A large amount of variation was explained by PCo1 , and our attempts to determine the factors driving this variation led us to look at specific taxonomic groups that may be important. We did this in two ways. First, we produced a biplot with the make emperor.py script, showing the prevalence of bacterial families in the PCoA space defined by the weighted unifrac distance between the 15 meals . A cluster of 4 meals, including USDA snack 1, AMERICAN snack, AMERICAN lunch, and USDA lunch, was comprised of samples that were dominated by Lactic Acid Bacteria. These are members of the order Lactobacillales, which are commonly found in association with both food products, especially in fermented milk products and human mucosal surfaces . The Vegan snack #1 was unique in that it was dominated by Xanthamonadaceae, a family containing many plant pathogens. A second cluster of 7 meals including VEGAN dinner, VEGAN breakfast, AMERICAN breakfast, AMERICAN dinner, USDA dinner, VEGAN snack 3, and USDA breakfast, was comprised of samples containing a large percentage of Thermus, a clade with many heat and dessication-resistant organisms. Second, we calculated correlations between the relative abundance of a single taxon and the PCo1 value for each meal using a simple regression . The bacterial family most tightly correlated with PCo1 was Streptococcaceae . We also asked whether the relative abundance of any particular taxonomic group was correlated with the nutritional content of the meals via pairwise Pearson’s correlations.

We limited this analysis to organisms that were present in all 15 meals. Due to the exploratory nature of this study, there were no specific hypotheses tested with these correlations,hydroponic nft channel and therefore no corrections for multiple hypothesis testing. Some taxa frequently abundant in human micro-biome studies were found to be significantly correlated with particular nutrients . For example, members of the genus Blautia are frequently observed in human fecal samples, and in our study, the relative abundance of this genus was found to be positively correlated with the sugar content of the meals p < 0.05 . We emphasize here that due to the large numbers of OTUs present in this study, corrected p values were always non-significant. However, the goal of this small-scale study is to inform the development of future hypotheses, not test current ones. Nevertheless, this result suggests that there could be interesting relationships between the nutritional content of the foods that we eat, the microbes that associate with those foods, and our gut micro-biome, not just because we are “feeding” our gut microbes, but because we are eating them as well Because of the vast, historical effort to make the 16S rRNA gene sequence available for hundreds of thousands of organisms, we are typically able to characterize well the taxonomic diversity of most microbial communities. One might assume that each organism present in a community has some functional role to play, and the most straightforward way to predict what that role each organism might play is to use metagenomic sequencing to interrogate the genomes of all members of the community. Unfortunately, in many cases and with current sequencing technology, the amount of microbial DNA relative to host or other environmental DNA is small enough to make metagenomic sequencing infeasible. This is the case here, where the plant and animal DNA present in the food we eat is typically much more abundant than the microbial DNA.

Some exceptions may exist with respectto fermented foods, but we are equally interested in the micro-biota associated with a wide variety of food types. In a case like this for which metagenomic sequencing is infeasible, another approach suggests itself. There is evidence that a correlation exists between the evolutionary relatedness of two organisms and the similarity of their genomic content . This allows us to leverage the information obtained by sequencing the genome of one organism to predict the functional potential of another, even if the other genome is represented only by a 16S rRNA sequence. The power of this approach is increased when very many, very closely-related genome sequences are available. This predictive approach has recently been implemented in the software package PICRUSt. PICRUSt uses the phylogenetic placement of a 16S rRNA sequence within a phylogeny of sequenced genomes to infer the content of the genome of the organism represented by that 16S rRNA sequence. With PICRUSt one can calculate a metric that measures how closely related the average 16S rDNA sequence in an environmental sample is to an available sequenced genome. When this number is low, PICRUSt is likely to perform well in predicting the genomes of the organisms in an environmental sample . The average NSTI for our 15 meals was 0.038, which is on par with the NSTI for the Human micro-biome Project samples , for which a massive effort has been made to obtain reference genome sequences . This low NSTI metric suggests that PICRUSt may perform well when predicting the metabolic potential of the microbial communities found in the meals prepared for this study. Here, we have shown the most significant KEGG functional category, for “Other N-glycan degradation” , which was highest in the VEGAN dietary pattern . Again, this is not a significant result when a p-value correction is applied, but is nevertheless highlighted as a potential source of information when using a pilot study like this to inform future research questions. As a sanity check for the PICRUSt predictions, we compared the relative abundance of genes present in the KEGG functional category “Sporulation” between meals that were cooked were compared to those that were raw . As expected, because organisms that can form spores are more likely to survive the cooking process, Sporulation-associated genes are more abundant in cooked versus raw foods.

