AbstractThe human gut has an extremely diverse microbial community. This article reviews previous studies on the relationship between human diet and gut microbiome diversity. Diets can influence the enterotypes during a long time (). Seasonal diet changes drive the gut microbiome diversity (). Long-term diet also has effects on gut microbial community of the elderly (). Long-term low-fiber diet may decrease the diversity of gut microbiome (). Studies on humanized mice showed that changing macronutrient alter gut microbiome within couple days (). Short-term diet can rapidly and reversibly change the gut microbiome composition (). Gut microbiome depend on different regional dietary habits (). Traditional diet will keep gut microbiome diversity compared with the western’s diet (). In the future, further investigations are required to figure out the mechanisms about how gut microbiome result in some diseases. IntroductionHuman gut microbiome reside in human intestinal tract from the oral cavity to the rectum. Bacteria usually attach to the mucosa, but do not penetrate the bowel wall (Gorbach SL 1996). Obligate anaerobes are more than facultative anaerobes in the intestine which is a relatively closed environment. The upper intestinal tract (oral cavity, throat, esophagus, stomach) normally contains a little microbiome because of rapid transit rate and low pH conditions (Gorbach SL 1996). In contrast, lower intestine is easy to establish a rich microbial community donated by obligate anaerobes. The human gut has an extremely complex and diverse microbial community, known as gut microflora or microbiota. The human gut microbiota contains more than 100 trillion bacteria, archaea, viruses, fungi, and other eukaryotes (). Approximately 1100 prevalent bacteria species exist in human populations. Each individual has at least 160 such species. The gene of microflora is about 150 times larger than our own genomes (). As the gut microorganisms encode a large number of genes, they are called the second genome. Human genes are innate and immutable, but the second genome is controllable that can be altered by diet (3). Fig. 1 the history of human gut microbiology research Rajilic-Stojanovic and de Vos (2014) reported three turning points (or periods) in human gut microbiology research (Fig. 1). First, German pediatrician Teodor Escherich found the first gut bacteria (E. coli) in 1885. From that time until 1960s, Bifidobacterium and Bacteroides spp. were considered to be dominant in human gut. Second, from 1970s till the beginning of this century, bacteria were mainly divided into several species: Bacteroides, Clostridium, Eubacterium, Veillonella, Ruminococcus, Bifidobacterium, Fusobacterium, Lactobacillus, Peptostreptococcus, and Peptococcus. The third period is from the beginning of this century until nowadays with the development of molecular technology. Bacteroidetes and Firmicutes were generally dominant in the gut, comprising more than 90% of the microbiome (Johnson et al. 2016). Johnson et al. (2016) indicated that Bacteroidetes genera has three main clades: Bacteroides, Prevotella, and Porphyromonas.Arumugam et al. (2011) indicated that healthy human microbial communities consist of three main variants, or named “enterotypes” : Bacteroides, Prevotella, and Ruminococcus. Most of the studies mainly focus on Bacteroides and Prevotella. The enterotype is a pattern related with diet, which is normally stratified, but not continuous ? may make different responses to different diet intake (Arumugam et al. 2011).In the last decade, within the widespread use of PCR and DNA sequencing, 16S rDNA sequencing has played a vital role in the accurate identification of bacteria in microbiology laboratories (Woo et al. 2008). 16S ribosomal RNA (rRNA) sequencing is a common amplicon sequencing method used to identify bacteria present within a given sample. For bacterial identification, 16S rDNA sequencing is particularly important because it is difficult to identify some bacteria through traditional methods such as rare bacteria, slow-growing bacteria, uncultivable bacteria and so on. In recent years, researchers prefer to used 16S rDNA sequencing which more accurately identified gut biome. Dietary habits are considered to one of the main factors result in human gut microbiome diversity (Conlon and Bird 2015). A series of changes in social and demographic led to the changes in human diet and lifestyle during “Neolithic revolution” about 10,000 years ago. It is speculated that human-related bacteria have undergone dramatic changes during that time (Mira et al. 2006). Filippo et al. (2010) compared the gut microbiota of children living in a village of rural Africa in an environment still resembles Neolithic, far away from globalization and industrialization, with that of European children who are eating and living in typical western ways.Human gut microbiome diversity deponds on a variety of factors by diet. In my paper, I will review the effects of long-term diet and short-term diet on human gut microbiome as well as discussing the regional dietary habits. Long-Term Dietary EffectWu et al. (2011) surveyed the association of diet with human gut microbiome. In a cross-sectional analysis of 98 healthy volunteers (abbreviated “COMBO”), two questionnaires that queried recent diet (Recall, short-term) and food frequency questionnaire (FFQ, long-term) were used to collect diet information. Metagenomic analysis of bacterial DNA sequences from stool samples of 98 individuals were conducted by using pyrosequencing. 