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Dietary Effects on the Human Gut Microbiome

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Abstract

The human gut microbiome is home to trillions of microorganisms, but according to recent research, this number can be greatly altered depending on one’s daily dietary intake. Researchers have been studying effects of common diets such as vegetarian, vegan, carnivore, and ketogenic diets as well as infant diets on gut flora, which have provided insight on how consumption of specific foods could modify different phyla and affect metabolic rates. Variations in a person’s diet can cause alterations in the gut flora which can lead to downstream metabolic changes. As notable research has been collected on these different diets, it can be seen that a shift towards a vegetarian diet may result in higher metabolic rates. Additionally, it has been observed that a diet enriched with dietary fibres could be a potential treatment for diabetic patients. In summary, the food that is consumed in our day to day lives has crucial effects on our gut microbiome and more is to be studied on how different diets could affect one’s metabolism in adulthood.

Introduction

Human gastrointestinal microbiota, also called gut microbiota, are essential non-pathogenic microorganisms that reside in the digestive tract of humans. These microorganisms are vital to metabolism as they aid in several functions such as host nutrient metabolism, xenobiotic and drug metabolism, immunomodulation and protection against pathogens [1]. Figure one indicates that these effects on the host are followed by the various changes that occur in the gut microbiome[4]. In addition, certain species of gut bacteria have the ability to produce a variety of substances that have the potential to kill pathogens [2]. The gut microbiota and the host have a commensal relationship; the microbiota contribute to the homeostasis of the host immune system, while the host provides the bacteria with shelter and food. Several factors such as age, modes of childbirth, and our daily diets, play an important role in shaping our gut microbiome [1]. The diverse gut microbiome varies throughout the gastrointestinal tract. For example, Streptococcus is the dominant genus in the distal esophagus, while Firmicutes and Bacteroides are the most common phyla that inhabit the large intestine [1]. Infants’ gut microbiota increase and diversify over time from birth to two and a half years of age. Over one’s lifespan, one’s diet has a direct impact on the gut bacteria. Alterations in the gut microbiome may potentially lead to prevalent diseases such as inflammatory bowel disorder (IBD) and metabolic disorders, which are highlighted in figure one [1,4]. The gut microbiota produces lignans that protect against health complications such as cardiovascular disease and cancer [3]. An emerging topic in present research on the gut microbiota is the impact of daily diets on the gut microbiome. Daily diets such as plant-based diets, carnivorous diets, and ketogenic diets have been studied to evaluate their impact on the gut microbiome. This review will focus on the effect of diet on gut microbiome, and the subsequent consequences on metabolism and disease [4].

Dietary Fibres

1. Advantageous Bacterial Changes:

Several studies have shown the benefit of a high fibre diet and its effects on the gut microbiome. Fibres are nondigestible carbohydrates, also known as microbiota-accessible carbohydrates (MACs). It has been shown that diets with a significant proportion of fibre lead to higher levels of Prevotella and Bacteroides [5,6,7]. These increases in certain types of bacteria have also resulted in an increase in short chain fatty acids (SCFAs) [6, 8]. SCFA production occurs due to the fermentation of MACs, which may be created by the host diet or other varieties of bacteria. These MACs are broken down by carbohydrate-active enzymes, which play an important role in carbohydrate degradation and metabolism [9]. Although there has been an observed increase in the total amount of SCFAs with the consumption of dietary fibres, the faecal count was surprisingly low when compared to a weight loss or wheat bran diet [10]. In this study, high levels of fibre consumption led to a lower production of faecal SCFAs, which may have been due to a lack of Ruminococcin bromii that helps ferment resistant starch.

2. Metabolic Changes:

Researchers have also observed several metabolic changes associated with the inclusion of dietary fibres in a general diet, which can also be observed in figure one as the fourth step in improving the health of the host[4]. One specific study identified that the combination of barley kernel-based bread – a type of fibre – and high levels of Prevotella led to improved glucose metabolism [7]. An increase in Prevotella may increase glycogen storage and improve glucose resistance[5]. Other researchers studied the effects of a high fibre diet in Chinese Patients with Type 2 Diabetes and found that the different dominances in bacteria in a high fibre diet led to an increase in SCFAs [8]. An increase in SCFAs will increase the rate of energy metabolism in the host. The phylum of gut bacteria known as Bifidobacterium has been found to be the major producer of SCFAs. Inoculation of Type 2 Diabetics with the Bifidobacterium pseudocatenulatum strain C95 reduced weight gain and significantly improved insulin resistance. The increase in SCFAs due to the abundance in Bifidobacteria may be involved in weight loss in Type 2 Diabetics. Additionally, increased proportions of Bacteroides and Prevotella due to a high fibre diet have also been shown to increase the number of SCFAs such as propionate [6].

Dietary fibres have several health benefits not only on the gut microbiome but also on overall metabolism. Diets high in dietary fibres and specific probiotics could be a future treatment for Type 2 Diabetes patients. More research on this topic is needed to fully explain the relationship between fibre, gut microbiota, and glucose metabolism.

