Studies suggest that microbiota diversity is reduced in CD and UC (see Discussion). Therefore, we examined the effect of the dietary alternation on murine microbiota diversity in independent experiments from the DSS challenge. There was a tendency for decreased colonic mucosal microbiota diversity in the switching group (Fig. 3, SW vs R: P = 0.055; SW vs NIH-31: P = 0.125).
Principal component analysis showed separation between the 3 different diet groups. The dietary alternation microbiota clustered discretely from both control groups (Fig. 4). Four phyla (Archaea_Other, Bacteria_Actinobacteria, Bacteria_Other, Bacteria_Tenericutes) differed by t test between the switching and the R group. Meanwhile, there was 1 (Bacteria_Bacteriodetes) difference between the SW and the NIH-31 dietary group (P < 0.05, Table 2; supplemental Fig. 2 [http://links.lww.com/MPG/A181]).
There was a trend for an increase in Tenericutes in SW compared with both control dietary groups (SW vs R: P = 0.0477; SW vs NIH-31: P = 0.055; supplemental Fig. 2 [http://links.lww.com/MPG/A181]). Eight genera (Lachnospiraceae_Bryantella, Archaea_Other, Bifidobacteriales_Bifidobacteriaceae, Erysipelotrichaceae_Allobaculum, Staphylococcaceae_Staphylococcus, Erysipelotrichaceae_Other, Erysipelotrichaceae_Coprobacillus, Bacteria_Other) differed between SW and R, and 10 genera (Incertae Sedis XIII_Anaerovorax, Ruminococcaceae_Other, Lachnospiraceae_Hespellia, Staphylococcaceae_Staphylococcus, Porphyromonadaceae_Tannerella, Clostridiales_Other, Bacteroidales_Other, Deferribacteraceae_Mucispirillum, Lachnospiraceae_Oribacterium, Lachnospiraceae_Bryantella) between SW and NIH-31. Lachnospiraceae_Bryantella and Staphylococcaceae_Staphylococcus both increased in the alternating dietary group compared with controls (P < 0.05, Table 2; supplemental Fig. 3 [http://links.lww.com/MPG/A181]).
Only the Archaea phyla changed significantly when corrected for multiple testing that likely relates to the relatively low sample numbers in our group comparisons. Therefore, these individual taxa results only represent trends with respect to bacterial dysbiosis secondary to increased dietary diversity.
Multiple characteristics of the tremendously changing environment (including nutrition) have been implicated as potential causes of the rising IBD incidence during the last 5 to 6 decades. Among these are pollution (31), refrigeration (32), increased hygiene (33), decreased infection with pathogenic organisms (34), and increased consumption of total fats, omega-6 fatty acids, and meat with a decreased intake of fruits, vegetables, and fiber (35). Interestingly, the increase in dietary diversity resulting from large-scale refrigeration and augmented worldwide trade (36) along with enhancing out-of-home eating habits (37) has not been blamed for the emergence of IBD. In the meantime, the success of EEN as a therapeutic modality in CD (see Introduction) emphasizes the potential etiologic importance of the latter dietary characteristic of industrialization. Some studies have suggested that higher socioeconomic status (average family income, family size, urbanization, education) may lead to a higher incidence rate of IBD (38,39). Such demographics usually associate with increased dietary diversity as well (40).
To support these epidemiologic observations, we examined the associations between agricultural import and IBD prevalence in a middle-eastern European country (Hungary, Fig. 5). The increase in agricultural import (41) paralleled a striking rise in the prevalence of both UC and CD in this region (42), indicating a possible connection between dietary diversity and IBD. Naturally, other correlates of agricultural import increase (eg, increased antigen load), concomitant lifestyle, and environment changes may also contribute to this observation emphasizing the difficulties in drawing direct association between nutrition and disease etiology. Nevertheless, epidemiologic observations support our theory that nutritional monotony, which characterizes rural populations consuming locally produced seasonal products (43), may be protective against immune-mediated chronic forms of intestinal inflammation. The findings of this work on increased severity of chemically induced colitis in mice receiving rather modestly alternating diets further sustain this possibility.