16S rDNA sequence information of bacteria were used to compare with what 98 subjects have eaten recently and what they usually eat in a long-term.Specific nutrients associated with gut microbiome were extracted from the 98 sample. The researchers used PERMANOVA to detect nutrient microbiome association for each nutrient. The nutrients from fat versus plant products and fiber showed inverse associations with microbiome. There were inverse associations between amino acids and proteins versus carbohydrates, fat versus carbohydrates as well. Bacteroidetes and Actinobacteria were positively associated with fat but negatively associated with fiber. Nutrients from FFQ but not Recall questionnaire were associated with microbiome composition, indicating that long-term diet strongly correlates with enterotype. The Bacteroides enterotype was highly associated with animal protein and fat, while the Prevotella enterotype was highly associated with fiber and carbohydrates.The researchers observed ten individuals in a hospital environment for controlled-feeding study (CAFE) as a short-term test. Wu et al. (2011) divided them into high-fat/low-fiber or low-fat/high-fiber diets randomly and sampled during 10 days. Although ten individuals’ gut microbiome changed within couple days, their enterotype still stayed in the same group (didn’t switch between Bacteroides and Prevotella). By comparing long-term and short-term dietary studies, it suggested that only the long-term diet was particularly related to enterotype. In another study, Davenport et al. (2014) focused on the relationship between seasonal diet changes and the gut microbiome. The composition of microbial community from the same group of people were recorded and analyzed in summer and winter respectively. The researchers found clear seasonal effects on microbiome composition. The same trend of bacterial changes were observed during the same season, but mirobiome composition differed in two seasons. The researchers used questionnaires to collect diet information, and found that diet differed mostly in fresh produce ? more fruit and vegetable intake in the summer. The Bacteroidetes were higher in summer than in winter. The Actinobacteria that negatively associated with fiber, decreased in the summer compared to the winter. The researchers indicated that seasonal diet changes drive the difference in microbial community (Fig. 2). Although richer food resource are available, the gut microbiome diversity was less in summer than in winter. Fig. 2 The composition of human gut microbiome differed in two seasons.Claesson et al. (2012) reported the long-term dietary effects on the gut microbiome diversity of the elderly. Two groups of elderly were tested: city residents and the elderly who had been in nursing home for one year. The researchers found that the microbial community diversity of the elderly in nursing home significantly less than that of city elderly residents. Long-term limited types of diet reduced the microbiome diversity of elderly in nursing home, and make their gut system more fragile.Sonnenburg et al. (2016) reported that long-term low fiber diet may lead to the loss of gut microbiome diversity. The researchers found that modern diet has lower fiber intake compared with traditional diet, resulting in fewer MACs (microbiota-accessible carbohydrates). The more MACs are in the diet, the more diverse of microbial community can be driven. To ensure their finding, researchers studied on humanized mice. After a long-term feeding in low fiber (low MACs), the gut microbiome diversity significantly decreased in mice, especially in their offspring. Short-Term Dietary EffectPrevious studies have shown that long-term diets affect the enterotypes of human gut microbiome, but researchers still had limited understanding of the role short-term diets play on the gut microbiome. Turnbaugh et al. (2009) studied on inbred mice and found that changing dietary intake can rapidly alter the gut microbiome. Researchers transplanted the human intestinal flora into mice gut to form stable microbial structures with bacterial diversity. Diet of mice was switched from low fat, high polysaccharide to high fat, high sugar. This change altered the structure of gut microbial community and their metabolic pathways during a single day.Another study on humanized mice also showed that gut microbiome can be altered rapidly by diet. Faith et al. (2011) transplanted ten human gut bacteria into mice. Four kinds of macronutrients intake (protein, fat, fiber, sugar) of these mice were systematically varied. Researchers established a model to figure out the association between specific macronutrients and each microbial community member. Further study focus on the community structure of human gut biome respond to dietary changes. David et al. (2014) tested the volunteers’ normal daily intake (baseline) at first. Then, they tested the effects of two types of diets group: plant-based diet and animal-based diet. Each group significantly changed subjects’ macronutrient intake. Researchers quantified the microbial diversity to ?