance to humans has been questioned.

Dietary fiber has a large impact on the microbiota composition and metabolic activity via provision of fermentable substrates; yet, to date, there has been very little attention paid to modeling the fiber composition of rodent diets to that of humans. Thus, there is a critical need to establish how the microbiota of mice responds to the range of human dietary fiber intakes and whether the changes are consistent with health benefits provided by dietary fiber in humans. According to data from NHANES, the average American diet contains 60% of the Adequate Intake (AI) of dietary fiber recommended by the Institute of Medicine (IOM).

The AI for fiber is scaled to energy and is 14 g per 4184 kj, which often is simplified to 25 g/d for women and 38 g/d for men. According to What We Eat in America, the 2015-2016 NHANES, Americans eat an average of 16.7 g of dietary fiber per 8807 kj (~8 g/4184 kj. In 2001, the Food and Nutrition Board of the Institute of Medicine set the AI for total fiber at 14 g/4184 kj, which was based on a number of prospective cohort studies that showed significant reductions in the risk for coronary heart disease and type 2 diabetes in individuals consuming the most fiber.

It is estimated that only ~5% of Americans consume the AI for fiber, whereas the average intake (from NHANES) is only 60% of the recommended level. Fiber intakes have increased about 20% since the 2001-2002 NHANES survey yet are still far less than levels shown in prospective cohort studies to reduce the risk of heart disease and diabetes. Evidence from prospective cohort studies and randomized clinical trials suggests that increasing fiber intake reduces gut and systemic inflammation and provides protection against the development of coronary heart disease and type 2 diabetes (T2D).

In a recent meta-analysis, the risk for a number of clinical outcomes, such as coronary heart disease and T2D, was reduced when the fiber intake was between 25 and 29 g/d . Interestingly, dose-response curves from this study indicated that higher intakes might even provide more protection. Although the evidence that dietary fiber promotes gut and metabolic health is well documented in humans, the mechanisms via which this is done are not well known. The difference between recommended and actual intakes of fiber has been called the fiber gap.

Food processing and the microbiome

In terms of providing substrates to the gut microbiome, human diets are much more complicated than the sum of their macro- and micronutrient components. Cooking and processing of food can lead to the introduction of protein and lipid oxidation products into the diet. Moreover, dietary emulsifiers are commonly added to foods to improve sensory aspects of processed foods.

All of these food matrix factors can independently affect health and the composition of the microbiome but are rarely considered in preclinical disease models despite being common components in human diets. In a recent investigation by Johnson et al, human volunteers kept 24-hour food records, and their gut microbiomes were tracked for 17 days. The dietary records were then used to predict changes to the microbiome.

They reported that conventional methods of describing foods based on nutrients were a poor predictor of the microbiome composition compared to a whole food-based, hierarchical tree of foods developed for the study. This observation suggests that the food matrix is more important for shaping the microbiome than the micro- and macronutrient content of the diet. Aside from the nutrient content, varying methods of food processing or preparation may also impact the composition and/or function of the gut microbiome.

For example, one study explored the impact of consumption of raw or cooked meat and tubers on the gut microbiome in mice. Researchers noted that differences in the mice microbiomes were evident when comparing raw vs cooked tubers but not raw vs cooked meat. Also, α diversity was lower in mice fed raw tubers compared to cooked tubers, whereas Bacteroidetes were increased.

Although mice are the most commonly used species for microbiota studies, the translational relevance of preclinical studies using mice as models for studying the intersection of nutrition and the microbiome as pertains to health and disease in humans is unclear. Although individual food matrix components have been tested in rodent models as reviewed herein, the effects of all of these factors combined on the microbiome in preclinical models of chronic disease are unclear, representing a critical knowledge gap.

Future research to address this issue could increase the translatability of these models. Unless mice are provided with diets that reflect actual human intakes of fiber and possibly other components, such as oxidized protein and fat or emulsifiers, and the resulting phenotypes are characterized, translatability of preclinical models in studies focused on diet and the gut microbiome to human populations may be hampered because all of these components can independently affect chronic disease and the microbiome in mouse models.

Semipurified rodent diets only contain cellulose as a source of dietary fiber, which promotes a microbiome that degrades the mucin barrier, promotes intestinal inflammation, and changes to the microbiome. A possible first step to improve the translatability of microbiota/chronic-disease models would be to use a diverse portfolio of fiber in semipurified diets that reflect human intakes instead of cellulose. This approach would address an important source of variability in the gut microbiome between humans and experimental animals.


Author: Robert E. Ward, Abby D. Benninghoff, Korry J. Hintze