Colorectal cancer (CRC) is the second most commonly diagnosed cancer in females and the third in males worldwide [1]. Approximately 25% of individuals diagnosed with CRC have a family history of the disease, but 75% of CRC cases are not hereditary, indicating that genetics and environmental factors contribute to the pathogenesis of CRC [2]. Accumulating evidence suggests that the gut microbiota and its metabolites may be the proximate environmental factors for CRC. The initiation and progression of CRC occurs in an altered intestinal environment that includes changes in the gut microbiota [3]. The intimate crosstalk between the gut microbial community and the host’s epithelium layer is a crucial factor for cell proliferation and differentiation, gene expression in host epithelial cells, and the regulation of inflammation, which is a significant driver of rectal carcinogenesis [4].

The human gut hosts roughly a thousand different bacterial species. Gut microbial diversity is affected by host genotype [5] and a range of environmental factors [6]. Among all environmental factors, dietary parameters play a critical role in shaping the gut microbiota [7]. The diet has an essential impact on the composition and function of the gut microbiota, which is more relevant to environmental factors rather than genetic background [8]. Numerous epidemiologic studies have identified that specific dietary patterns can either promote the development of CRC or offer protection from it. The two most studied diets are the Western diet and the Mediterranean diet (MD). The Western diet, characterized by high red meat, high fat, and low fiber content, is thought to be a significant contributor to CRC incidence, while the MD, consisting of high fiber foods, i.e., fruits, vegetables, and whole grains, has been shown to be protective against CRC [9]. However, the effect of food intake on the species of intestinal bacteria is unclear, and inconsistent results also exist [10]. The inner mechanisms of diet that induce CRC may be complicated, and require elucidation.

Dietary compounds are a source of energy and metabolites for gut bacteria [7]. Cereals contain resistant starch and non-starch polysaccharides such as β-glucan and arabinoxylans, which resist digestion in the upper gastrointestinal tract, making them an essential fuel for the microbiota of the gut [11]. Consumption of whole cereal grains (WCGs) has been linked to improvements in metabolic syndrome (Mets) by altering the composition and function of the gut microbiota in humans and other mammals [11]. An animal study revealed that commercial oat bran or hulled barley-derived β-glucan significantly increased Lactobacillus and Bifidobacterium populations and decreased the number of Enterobacteriaceae in a dose-dependent manner in male rats [12]. In rats, switching from a low-fat diet to a high-fat diet altered the microbiota composition with an increase in Firmicutes and decrease in Bacteriodetes [13].

In humans, evidence for the direct effect of fat on the gut microbiota is still lacking due to the constant mixing of meat and fat with fiber in the human diet [10]. Compared to a single type of food, i.e., meat or vegetable, the dietary structure may play a more significant role in the composition of the gut flora. The analysis of the effect of a particular food on the bacterial flora based on the dietary pattern may provide insight on the relationship between diet and CRC carcinogenesis. Unfortunately, most studies examining nutrition and gut flora focus on a single food for a short amount of time, such as administering a diet consisting solely of animal foods and then observing the immediate changes in the gut microbiota [14]. The long-term dietary intake may alter the microbial community structure and overwhelm inter-individual differences in microbial gene expression, which may subsequently play a significant role in CRC carcinogenesis compared with short-term dietary habits [14]. Quantitative analysis of the role of long-term diet in CRC is complicated, either in perspective or in a retrospective study. Given that the intestinal flora can potentially contribute to the development of diseases in genetically at-risk individuals, the intestinal flora could be a promising tool to study the relationship between diet and CRC. Understanding the role of long-term dietary patterns in the intestinal flora will help further our comprehension of the influence of food on the intestinal environment [15].

To elucidate the effects of food intake on the intestinal flora based on the southern Chinese dietary pattern, we recruited healthy individuals and patients with CRC. The long-term nutritional habits were derived from a fFood Frequency Questionnaire (FFQ), and the association between food intake and the species and abundance of intestinal flora was assessed.