- diversity (at a given time-point) and ?- diversity (difference between baseline and diet-associated biome). They observed no significant changes of ?- diversity in both groups, but ?-diversity increased a single day after food reached the distal gut microflora. The microbial community reverted to their original structure two days after animal-based diet ended (Fig. 3). The rapid and reversible responses to dietary changes may reflect strong plasticity of gut microbial community and the human diet’s flexibility. Besides, researchers found that the diet can introduce foreign microbes into the gut. Dairy-associated microbes (such as Lactobacillus) and plant virus (such as Rubus chlorotic mottle virus) were detected in two diet groups respectively.Fig.3 The human gut microbiome can be changed by short-term diet.Spencer et al. (2011) surveyed how the choline in diet influence the microbial community in human gut. They switched subjects from a normal diet to a low-choline diet. The subjects’ microbial community composition began to change from the first day, and changed with choline levels of diets.Combined with the studies on short-term diet shown above, human gut microbiome can respond rapidly to changes in diet, and take less time than people thought before. The new diet can reshape microbial community more or less in couple days, and the changes are reversible. Regional Dietary Habit The composition of gut microbiome may depend on different dietary habits in different regions (3). Geography, cultural traditions and other factors decide the different regional dietary habits. Filippo et al. (2010) surveyed two groups of children: modern European children (EU) and rural African children from a village of Burkina Faso (BF) that rarely affected by globalization and industrialization. EU children were eating typical western diets that high in animal protein, sugar, and fat, and low in fiber. BF children mainly ate vegetarian diets that low in fat and animal protein, and rich in fiber, and plant polysaccharide. Researchers found big differences in enterotypes between the two groups. The enterotype of BF children was dominated by Actinobacteria and Bacteroidetes; and the enterotype of EU children was dominated by Firmicutes and Proteobacteria (Fig. 4). Besides, Prevotella made up 53% of the gut bacteria in BF children, but were lacking in EU children because of the less fiber intake, which agrees with the studies of Wu et al. (2011) Fig. 4 The composition of gut microbiome differed in EU children and BF children. The diet of BF children that rich in plant polysaccharide and low in sugar and fat can result in more SCFAs (short-chain fatty acids). SCFAs are more likely to prevent enterobacteria such as Shigella from representing in human gut. That means the gut microbiome and the polysaccharide-rich diet of BF children worked together, protecting them from some gut diseases.The western diets became high in fat, and may decrease human gut microbiome diversity (). Yatsunenko et al. (2012) studied on three groups of people: American citizens, Malawian rural residents, and Amerindians from Venezuela. American diets were rich in fat and sugar, while diets in Malawian and Amerindian were donated by corn and cassava. The American low-fiber diets had claer effects on their gut microbiome, leading to the least richness of microbial community diversity among the three groups. Conclusion, and Future DirectionsHuman gut microbial community has a diverse system with variety of microbiome. The interactions between individual, diet and gut microbiome are extremely complex. Based on the review of previous studies and data, long-term diet appears to have the largest effect among all the foreign factors affecting human gut microbiome. Diet can also rapidly and reversibly alter the gut microbiome composition during couple days. Different human gut microbial community in different regions mostly result from different dietary habits. In one word, diet obviously has undeniable effects on human gut microbiome diversity.In the future, we’d better study more on the mechanisms of gut microbiome works on chronic disease such as obesity and diabetes or some other acute diseases. If there is a causal relationship between enterotype and disease, long-term and short-term dietary interventions may be used to rebuild individual’s enterotype to prevent diseases or improve health. Besides, the analysis data were mainly collected from western countries in Europe and the United States. More data are required from some eastern regions of the world. In addition, the observations of experiments were usually focused on mice so far, we need further investigations for human research.