General Diet

Different changes to our regular diets can result in several differences in our gut microbiome. These two factors are indicated as the second and third steps in affecting the host’s metabolism which can be seen in figure one[4]. Various diets such as vegetarian, vegan, omnivore, carnivore and ketogenic diets have been studied to identify their effects on gut microbiota. In one specific study that compared vegan and omnivore diets, it was observed that vegans had a more diverse gut microbiome [11]. A different study found that a vegetarian diet led to an increase in Bifidobacterium in rural Japanese people, while another study proposed that a plant-based diet led to an increase in Prevotella [5,12,13]. The results from these studies indicate that plant-based diets cause the gut microbiome to become highly diverse, by increasing the amounts of specific bacterial phyla. Similarly, when solely focusing on a diet consisting of cruciferous vegetables such as broccoli and cabbage, it can be seen that certain bacterial species improved metabolism. When there was a dominance of Eggerthella, improved lignan metabolism followed [5]. Furthermore, the dominance of Bacteroidetes led to the degradation of fibres and glucosinolates. Meanwhile, in a complete meat-based diet consisting of three different meats (chicken, beef, and fish), the amount of Clostridium and Bacteroides significantly increased when beef was consumed [14]. This completely differed from a vegetarian diet, in which there was no observed growth of Clostridium. Fish digestion produced fewer SCFAs such as acetic and propionic acids, contrasting with the results of fibre consumption. This study also focused on certain cooking methods and found that there was a higher Clostridium growth due to fried meat consumption when compared to boiled meats [5]. Another diet known as the ketogenic diet (high fat and low carbohydrate diet) was associated with a decrease of the phylum E. rectale, which is responsible for producing butyrate[5,15]. An additional change that occurred in children with epilepsy that consumed the ketogenic diet is the depletion of Bifidobacterium, which may be associated with a decreased production of SCFAs. The effects of the ketogenic and vegetarian diets are similar because both reduced the production of SCFAs. The depletion of Bifidobacterium in the ketogenic diet is also directly linked to the decrease in E. rectale because Bifidobacterium produces acetate which is needed for E. rectale. All in all, plant-based diets have been shown to increase gut microbiome diversity, while carnivorous diets have been observed to have increased amounts of Clostridium and Bacteroides, which could be harmful to the host, but no specific effect has been found. A diet that consists of a high amount of red or processed meats could lead to different chronic diseases. This research holds high significance today as many people have explored different diets. A push towards a vegetarian or cruciferous vegetable diet could be more beneficial as increased phylum diversity may be associated with increased metabolism. Further research studies on how certain bacterial changes result in metabolic changes, could potentially resolve the relationship between different dietary components, the gut microbiome, and human metabolism.

Infant diet

There are different variations in infant diets that have been associated with several changes in the gut microbiome. One specific study focused on three infant diets: mother’s own milk (MOM), donor pasteurized human milk (DHM), and formula milk [16]. These researchers studied the effects of these three diets on the gut microbiota of premature infants. The Acinetobacter genus was widely present in the MOM group, while the Coprococcus genus was mainly found in the DHM group [5] . The DHM and formula milk groups had lower amounts of Clostridiales, Lactobacillus, and Bacillales when compared to the MOM group of infants. Another study showed that formula fed infants had an increased richness of Clostridium difficile, which contradicts the statement made by the previous study [17]. Parra-Llorca et al. also found a substantial decrease in LPS biosynthesis as well as proteins in formula fed infants[5]. Going a step further, the formula milk not only affected the gut microbiome, it also enriched the function of sugar metabolism [16]. A study that was done on 24 healthy infants in China found that Proteobacteria was more predominant in formula fed infants [18]. By further observing faecal samples and performing pyrosequencing, it was found that Firmicutes was present in all three groups. Specifically, Firmicutes was found to be more abundant in breastfed infants when compared to the other infants. These results signify that Firmicutes is the most dominant phylum in the infant intestinal microflora. Additional research was performed in Korea, studying the effects of both formula and breast milk on the gut microbiota profile of infants [19]. Formula fed infants were found to have a more diverse gut microbiome, while breastfed infants had an increase in Bifidobacteriaceae and Lactobacillaceae. The lower bacterial richness in breastfed infants could be due to the oligosaccharides in the milk that serve as substrates to only a specific number of gut microbes [17]. The abundance in different types of gut microbiota could potentially explain how some subjects have a faster glucose metabolism than others. These research studies are highly significant today, but there is a gap in knowledge as to how infant diets could affect a human’s long-term metabolism. Researchers need to further study this topic in order to understand how different infant diets could contribute to metabolic disorders in later stages of human life.

Probiotics

Looking forward, researchers have proposed that probiotics could be a solution to counteract detrimental changes that occur in gut flora. These dietary strategies are now being used to alter the gut bacteria to help the body fight against diabetes and obesity [20]. Probiotics, which can also be found in foods such as yogurt, are dietary substitutions that help alter energy homeostasis. Addition of probiotics to the diet could activate the immune system by helping it produce more antibodies to fight infections and tumours [21]. Additionally, probiotics have the ability to block certain receptor sites for toxins, which may protect against disorders such as IBD. An increase in consumption of probiotics can also result in the production of SCFAs, which may improve insulin resistance. Some strains of probiotics have also been found to have anti-inflammatory effects which signifies that through future applications, probiotics may be used to prevent IBD. Although probiotics have their advantages, there are also several consequences associated with using them in our daily diets. In patients with IBD, it is possible that the probiotic species could translocate across the gut and cause systemic sepsis, which could be very harmful to the host. Moreover, increased mortality rates have been observed for patients with acute pancreatitis when treated with probiotics. Early supplementation of probiotics in an infant’s diet has not yet been proposed, so recommendations have not been made on this topic as yet [22].

In addition to altering our gut microbiome using probiotics, our bacteria can also be modified by changing our diets. In the future, a high fibre diet may be prescribed to fight against metabolic disorders. Exclusive trials must be conducted in order to examine the effects of probiotics on digestive disorders, along with investigations in the laboratory to analyze the in-depth mechanisms of probiotics in the gut. Potential research on this topic could resolve the relationship between the effects of probiotics and diet on the gut microbiome and its relationship with metabolism.

Results

Research on bacterial changes due to several dietary differences has suggested how these alterations affect a human’s metabolism. All of these alterations and their significant effects on the host’s health have been specified in table one[5]. Although some gut microbial phyla have not been specified to have any significant effect on the host, most species such as Bacteroides, Clostridia, and Firmicutes have been observed to greatly impact the gut microbiome. An increase in dietary fibres leads to an increase in Prevotella and Bacteroides, which has downstream effects on metabolism [6,7]. Additionally, a change from a more varied diet to a vegetarian, omnivore, carnivore, or ketogenic diet, could also lead to a number of modifications to our gut microbiome such as changes in certain bacterial phyla. For example, a vegetarian diet leads to an increase in Bifidobacteria and Prevotella, while a carnivorous diet results in an increase in Clostridium growth, which has not been found to have a positive nor a negative effect on the gut microbiome [12,13,14]. Another research focus has been differences in infant diets and changes in the gut microbiome. The Acinetobacter genus was mostly found in the MOM group, the Coprococcus genus was abundant in the DHM group, and Clostridium difficile predominated in the formula fed infants.

