The main objective of this paper is to critically argue against extrapolation in the context of an effect of GFD on health and the gut microbiota ( Figure 1 ). Extrapolation of results from one population to another is incorrect and risky for various reasons, both strictly statistical and scientific. As it will become clear throughout this manuscript, this concern is particularly important in the context of gut microbial ecology, health and disease. On a recent review of the relationship between the gut microbiota and dietary nutrients, Shortt et al. [ 71 ] acknowledgedthe fact that animal-derived data can hardly be extrapolated to humans, and there is a well-known bias to choose male rodents in studies from different fields of science [ 72 ], including microbial ecology [ 3 ]. However, the problem with extrapolating results among human populations is barely mentioned in the literature, even in papers from our own research group [ 73 ]. We do not generally mention this because we consider it to be common knowledge and implicit in the results of our publications. However, we strongly believe that this concern should be discussed, especially within the context of health benefits derived from a change in the gut microbial ecosystem.

Different studies have evaluated the gut microbiota over short periods of time but very few studies have analyzed changes in the gut microbiota over long periods of time. One study showed a pronounced variability in an individual’s microbiota across months, weeks and even days, and that only a small fraction of all taxa appear to be present across all time points (in this study, 396 time points were analyzed [ 85 ]). Interestingly, baseline populations (i.e., before any major dietary or other change) can also predict the response of the gut microbiota in some situations [ 86 ].

Another reason each individual is unique is because they live in vastly different geographic and sociocultural regions having unique foods and dietary habits. For example, Mexican people possess one of the most genome-wide variation, a fact that can affect biomedical traits as well as disease presentation, progression and response to treatment [ 83 ]. Interestingly, one seminal study about inflammatory bowel disease (IBD) and the gut microbiota showed that the patient’s geographical origin was strongly associated with disease presentation and involvement of specific microbes [ 84 ].

The question of why the microbiota is so unique in each individual deserves thorough examination. The first studies on the gut microbiota soon revealed that each subject harbors a unique blend of microbes [ 77 ]. Microbial carriage varies between subjects down to the species and strain level [ 78 79 ]. Virtually all host-associated and environmental factors can have an effect on an individual’s gut microbiota, either individually or collectively. Sex is also an important but often neglected topic in gut microbial ecology [ 80 ]. This is important because some GRD are known to be more prevalent in women [ 81 ]. On top of the well-known high inter-individual differences, there is considerable horizontal gene transfer happening inside the gut [ 64 ], which have the potential of increasing the uniqueness of each individual microbiome, and some microbes show bistable abundance distributions that are affected differently than the rest [ 82 ].

Each human being harbors a unique blend of trillions of microorganisms and viruses in the gut and other organs, and growing evidence suggest that colonization starts before birth [ 74 ]. The microbiota is not only highly different among individual subjects but it also shows a highly individualized response to environmental challenges such as antibiotic perturbation [ 75 ]. One study showed that variation in composition of the microbiota across different body sites was consistently larger than technical variability (e.g., PCR primers, 16S rRNA gene region, sequencing platform) across studies [ 76 ]. Overall, this means that the many different analyses showing inter-individual variation are biologically meaningful and not the result of technical artifacts.

5.2. Dietary Differences in Gluten-Containing and GFD

Gluten-containing foods provide many nutrients (e.g., prebiotics such as inulin) which may not be equally abundant in gluten-free foods. The potential issues associated with GFD have been discussed since the 1950s [ 87 ] and the concern that a GFD could produce potentially adverse effects in the microbiota solely based on a marked reduction in intake of naturally occurring prebiotics has been raised [ 88 ]. On the one hand, a recent review showed that long-term morbidities associated with CD, such as nutritional deficiencies, impaired bone health, and reproductive abnormalities, can substantially improve after strict adherence to a GFD [ 89 ]. However, a study in Italy reveals an overall low nutritional quality of gluten-free bakery products [ 90 ], and gluten-free products contribute to imbalanced diets in children from Spain [ 91 ]. In addition, a recent review showed that reduced intake of calcium, vitamins and fiber as well as enhanced consumption of fat and carbohydrates have been consistently reported in patients on GFD [ 92 ]. Moreover, there is evidence that some gluten-free foods are not enriched and may be deficient in several nutrients, including dietary fiber, folate, iron, niacin, riboflavin, and thiamine [ 93 94 ], although this would not necessarily lead to dietary deficiency of these nutrients because other gluten-free foods such as vegetables, beef, eggs and cheese are rich in these compounds. Other studies evaluating the nutritional composition of processed gluten-free products have demonstrated higher levels of lipids, trans-fat, protein, and salt compared to their gluten-containing counterparts. Furthermore, recent evidence has shown that patients under a GFD are at risk of metabolic syndrome and hepatic steatosis [ 95 ] and the concerns regarding the association between micronutrient deficiencies and increased exposure to toxins such as arsenic in GFD [ 96 ]. Moreover, some varieties of GFD do not necessarily lead to a healthier physiological state. Ercolini et al. [ 97 ], for example, showed that changing from an African-style GFD to an Italian-style GFD provoked significant changes in the salivary microbiota and metabolome of Saharawi (Western Sahara) celiac children and, more importantly, that these changes suggested metabolic dysfunction.

Another issue with GFD is its availability and costs. While some regions in the industrialized world have the luxury of having access to a wide variety of foods and dietary ingredients, most regions of the world have limited access to different foods. This translates into wide differences in GFD, even within the same geographical region. Importantly, not all gluten-free products are certified ( http://www.gfco.org/ ) and some supposedly gluten-free products are actually contaminated with gluten [ 98 ]. Moreover, the mere availability of dietary foods in one region does not imply that all people have access to it. In México, for example, differences in income may involve as much as 27-fold difference between the average incomes of the top and the bottom deciles, a difference that stark contrasts with the average ratio of 10 to 1 in the Organization for Economic Co-operation and Development (OECD 2014, https://www.worldeconomicsassociation.org/newsletterarticles/inequality-in-mexico/ ). Therefore, the purchasing power is likely to be involved in the maintenance of life-long GFD.

An interesting argument emerged from one anonymous reviewer during the review process. Indeed, other grains such as corn and rice are the primary grains consumed in many different countries. In the case of maize, which is often used as an alternative to elaborate GFD for CD patients, there are some maize prolamins (called zeins) containing amino acid sequences that resemble the wheat gluten peptides that may in fact be clinically relevant [ 99 ]. The case of rice is also interesting, especially because several countries in Asia have considerably reduced their consumption of rice [ 100 ] and increased the consumption of other grains. In addition, it has been recognized that CD epidemiology has changed, in particular in areas where previously CD was unrecognized or rare such as India, China and Latin America. Several hypotheses may explain this phenomenon such as a change in the pattern of food consumption to try to beat malnutrition that has led to a wheat–rice shift in poor countries, but dysbiosis and genetic predisposition may be also related [ 101 ]. Overall, we agree with the notion that the cost and availability of GFD may be of lesser clinical importance in some regions of the world.