Dietary patterns play important roles in CRC carcinogenesis. In this study, all participants were Chinese who lived in a southern coastal area where the staple foods consisted of rice and vegetables, with a small amount of meat (either red meat, fish, or seafood). Rice and vegetables occupied two-thirds of the total diet. Vegetables and meat were cooked mainly by frying and steaming, with vegetable oil or animal fat (mainly lard). Although the eating habits are similar to those of the Mediterranean diet, there has recently been a significant increase in the incidence of CRC in this area.

Although the eating habits of the inhabitants are generally similar under the entire demographic background in this study, we still found that there was a significant difference in food preferences between CRC patients and healthy people. In this study, individuals with CRC were inclined to consume higher amounts of red meat and pickled foods, and lower amounts of fish, shrimp, and other seafood. Significantly lower consumption of pulses and soy products, fruits, vegetables, coarse grains, and dairy products was also found in CRC patients. A more hostile gut environment can occur as a result of higher consumption of red meat or processed meat. The gut microbiota metabolizes proteins from red meat to nitrosamine and heterocyclic amines, and these metabolites are risk factors for CRC development [17]. Therefore, higher red meat consumption is a well-recognized factor that is associated with a higher CRC risk [18], although it does not seem to apply to all people [10]. However, our data showed that pickled foods play a more important role in CRC pathogenesis rather than red meat.

The impact of diet on intestinal flora has been extensively studied, indicating that diet could re-shape the community structure of the gut microbiota [10,14]. An animal-based diet was observed to increase the abundance of bile-tolerant microorganisms (Alistipes, Bilophila, and Bacteroides) and decrease the levels of Firmicutes [14]. Specifically, high-fat consumption may increase the proportion of gram-negative bacteria in the gut while reducing the abundance of some gram-positive bacteria such as Bifidobacterium [19]. In our study, the CRC group exhibited enrichment of Proteobacteria and a depletion of Firmicutes, which was closely related to food preference. Based on logistic regression analysis, we found that pickled food had significant effects on the abundance of Fusobacteria, which accounted for the greater impact of pickled food on Fusobacteria than that of red meat. Pickled foods are a favorite food of the local inhabitants, and previous epidemiological studies determined that pickled foods were closely related to CRC carcinogenesis in China [20]. Our study reveals that pickled foods may induce CRC through increasing Fusobacteria.

Gut dysbiosis can lead to over-representation of certain bacterial species that can promote colon carcinogenesis by either favoring chronic inflammation or local immunosuppression [21]. Escherichia was the main pathogenic bacteria found in our CRC patients, and it occurred at increased frequency in patients with CRC and inflammatory bowel disease [22]. Escherichia and Fusobacterium have been shown to be highly correlated with CRC by activating immune cells that release cytokines, such as interleukin (IL)-6 and IL-17, which drives inflammation and affects carcinogenesis [23]. The Western diet enhances susceptibility toward the pathogenic potential of adherent invasive Escherichia coli [24]. Our results revealed that fish, beans, and nuts significantly influence the abundance of Escherichia, and healthy individuals with more fish intake had far less Escherichia, indicating that intestinal flora is primarily affected by food intake that may shape the gut bacterial communities in a dose-dependent manner. Species- and strain-level variations can contribute to functional differences between individuals that are important in a clinical context [25]. Our study found that the effect of food on the intestinal flora may be different between CRC patients and healthy people, but the mechanism remains to be further studied.

The gut microbiota composition varies among individuals within and between communities [26]. A strong association was observed between long-term consumption of a protein and animal fat-rich diet with Bacteroides predominance and that of a carbohydrate-rich diet with Prevotella predominance [7]. This phenomenon is remarkable in native Africans (with high consumption of complex fiber) and African-Americans (with high consumption of protein), with the microbiota dominated by Bacteroides in African-Americans and by Prevotella in native Africans [27]. Bacteroides and Prevotella act as the driving taxa that explain inter-individual differences and delineate the main sources of variation [28]. A differential abundance of Bacteroidetes and Prevotella was found in Chinese and Indian subjects, due to the difference in their diet [29].