Conclusion

Overall, these various bacterial changes that occur due to different dietary components are greatly affecting the human gut microbiome, and research studies have shown insight on how these alterations would affect human metabolism. In regard to future medicine, it has been shown that probiotics could be used to improve our metabolism and more research needs to be performed to further analyze the positive effects of probiotics on our gut microbiome. To conclude, our understanding of the world of gut microbiota has just begun, and much more is to be learned before manipulating it for our therapeutic use.

Acknowledgments

I would like to thank Dr. Sarah Singer for helping me throughout every step of this process and for providing me with valuable feedback on my research paper. I couldn’t have done it without your support. I would also like to say thank you to Dr. Kartik Angara for taking the time out of his busy schedule to peer review my paper and give me wonderful comments.

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Figure 1: Relationship between Diet and the Gut Microbiome

This image represents the step by step process of how different dietary components affect the gut microbiome. The different diets that are ingested, the effects of these dietary components, diseases that could occur, and the altered gut microbiome as a result, is shown in this diagram.

Dietary component Bacterial Changes Result
Dietary Fibres Increase in Prevotella and Bacteroides Higher production of SCFAs
Vegetarian Diet Increase in Prevotella and Bifidobacteria -no observed effect-
Cruciferous Vegetable Diet Increase in Eggerthella and Bacteroidetes Improved lignan metabolism and degradation of fibres and glucosinolates
Ketogenic Diet Decrease in E. rectale and Bifidobacteria Decrease in the amount of butyrate
Carnivorous Diet Increase in Clostridium (fried meat) -no observed effect-
MOM Infant Diet Increase in Acinetobacter, Bifidobacteriaceae and Lactobacillaceae -no observed effect-
DHM Infant Diet Increase in Coprococcus

Decrease in Clostridiales, Lactobacillus, and Bacillales

-no observed effect-
Formula Milk Infant Diet Increase in Clostridium Difficile and proteobacteria

Decrease in Clostridiales, Lactobacillus, and Bacillales

Reduction in LPS and protein biosynthesis

Faster sugar metabolism

Table 1: Bacterial Changes Due to Different Dietary Components

This table shows the bacterial changes that occur in the gut microbiome as a result of the ingestion of different diets. The changes that occur in the body due to these bacterial changes are also represented in the table above.

References

[1] Jandhyala, Sai Manasa. 2015. “Role of The Normal Gut Microbiota”. World Journal Of Gastroenterology 21 (29): 8787. https://doi.org/10.3748/wjg.v21.i29.8787.

[2] M M. Quigley, Eamonn. 2020. “Gut Bacteria In Health And Disease”. Gastroenterology And Hepatology 9 (9): 560-569.

[3] Zhang, Yu-Jie, Sha Li, Ren-You Gan, Tong Zhou, Dong-Ping Xu, and Hua-Bin Li. 2015. “Impacts Of Gut Bacteria On Human Health And Diseases”. International Journal Of Molecular Sciences 16 (12): 7493-7519. https;//doi.org/10.3390/ijms16047493.

[4] Ramakrishnan, Akshaya. “Relationship between Diet and the Gut Microbiome”. Case Western Reserve University.2020

[5] Ramakrishnan, Akshaya. “Bacterial Changes Due to Different Dietary Components”. Case Western Reserve University.2020

[6] Gray, Lawrence E. K., Martin O’Hely, Sarath Ranganathan, Peter David Sly, and Peter Vuillermin. 2017. “The Maternal Diet, Gut Bacteria, And Bacterial Metabolites During Pregnancy Influence Offspring Asthma”. Frontiers In Immunology 8. https://doi.org/10.3389/fimmu.2017.00365.

[7] Kovatcheva-Datchary, Petia, Anne Nilsson, Rozita Akrami, Ying Shiuan Lee, Filipe De Vadder, Tulika Arora, Anna Hallen, Eric Martens, Inger Björck, and Fredrik Bäckhed. 2015. “Dietary Fiber-Induced Improvement In Glucose Metabolism Is Associated With Increased Abundance Of Prevotella”. Cell Metabolism 22 (6): 971-982. https://doi.org/10.1016/j.cmet.2015.10.001.

[8] Zhao, Liping, et al. 2018. “Gut Bacteria Selectively Promoted By Dietary Fibers Alleviate Type 2 Diabetes”. Science 359 (6380): 1151-1156. https://doi.org/10.1126/science.aao5774.

[9] Soverini, Matteo, Silvia Turroni, Elena Biagi, Sara Quercia, Patrizia Brigidi, Marco Candela, and Simone Rampelli. 2017. “Variation Of Carbohydrate-Active Enzyme Patterns In The Gut Microbiota Of Italian Healthy Subjects And Type 2 Diabetes Patients”. Frontiers In Microbiology 8. https://doi.org/10.3389/fmicb.2017.02079.

[10] Salonen, Anne, Leo Lahti, Jarkko Salojärvi, Grietje Holtrop, Katri Korpela, Sylvia H Duncan, and Priya Date et al. 2014. “Impact Of Diet And Individual Variation On Intestinal Microbiota Composition And Fermentation Products In Obese Men”. The ISME Journal 8 (11): 2218-2230. https://doi.org/10.1038/ismej.2014.63.

[11] Wu, Gary D, Charlene Compher, Eric Z Chen, Sarah A Smith, Rachana D Shah, Kyle Bittinger, and Christel Chehoud et al. 2014. “Comparative Metabolomics In Vegans And Omnivores Reveal Constraints On Diet-Dependent Gut Microbiota Metabolite Production”. Gut 65 (1): 63-72. https://doi.org/10.1136/gutjnl-2014-308209.

[12] Hayashi, Hidenori, Mitsuo Sakamoto, and Yoshimi Benno. 2002. “Fecal Microbial Diversity In A Strict Vegetarian As Determined By Molecular Analysis And Cultivation”. Microbiology And Immunology 46 (12): 819-831. https://doi.org/10.1111/j.1348-0421.2002.tb02769.x.