All KEGG pathways that vary significantly between dietary patterns are presented in Table 8. These findings suggest that there are functional differences in bacterial populations associated with different foods and meals, and that these may be related not only to bacterial substrate preferences, but also techniques used in meal preparation. We live in an intimate relationship with microorganisms that are present on the surfaces and cavities of the human body. During birth, or shortly thereafter, microbes from the mother’s skin and milk, the air, and inanimate objects enter the virtually germ-free system of the neonate and proliferate to a dramatic extent. The gastrointestinal tract is the most densely populated microbial ecosystem of the mammalian host. Bacterial cells are most abundant, but other types of microbes are also present in the GI tract, such as archaea, viruses, protozoa, and fungi. The intestinal lumen alone harbors 10 times more bacterial cells than eukaryotic cells in the entire human body, an amount equivalent to approximately 1 kg of human mass.This fact leads us to view ourselves as “superorganisms”, being composed of our cells as well as microbial cells that are dependent on each another for survival.Food is a major source of energy that promotes growth and development, immunity, and tissue repair, as well as homeostatic regulation. It is also an important energy source for gut micro-biota.Although most nutrient absorption occurs in the small intestine, the colon harbors the majority of bacterial colonists. The colon can be viewed as the major site for “co-metabolic” activity,nft growing system which enhances the efficiency of the energy harvest from foods and influences the synthesis, bio-availability, and function of nutrients,vitamins,and drugs.Thus, the functional interaction between microbes and their host explains individual variability of nutrient metabolism and bio-availability.Understanding the relationship between the gut micro-biome and diet is important for the development of next-generation therapeutic foods that target these microbes in health-promoting ways and will ultimately usher us toward an era of personalized nutrition and medicine. In this paper, current knowledge of the gut micro-biome from the perspective of human dietary history and the coevolutionary relationship with the host will be broadly reviewed. The impact of major dietary components as well as single food ingredients that favor changes in the gut micro-biome will be explored.Dietary transition during human history has been suggested to play a central role in the evolution of mankind.Unlike the diets of other higher primates, which consist of mainly fiber-rich plants supplemented with insects and a small amount of animal flesh,humans consume easily digested, energy-dense food. This distinction has resulted in substantial differences in the human GI tract including a smaller gut volume, longer small intestine, smaller cecum and colon, and faster gut passage rate.The discovery of fire and use of cooking techniques are also contributed to the evolution of human GI physiology by softening food texture, elevating calorie density, and reducing toxins.These differences are encompassed within the “expensive tissue hypothesis”, which suggests that a reduction in the of size of an energetically expensive GI tract yields a corresponding increase in the size of an energetically expensive brain, which in humans may have been facilitated by improvements in diet .

Another major advancement in human evolution was the shift from hunting and gathering to agriculture involving the domestication of animals and crops. Domesticated plants provided more calories than non-domesticated plants, which consequently drove the dietary pattern to focus more on a limited variety of foods, with a reduction in nutrient diversity.Today, economics, agriculture, and culture are strong forces that shape food availability, variety, and quality. With the advent and spread of global food production, additional changes in the human diet have occurred. Mass food production has allowed people to focus more intensively on the consumption of a few staples. The acquisition of a conserved and stable microbial consortium is constrained by the host GI tract morphology and long-term diet history.A recent study examined the gut micro-biome of 39 different mammalian species , grouping them into herbivores , carnivores, and omnivores.Comparisons between the groups revealed only three bacterial genera are significantly associated with the overall mammalian phylogenetic tree, namely Prevotella, Barnesiella, and Bacteroides. Although there were differences in the anatomy and function of the gut in each group, as well as a varied rate of microbial fermentation among the hosts, herbivores appeared to be enriched in functional enzymes essential to the biosynthesis of amino acids, whereas carnivores were enriched in enzymes involved with branched-chain amino acid degradation.Notably, a gut micro-biome that is low in diversity is less resilient to various disturbances from diet.These results support the notion that, over time, the intestinal microbial community has coevolved with the host.Part of the coevolution of the gut micro-biota with its host involves horizontal gene transfer to gain function and adapt to new environmental conditions. For example, the acquisition of carbohydrate-active enzymes , both glycoside hydrolases and glycosyltransferases, in human gut micro-biota is largely due to horizontal gene transfer rather than functional gene expansion.Indeed, the human genome lacks the large repertoire of glycoside hydrolases and polysaccharide lyases to digest a wide variety of plant material, whereas the distal gut micro-biome provides diverse CAZymes that cleave the many glycosidic linkages present in complex dietary polysaccharides . More recently, a comparative genomic analysis demonstrated the high prevalence of horizontal gene transfer in the human gut micro-biome.Therefore, horizontal gene transfer contributes to the complexity of the metabolic function of the gut micro-biome, allowing the host and its resident micro-biota to adapt to changing environmental conditions. Thus, the ability of a host to acclimatize to environmental shifts is dictated by the co-metabolic capabilities of both the gut microbes and the host. For instance, in Japanese communities where nonsterile, uncooked seaweed is regularly consumed, the genome of the human gut symbiont Bacteroides plebeius has retained β-porphyranase, a beneficial enzyme capable of digesting algal cell walls from Zobellia galactanivorans. Indeed, low microbial complexity has been associated with a Western diet and sedentary lifestyle and potentially could contribute to disorders associated with excessive weight gain.Studies on intestinal micro-biota raise questions as to whether consuming a modern diet that is hyperhygienic and highly processed results in reduction of microbial functional maturity by preventing the exchange of beneficial genes between gut micro-biota and microbes from the diet and environment. In addition, the increasing use of sanitization and antibiotics in food processing may contribute to a profound impact on the gut micro-biome .