Both Bacteroides and Prevotella were the dominant flora in the individuals included in our study. Bacteroides abundance is relatively constant regardless of the foods consumed. Prevotella is known to be associated with an indigestible carbohydrate-rich diet, particularly grains such as whole wheat and barley [30]. Studies revealed that Prevotella is more prevalent in populations that consume a vegan or vegetarian diet [31]. Among the foods we studied, only fruits, beans, and nuts were found to play a significant role in the amount of Prevotella. The studied individuals consumed rice as a staple food, and whether the effect of fruits and nuts on Provetella is based on the premise of rice as a staple food, or whether fruits and nuts exert additional effects on Provetella requires further studies.

Recent studies raise the possibility that the intake of WCGs and their components can selectively modulate the microbiota composition, suggesting that WCGs can exert a prebiotic effect on Bifidobacterium and Lactobacillus spp. [32]. Bifidobacterium prevents gastrointestinal disorders such as diarrhea, IBD, and CRC [33]. Consumption of plant protein was observed to increase the Bifidobacterium and Lactobacillus genera, and decrease the pathogenic bacterial species of the Bacteroides and Clostridium genera [34]. The carbohydrate-based Asian diet drives the colonization of Bifidobacteria [29], but the abundance of Bifidobacteria was only found in our healthy individuals, revealing that individual differences still exist. There is the possibility that an overall association was modified or confounded by other dietary factors. The composition of the gut microbiota is highly dynamic and different for each human individual and changes over time [35].

In CRC carcinogenesis, the species and abundance of flora are equally important. Some bacteria are easily ignored due to their very low abundance. The diversity of the flora, especially those important but less abundant flora existing in the gut, increases the difficulty of the analysis. The gut microbiota may be successfully enriched with a beneficial bacterium or a selected cocktail of bacteria so as to improve the antitumor immunity [3]. Therefore, a classification based on compositional patterns would potentiate microbiota-based diagnostics, therapies, or prevention of disease, with implications for personalized treatment through nutritional, microbial, and pharmaceutical interventions [28]. Classification of flora according to probiotics or pathogenicity will be beneficial for evaluating the role of flora in the genesis of CRC. Firmicutes and Bacteroidetes are the dominant phyla in the gut [36]. A previous analysis of gut microbial communities resulted in proposed “enterotypes” that were dominated by Bacteroides, Prevotella, and Ruminococcus [37]. The dichotomy in the Prevotella/Bacteroides ratio was also observed between human populations with intake of significantly higher proportions of dietary fiber and meat [38]. Prevotella (when no enterotype was reported) was enriched in individuals with non-Western and/or fiber-rich diets [14,39]. An increase in Bacteroides, which tends towards lower overall diversity, has been linked to CRC [27]. In the current study, we attempted to analyze the effects of various foods on the Prevotella/Bacteroides ratio that was significant in the healthy group as compared to the CRC group, indicating that food affects the intestinal flora with different efficacies in CRC patients and in healthy people.

Identification and characterization of the significant patterns related to human gut microbiota configurations remain challenging [28]. Presently, there is no simple description of this complex landscape across large populations and geographies, in part because some taxa vary monotonically among individuals, while most others show bimodal or more complex distributions [28]. The role played by a gut bacterium in cancer occurrence and response to therapy is still in its infancy and needs to be transferred from mouse models to human beings [3]. Dietary modulation of CRC risk may be a result of the effects on the gut microbiota composition [40]. Understanding how dietary intake contributes to microbiota composition and stability in early life is essential for dietary recommendations and for designing clinical interventions for microbiota-associated diseases [15].