[13] Losasso, Carmen, Ester M. Eckert, Eleonora Mastrorilli, Jorg Villiger, Marzia Mancin, Ilaria Patuzzi, and Andrea Di Cesare et al. 2018. “Assessing The Influence Of Vegan, Vegetarian And Omnivore Oriented Westernized Dietary Styles On Human Gut Microbiota: A Cross Sectional Study”. Frontiers In Microbiology9. https://doi.org/10.3389/fmicb.2018.00317.

[14] Shen, Qing, Yin An Chen, and Kieran M. Tuohy. 2010. “A Comparative In Vitro Investigation Into The Effects Of Cooked Meats On The Human Faecal Microbiota”. Anaerobe 16 (6): 572-577. https://doi.org/10.1016/j.anaerobe.2010.09.007.

[15] Lindefeldt, Marie, Alexander Eng, Hamid Darban, Annelie Bjerkner, Cecilia K Zetterström, Tobias Allander, Björn Andersson, Elhanan Borenstein, Maria Dahlin, and Stefanie Prast-Nielsen. 2019. “The Ketogenic Diet Influences Taxonomic And Functional Composition Of The Gut Microbiota In Children With Severe Epilepsy”. Npj Biofilms And Microbiomes 5 (1). https://doi.org/10.1038/s41522-018-0073-2.

[16] Parra-Llorca, Anna, María Gormaz, Cristina Alcántara, María Cernada, Antonio Nuñez-Ramiro, Máximo Vento, and Maria C. Collado. 2018. “Preterm Gut Microbiome Depending On Feeding Type: Significance Of Donor Human Milk”. Frontiers In Microbiology 9. https://doi.org/10.3389/fmicb.2018.01376.

[17] Azad, M. B., T. Konya, H. Maughan, D. S. Guttman, C. J. Field, R. S. Chari, M. R. Sears, A. B. Becker, J. A. Scott, and A. L. Kozyrskyj. 2013. “Gut Microbiota Of Healthy Canadian Infants: Profiles By Mode Of Delivery And Infant Diet At 4 Months”. Canadian Medical Association Journal 185 (5): 385-394. https://doi.org/10.1503/cmaj.121189.

[18] Fan, Wenguang, Guicheng Huo, Xiaomin Li, Lijie Yang, and Cuicui Duan. 2014. “Impact Of Diet In Shaping Gut Microbiota Revealed By A Comparative Study In Infants During The Six Months Of Life”. Journal Of Microbiology And Biotechnology 24 (2): 133-143. https://doi.org/10.4014/jmb.1309.09029.

[19] Lee, Sang A, Ji Ye Lim, Bong-Soo Kim, Su Jin Cho, Nak Yon Kim, Ok Bin Kim, and Yuri Kim. 2015. “Comparison Of The Gut Microbiota Profile In Breast-Fed And Formula-Fed Korean Infants Using Pyrosequencing”. Nutrition Research And Practice 9 (3): 242. https://doi.org/10.4162/nrp.2015.9.3.242.

[20] Wang, Peng-Xu, Xin-Ru Deng, Chen-Hong Zhang, and Hui-Juan Yuan. 2020. “Gut Microbiota And Metabolic Syndrome”. Chinese Medical Journal 133 (7): 808-816. https://doi.org/10.1097/cm9.0000000000000696.

[21] Fooks, Laura J., Roy Fuller, and Glenn R. Gibson. 1999. “Prebiotics, Probiotics And Human Gut Microbiology”. International Dairy Journal 9 (1): 53-61. https://doi.org/10.1016/s0958-6946(99)00044-8.

[22] Quigley, Eamonn MM. 2011. “Gut Microbiota And The Role Of Probiotics In Therapy”. Current Opinion In Pharmacology 11 (6): 593-603. https://doi.org/10.1016/j.coph.2011.09.010.

Biography

Abstract

The human gut microbiome is home to trillions of microorganisms, but according to recent research, this number can be greatly altered depending on one’s daily dietary intake. Researchers have been studying effects of common diets such as vegetarian, vegan, carnivore, and ketogenic diets as well as infant diets on gut flora, which have provided insight on how consumption of specific foods could modify different phyla and affect metabolic rates. Variations in a person’s diet can cause alterations in the gut flora which can lead to downstream metabolic changes. As notable research has been collected on these different diets, it can be seen that a shift towards a vegetarian diet may result in higher metabolic rates. Additionally, it has been observed that a diet enriched with dietary fibres could be a potential treatment for diabetic patients. In summary, the food that is consumed in our day to day lives has crucial effects on our gut microbiome and more is to be studied on how different diets could affect one’s metabolism in adulthood.

Introduction

Human gastrointestinal microbiota, also called gut microbiota, are essential non-pathogenic microorganisms that reside in the digestive tract of humans. These microorganisms are vital to metabolism as they aid in several functions such as host nutrient metabolism, xenobiotic and drug metabolism, immunomodulation and protection against pathogens [1]. Figure one indicates that these effects on the host are followed by the various changes that occur in the gut microbiome[4]. In addition, certain species of gut bacteria have the ability to produce a variety of substances that have the potential to kill pathogens [2]. The gut microbiota and the host have a commensal relationship; the microbiota contribute to the homeostasis of the host immune system, while the host provides the bacteria with shelter and food. Several factors such as age, modes of childbirth, and our daily diets, play an important role in shaping our gut microbiome [1]. The diverse gut microbiome varies throughout the gastrointestinal tract. For example, Streptococcus is the dominant genus in the distal esophagus, while Firmicutes and Bacteroides are the most common phyla that inhabit the large intestine [1]. Infants’ gut microbiota increase and diversify over time from birth to two and a half years of age. Over one’s lifespan, one’s diet has a direct impact on the gut bacteria. Alterations in the gut microbiome may potentially lead to prevalent diseases such as inflammatory bowel disorder (IBD) and metabolic disorders, which are highlighted in figure one [1,4]. The gut microbiota produces lignans that protect against health complications such as cardiovascular disease and cancer [3]. An emerging topic in present research on the gut microbiota is the impact of daily diets on the gut microbiome. Daily diets such as plant-based diets, carnivorous diets, and ketogenic diets have been studied to evaluate their impact on the gut microbiome. This review will focus on the effect of diet on gut microbiome, and the subsequent consequences on metabolism and disease [4].