The commensal microbiota is a major communicator of dietary modification toward the intestinal immune system of the host and can rapidly change its composition upon nutritional challenges (44,45). A modest level of microbiota composition disturbance (or dysbiosis) and decreased diversity has been observed in IBD (46,47). Therefore, it is commonly accepted that the intestinal microbiota plays an important role in the pathogenesis of these disorders (2). In spite of the success of EEN for the treatment of CD, there is surprisingly limited information about its effects on the intestinal microbiota. Temperature gradient gel electrophoresis revealed significant fecal bacterial composition changes following EEN therapy in children with CD (18). Similarly, denaturing gel electrophoresis indicated marked shifts in mucosal bacterial populations upon EEN (48). Consistent with these observations, EEN significantly decreased fecal Enterobacteria, Bifidobacteria, Bacteroides, Clostridium coccoides, and C leptum diversity in pediatric CD (49) and Faecalibacterium prausnitzii in adult CD (50). On the contrary, EEN (control formula) in critically ill children did not influence bacterial diversity in stool following 7 days of therapy (by denaturing gel electrophoresis), but induced a trend for increase in Lactobacillus and Enterococcus sp and a decrease in Bifidobacterium sp and Enterobacteriaceae by standard culture methods (51). Therefore, it is presently difficult to make convincing conclusions about the effects of EEN on human intestinal microbiota composition. It is also unknown whether EEN has different microbiota effects in people without intestinal inflammation and in patients with IBD where dysbiosis can be present. Importantly, if approached with the concept presented here, traditional mouse models of IBD are already maintained on EEN, since they receive the same composition diet (ie, monotonous diet) day by day. In light of this concept, mice consuming the monotonous diets (control and NIH-31) represented 2 different forms of EEN “therapy” and the switching group corresponds to animals on a modest form of “industrialized” (augmented diet diversity) nutrition.
Interestingly, microbiota diversity decreased upon the alternating nutrition in the study. This would indicate increased susceptibility to inflammation in light of the decreased microbiota diversity observed in IBD (46,47); however, EEN (ie, monotonous) appears to further reduce microbiota diversity in patients with CD according to the limited (not high-throughput) investigations already discussed above (49,50). These later observations would contradict our theory that monotonous (but complete: containing all required micro- and macronutrients) diets may protect against IBD by increasing diversity and optimizing microbiota composition. In the meantime, repetitive nutrition may have differing microbiota effects under inflamed and normal intestinal conditions as supported by observations in critically ill (but devoid of intestinal inflammation) children where EEN had both diversifying and simplifying effects on bacterial taxa (51). In fact, 2-species model microbiota experiments in gnotobiotic mice indicate that modification in host diet can induce selective pressure on bacterial species depending on their fermentative capacity (52). Therefore, our findings indicate that dietary alternation may decrease microbiota diversity in mammals by providing selective advantage to bacterial strains with a broad range of metabolic competence under normal (noninflamed) conditions.
Tenericutes increased in abundance on the switching diet. There are conflicting results on this phylum in regards to murine models of IBD where Tenericutes decreased during DSS challenge (53), but increased at some point of Citrobacter rodentium infection (54). Similar to microbiota diversity, it is difficult to determine from these observations how the abundance of Tenericutes may influence colitis susceptibility under noninflamed (“normal”) conditions. Our findings would suggest that an increase in this phylum may promote vulnerability to mammalian colitis.
This article includes the first high-throughput analysis to test the effects of alternating and monotonous dietary intake on commensal microbiota composition and associated susceptibility to acute colitis in mice. Our results implicate that a consistent (monotonous) diet may have preventative effects against intestinal inflammation in mammals. The relevance of our findings in regard to the emergence of IBD upon industrialization, and for nutritionally based therapeutic modalities for the disease group must be further explored.
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