Dietary Fibres

1. Advantageous Bacterial Changes:

Several studies have shown the benefit of a high fibre diet and its effects on the gut microbiome. Fibres are nondigestible carbohydrates, also known as microbiota-accessible carbohydrates (MACs). It has been shown that diets with a significant proportion of fibre lead to higher levels of Prevotella and Bacteroides [5,6,7]. These increases in certain types of bacteria have also resulted in an increase in short chain fatty acids (SCFAs) [6, 8]. SCFA production occurs due to the fermentation of MACs, which may be created by the host diet or other varieties of bacteria. These MACs are broken down by carbohydrate-active enzymes, which play an important role in carbohydrate degradation and metabolism [9]. Although there has been an observed increase in the total amount of SCFAs with the consumption of dietary fibres, the faecal count was surprisingly low when compared to a weight loss or wheat bran diet [10]. In this study, high levels of fibre consumption led to a lower production of faecal SCFAs, which may have been due to a lack of Ruminococcin bromii that helps ferment resistant starch.

2. Metabolic Changes:

Researchers have also observed several metabolic changes associated with the inclusion of dietary fibres in a general diet, which can also be observed in figure one as the fourth step in improving the health of the host[4]. One specific study identified that the combination of barley kernel-based bread – a type of fibre – and high levels of Prevotella led to improved glucose metabolism [7]. An increase in Prevotella may increase glycogen storage and improve glucose resistance[5]. Other researchers studied the effects of a high fibre diet in Chinese Patients with Type 2 Diabetes and found that the different dominances in bacteria in a high fibre diet led to an increase in SCFAs [8]. An increase in SCFAs will increase the rate of energy metabolism in the host. The phylum of gut bacteria known as Bifidobacterium has been found to be the major producer of SCFAs. Inoculation of Type 2 Diabetics with the Bifidobacterium pseudocatenulatum strain C95 reduced weight gain and significantly improved insulin resistance. The increase in SCFAs due to the abundance in Bifidobacteria may be involved in weight loss in Type 2 Diabetics. Additionally, increased proportions of Bacteroides and Prevotella due to a high fibre diet have also been shown to increase the number of SCFAs such as propionate [6].

Dietary fibres have several health benefits not only on the gut microbiome but also on overall metabolism. Diets high in dietary fibres and specific probiotics could be a future treatment for Type 2 Diabetes patients. More research on this topic is needed to fully explain the relationship between fibre, gut microbiota, and glucose metabolism.

General Diet

Different changes to our regular diets can result in several differences in our gut microbiome. These two factors are indicated as the second and third steps in affecting the host’s metabolism which can be seen in figure one[4]. Various diets such as vegetarian, vegan, omnivore, carnivore and ketogenic diets have been studied to identify their effects on gut microbiota. In one specific study that compared vegan and omnivore diets, it was observed that vegans had a more diverse gut microbiome [11]. A different study found that a vegetarian diet led to an increase in Bifidobacterium in rural Japanese people, while another study proposed that a plant-based diet led to an increase in Prevotella [5,12,13]. The results from these studies indicate that plant-based diets cause the gut microbiome to become highly diverse, by increasing the amounts of specific bacterial phyla. Similarly, when solely focusing on a diet consisting of cruciferous vegetables such as broccoli and cabbage, it can be seen that certain bacterial species improved metabolism. When there was a dominance of Eggerthella, improved lignan metabolism followed [5]. Furthermore, the dominance of Bacteroidetes led to the degradation of fibres and glucosinolates. Meanwhile, in a complete meat-based diet consisting of three different meats (chicken, beef, and fish), the amount of Clostridium and Bacteroides significantly increased when beef was consumed [14]. This completely differed from a vegetarian diet, in which there was no observed growth of Clostridium. Fish digestion produced fewer SCFAs such as acetic and propionic acids, contrasting with the results of fibre consumption. This study also focused on certain cooking methods and found that there was a higher Clostridium growth due to fried meat consumption when compared to boiled meats [5]. Another diet known as the ketogenic diet (high fat and low carbohydrate diet) was associated with a decrease of the phylum E. rectale, which is responsible for producing butyrate[5,15]. An additional change that occurred in children with epilepsy that consumed the ketogenic diet is the depletion of Bifidobacterium, which may be associated with a decreased production of SCFAs. The effects of the ketogenic and vegetarian diets are similar because both reduced the production of SCFAs. The depletion of Bifidobacterium in the ketogenic diet is also directly linked to the decrease in E. rectale because Bifidobacterium produces acetate which is needed for E. rectale. All in all, plant-based diets have been shown to increase gut microbiome diversity, while carnivorous diets have been observed to have increased amounts of Clostridium and Bacteroides, which could be harmful to the host, but no specific effect has been found. A diet that consists of a high amount of red or processed meats could lead to different chronic diseases. This research holds high significance today as many people have explored different diets. A push towards a vegetarian or cruciferous vegetable diet could be more beneficial as increased phylum diversity may be associated with increased metabolism. Further research studies on how certain bacterial changes result in metabolic changes, could potentially resolve the relationship between different dietary components, the gut microbiome, and human metabolism.

Infant diet

There are different variations in infant diets that have been associated with several changes in the gut microbiome. One specific study focused on three infant diets: mother’s own milk (MOM), donor pasteurized human milk (DHM), and formula milk [16]. These researchers studied the effects of these three diets on the gut microbiota of premature infants. The Acinetobacter genus was widely present in the MOM group, while the Coprococcus genus was mainly found in the DHM group [5] . The DHM and formula milk groups had lower amounts of Clostridiales, Lactobacillus, and Bacillales when compared to the MOM group of infants. Another study showed that formula fed infants had an increased richness of Clostridium difficile, which contradicts the statement made by the previous study [17]. Parra-Llorca et al. also found a substantial decrease in LPS biosynthesis as well as proteins in formula fed infants[5]. Going a step further, the formula milk not only affected the gut microbiome, it also enriched the function of sugar metabolism [16]. A study that was done on 24 healthy infants in China found that Proteobacteria was more predominant in formula fed infants [18]. By further observing faecal samples and performing pyrosequencing, it was found that Firmicutes was present in all three groups. Specifically, Firmicutes was found to be more abundant in breastfed infants when compared to the other infants. These results signify that Firmicutes is the most dominant phylum in the infant intestinal microflora. Additional research was performed in Korea, studying the effects of both formula and breast milk on the gut microbiota profile of infants [19]. Formula fed infants were found to have a more diverse gut microbiome, while breastfed infants had an increase in Bifidobacteriaceae and Lactobacillaceae. The lower bacterial richness in breastfed infants could be due to the oligosaccharides in the milk that serve as substrates to only a specific number of gut microbes [17]. The abundance in different types of gut microbiota could potentially explain how some subjects have a faster glucose metabolism than others. These research studies are highly significant today, but there is a gap in knowledge as to how infant diets could affect a human’s long-term metabolism. Researchers need to further study this topic in order to understand how different infant diets could contribute to metabolic disorders in later stages of human life.

Probiotics

Looking forward, researchers have proposed that probiotics could be a solution to counteract detrimental changes that occur in gut flora. These dietary strategies are now being used to alter the gut bacteria to help the body fight against diabetes and obesity [20]. Probiotics, which can also be found in foods such as yogurt, are dietary substitutions that help alter energy homeostasis. Addition of probiotics to the diet could activate the immune system by helping it produce more antibodies to fight infections and tumours [21]. Additionally, probiotics have the ability to block certain receptor sites for toxins, which may protect against disorders such as IBD. An increase in consumption of probiotics can also result in the production of SCFAs, which may improve insulin resistance. Some strains of probiotics have also been found to have anti-inflammatory effects which signifies that through future applications, probiotics may be used to prevent IBD. Although probiotics have their advantages, there are also several consequences associated with using them in our daily diets. In patients with IBD, it is possible that the probiotic species could translocate across the gut and cause systemic sepsis, which could be very harmful to the host. Moreover, increased mortality rates have been observed for patients with acute pancreatitis when treated with probiotics. Early supplementation of probiotics in an infant’s diet has not yet been proposed, so recommendations have not been made on this topic as yet [22].

In addition to altering our gut microbiome using probiotics, our bacteria can also be modified by changing our diets. In the future, a high fibre diet may be prescribed to fight against metabolic disorders. Exclusive trials must be conducted in order to examine the effects of probiotics on digestive disorders, along with investigations in the laboratory to analyze the in-depth mechanisms of probiotics in the gut. Potential research on this topic could resolve the relationship between the effects of probiotics and diet on the gut microbiome and its relationship with metabolism.

Results

Research on bacterial changes due to several dietary differences has suggested how these alterations affect a human’s metabolism. All of these alterations and their significant effects on the host’s health have been specified in table one[5]. Although some gut microbial phyla have not been specified to have any significant effect on the host, most species such as Bacteroides, Clostridia, and Firmicutes have been observed to greatly impact the gut microbiome. An increase in dietary fibres leads to an increase in Prevotella and Bacteroides, which has downstream effects on metabolism [6,7]. Additionally, a change from a more varied diet to a vegetarian, omnivore, carnivore, or ketogenic diet, could also lead to a number of modifications to our gut microbiome such as changes in certain bacterial phyla. For example, a vegetarian diet leads to an increase in Bifidobacteria and Prevotella, while a carnivorous diet results in an increase in Clostridium growth, which has not been found to have a positive nor a negative effect on the gut microbiome [12,13,14]. Another research focus has been differences in infant diets and changes in the gut microbiome. The Acinetobacter genus was mostly found in the MOM group, the Coprococcus genus was abundant in the DHM group, and Clostridium difficile predominated in the formula fed infants.

Conclusion

Overall, these various bacterial changes that occur due to different dietary components are greatly affecting the human gut microbiome, and research studies have shown insight on how these alterations would affect human metabolism. In regard to future medicine, it has been shown that probiotics could be used to improve our metabolism and more research needs to be performed to further analyze the positive effects of probiotics on our gut microbiome. To conclude, our understanding of the world of gut microbiota has just begun, and much more is to be learned before manipulating it for our therapeutic use.

Acknowledgments:

I would like to thank Dr. Sarah Singer for helping me throughout every step of this process and for providing me with valuable feedback on my research paper. I couldn’t have done it without your support. I would also like to say thank you to Dr. Kartik Angara for taking the time out of his busy schedule to peer review my paper and give me wonderful comments.

A close up of text on a white background

Description automatically generated

Figure 1: Relationship between Diet and the Gut Microbiome

This image represents the step by step process of how different dietary components affect the gut microbiome. The different diets that are ingested, the effects of these dietary components, diseases that could occur, and the altered gut microbiome as a result, is shown in this diagram.

Dietary component Bacterial Changes Result
Dietary Fibres Increase in Prevotella and Bacteroides Higher production of SCFAs
Vegetarian Diet Increase in Prevotella and Bifidobacteria -no observed effect-
Cruciferous Vegetable Diet Increase in Eggerthella and Bacteroidetes Improved lignan metabolism and degradation of fibres and glucosinolates
Ketogenic Diet Decrease in E. rectale and Bifidobacteria Decrease in the amount of butyrate
Carnivorous Diet Increase in Clostridium (fried meat) -no observed effect-
MOM Infant Diet Increase in Acinetobacter, Bifidobacteriaceae and Lactobacillaceae -no observed effect-
DHM Infant Diet Increase in Coprococcus

Decrease in Clostridiales, Lactobacillus, and Bacillales

-no observed effect-
Formula Milk Infant Diet Increase in Clostridium Difficile and proteobacteria

Decrease in Clostridiales, Lactobacillus, and Bacillales

Reduction in LPS and protein biosynthesis

Faster sugar metabolism

Table 1: Bacterial Changes Due to Different Dietary Components

This table shows the bacterial changes that occur in the gut microbiome as a result of the ingestion of different diets. The changes that occur in the body due to these bacterial changes are also represented in the table above.

References

[1] Jandhyala, Sai Manasa. 2015. “Role of The Normal Gut Microbiota”. World Journal Of Gastroenterology 21 (29): 8787. https://doi.org/10.3748/wjg.v21.i29.8787.

[2] M M. Quigley, Eamonn. 2020. “Gut Bacteria In Health And Disease”. Gastroenterology And Hepatology 9 (9): 560-569.

[3] Zhang, Yu-Jie, Sha Li, Ren-You Gan, Tong Zhou, Dong-Ping Xu, and Hua-Bin Li. 2015. “Impacts Of Gut Bacteria On Human Health And Diseases”. International Journal Of Molecular Sciences 16 (12): 7493-7519. https;//doi.org/10.3390/ijms16047493.

[4] Ramakrishnan, Akshaya. “Relationship between Diet and the Gut Microbiome”. Case Western Reserve University.2020

[5] Ramakrishnan, Akshaya. “Bacterial Changes Due to Different Dietary Components”. Case Western Reserve University.2020

[6] Gray, Lawrence E. K., Martin O’Hely, Sarath Ranganathan, Peter David Sly, and Peter Vuillermin. 2017. “The Maternal Diet, Gut Bacteria, And Bacterial Metabolites During Pregnancy Influence Offspring Asthma”. Frontiers In Immunology 8. https://doi.org/10.3389/fimmu.2017.00365.

[7] Kovatcheva-Datchary, Petia, Anne Nilsson, Rozita Akrami, Ying Shiuan Lee, Filipe De Vadder, Tulika Arora, Anna Hallen, Eric Martens, Inger Björck, and Fredrik Bäckhed. 2015. “Dietary Fiber-Induced Improvement In Glucose Metabolism Is Associated With Increased Abundance Of Prevotella”. Cell Metabolism 22 (6): 971-982. https://doi.org/10.1016/j.cmet.2015.10.001.

[8] Zhao, Liping, et al. 2018. “Gut Bacteria Selectively Promoted By Dietary Fibers Alleviate Type 2 Diabetes”. Science 359 (6380): 1151-1156. https://doi.org/10.1126/science.aao5774.

[9] Soverini, Matteo, Silvia Turroni, Elena Biagi, Sara Quercia, Patrizia Brigidi, Marco Candela, and Simone Rampelli. 2017. “Variation Of Carbohydrate-Active Enzyme Patterns In The Gut Microbiota Of Italian Healthy Subjects And Type 2 Diabetes Patients”. Frontiers In Microbiology 8. https://doi.org/10.3389/fmicb.2017.02079.

[10] Salonen, Anne, Leo Lahti, Jarkko Salojärvi, Grietje Holtrop, Katri Korpela, Sylvia H Duncan, and Priya Date et al. 2014. “Impact Of Diet And Individual Variation On Intestinal Microbiota Composition And Fermentation Products In Obese Men”. The ISME Journal 8 (11): 2218-2230. https://doi.org/10.1038/ismej.2014.63.

[11] Wu, Gary D, Charlene Compher, Eric Z Chen, Sarah A Smith, Rachana D Shah, Kyle Bittinger, and Christel Chehoud et al. 2014. “Comparative Metabolomics In Vegans And Omnivores Reveal Constraints On Diet-Dependent Gut Microbiota Metabolite Production”. Gut 65 (1): 63-72. https://doi.org/10.1136/gutjnl-2014-308209.

[12] Hayashi, Hidenori, Mitsuo Sakamoto, and Yoshimi Benno. 2002. “Fecal Microbial Diversity In A Strict Vegetarian As Determined By Molecular Analysis And Cultivation”. Microbiology And Immunology 46 (12): 819-831. https://doi.org/10.1111/j.1348-0421.2002.tb02769.x.

[13] Losasso, Carmen, Ester M. Eckert, Eleonora Mastrorilli, Jorg Villiger, Marzia Mancin, Ilaria Patuzzi, and Andrea Di Cesare et al. 2018. “Assessing The Influence Of Vegan, Vegetarian And Omnivore Oriented Westernized Dietary Styles On Human Gut Microbiota: A Cross Sectional Study”. Frontiers In Microbiology9. https://doi.org/10.3389/fmicb.2018.00317.

[14] Shen, Qing, Yin An Chen, and Kieran M. Tuohy. 2010. “A Comparative In Vitro Investigation Into The Effects Of Cooked Meats On The Human Faecal Microbiota”. Anaerobe 16 (6): 572-577. https://doi.org/10.1016/j.anaerobe.2010.09.007.

[15] Lindefeldt, Marie, Alexander Eng, Hamid Darban, Annelie Bjerkner, Cecilia K Zetterström, Tobias Allander, Björn Andersson, Elhanan Borenstein, Maria Dahlin, and Stefanie Prast-Nielsen. 2019. “The Ketogenic Diet Influences Taxonomic And Functional Composition Of The Gut Microbiota In Children With Severe Epilepsy”. Npj Biofilms And Microbiomes 5 (1). https://doi.org/10.1038/s41522-018-0073-2.

[16] Parra-Llorca, Anna, María Gormaz, Cristina Alcántara, María Cernada, Antonio Nuñez-Ramiro, Máximo Vento, and Maria C. Collado. 2018. “Preterm Gut Microbiome Depending On Feeding Type: Significance Of Donor Human Milk”. Frontiers In Microbiology 9. https://doi.org/10.3389/fmicb.2018.01376.

[17] Azad, M. B., T. Konya, H. Maughan, D. S. Guttman, C. J. Field, R. S. Chari, M. R. Sears, A. B. Becker, J. A. Scott, and A. L. Kozyrskyj. 2013. “Gut Microbiota Of Healthy Canadian Infants: Profiles By Mode Of Delivery And Infant Diet At 4 Months”. Canadian Medical Association Journal 185 (5): 385-394. https://doi.org/10.1503/cmaj.121189.

[18] Fan, Wenguang, Guicheng Huo, Xiaomin Li, Lijie Yang, and Cuicui Duan. 2014. “Impact Of Diet In Shaping Gut Microbiota Revealed By A Comparative Study In Infants During The Six Months Of Life”. Journal Of Microbiology And Biotechnology 24 (2): 133-143. https://doi.org/10.4014/jmb.1309.09029.

[19] Lee, Sang A, Ji Ye Lim, Bong-Soo Kim, Su Jin Cho, Nak Yon Kim, Ok Bin Kim, and Yuri Kim. 2015. “Comparison Of The Gut Microbiota Profile In Breast-Fed And Formula-Fed Korean Infants Using Pyrosequencing”. Nutrition Research And Practice 9 (3): 242. https://doi.org/10.4162/nrp.2015.9.3.242.

[20] Wang, Peng-Xu, Xin-Ru Deng, Chen-Hong Zhang, and Hui-Juan Yuan. 2020. “Gut Microbiota And Metabolic Syndrome”. Chinese Medical Journal 133 (7): 808-816. https://doi.org/10.1097/cm9.0000000000000696.

[21] Fooks, Laura J., Roy Fuller, and Glenn R. Gibson. 1999. “Prebiotics, Probiotics And Human Gut Microbiology”. International Dairy Journal 9 (1): 53-61. https://doi.org/10.1016/s0958-6946(99)00044-8.

[22] Quigley, Eamonn MM. 2011. “Gut Microbiota And The Role Of Probiotics In Therapy”. Current Opinion In Pharmacology 11 (6): 593-603. https://doi.org/10.1016/j.coph.2011.09.010.

Biography

Abstract

The human gut microbiome is home to trillions of microorganisms, but according to recent research, this number can be greatly altered depending on one’s daily dietary intake. Researchers have been studying effects of common diets such as vegetarian, vegan, carnivore, and ketogenic diets as well as infant diets on gut flora, which have provided insight on how consumption of specific foods could modify different phyla and affect metabolic rates. Variations in a person’s diet can cause alterations in the gut flora which can lead to downstream metabolic changes. As notable research has been collected on these different diets, it can be seen that a shift towards a vegetarian diet may result in higher metabolic rates. Additionally, it has been observed that a diet enriched with dietary fibres could be a potential treatment for diabetic patients. In summary, the food that is consumed in our day to day lives has crucial effects on our gut microbiome and more is to be studied on how different diets could affect one’s metabolism in adulthood.

Introduction

Human gastrointestinal microbiota, also called gut microbiota, are essential non-pathogenic microorganisms that reside in the digestive tract of humans. These microorganisms are vital to metabolism as they aid in several functions such as host nutrient metabolism, xenobiotic and drug metabolism, immunomodulation and protection against pathogens [1]. Figure one indicates that these effects on the host are followed by the various changes that occur in the gut microbiome[4]. In addition, certain species of gut bacteria have the ability to produce a variety of substances that have the potential to kill pathogens [2]. The gut microbiota and the host have a commensal relationship; the microbiota contribute to the homeostasis of the host immune system, while the host provides the bacteria with shelter and food. Several factors such as age, modes of childbirth, and our daily diets, play an important role in shaping our gut microbiome [1]. The diverse gut microbiome varies throughout the gastrointestinal tract. For example, Streptococcus is the dominant genus in the distal esophagus, while Firmicutes and Bacteroides are the most common phyla that inhabit the large intestine [1]. Infants’ gut microbiota increase and diversify over time from birth to two and a half years of age. Over one’s lifespan, one’s diet has a direct impact on the gut bacteria. Alterations in the gut microbiome may potentially lead to prevalent diseases such as inflammatory bowel disorder (IBD) and metabolic disorders, which are highlighted in figure one [1,4]. The gut microbiota produces lignans that protect against health complications such as cardiovascular disease and cancer [3]. An emerging topic in present research on the gut microbiota is the impact of daily diets on the gut microbiome. Daily diets such as plant-based diets, carnivorous diets, and ketogenic diets have been studied to evaluate their impact on the gut microbiome. This review will focus on the effect of diet on gut microbiome, and the subsequent consequences on metabolism and disease [4].

Dietary Fibres

1. Advantageous Bacterial Changes:

Several studies have shown the benefit of a high fibre diet and its effects on the gut microbiome. Fibres are nondigestible carbohydrates, also known as microbiota-accessible carbohydrates (MACs). It has been shown that diets with a significant proportion of fibre lead to higher levels of Prevotella and Bacteroides [5,6,7]. These increases in certain types of bacteria have also resulted in an increase in short chain fatty acids (SCFAs) [6, 8]. SCFA production occurs due to the fermentation of MACs, which may be created by the host diet or other varieties of bacteria. These MACs are broken down by carbohydrate-active enzymes, which play an important role in carbohydrate degradation and metabolism [9]. Although there has been an observed increase in the total amount of SCFAs with the consumption of dietary fibres, the faecal count was surprisingly low when compared to a weight loss or wheat bran diet [10]. In this study, high levels of fibre consumption led to a lower production of faecal SCFAs, which may have been due to a lack of Ruminococcin bromii that helps ferment resistant starch.

2. Metabolic Changes:

Researchers have also observed several metabolic changes associated with the inclusion of dietary fibres in a general diet, which can also be observed in figure one as the fourth step in improving the health of the host[4]. One specific study identified that the combination of barley kernel-based bread – a type of fibre – and high levels of Prevotella led to improved glucose metabolism [7]. An increase in Prevotella may increase glycogen storage and improve glucose resistance[5]. Other researchers studied the effects of a high fibre diet in Chinese Patients with Type 2 Diabetes and found that the different dominances in bacteria in a high fibre diet led to an increase in SCFAs [8]. An increase in SCFAs will increase the rate of energy metabolism in the host. The phylum of gut bacteria known as Bifidobacterium has been found to be the major producer of SCFAs. Inoculation of Type 2 Diabetics with the Bifidobacterium pseudocatenulatum strain C95 reduced weight gain and significantly improved insulin resistance. The increase in SCFAs due to the abundance in Bifidobacteria may be involved in weight loss in Type 2 Diabetics. Additionally, increased proportions of Bacteroides and Prevotella due to a high fibre diet have also been shown to increase the number of SCFAs such as propionate [6].

Dietary fibres have several health benefits not only on the gut microbiome but also on overall metabolism. Diets high in dietary fibres and specific probiotics could be a future treatment for Type 2 Diabetes patients. More research on this topic is needed to fully explain the relationship between fibre, gut microbiota, and glucose metabolism.

General Diet

Different changes to our regular diets can result in several differences in our gut microbiome. These two factors are indicated as the second and third steps in affecting the host’s metabolism which can be seen in figure one[4]. Various diets such as vegetarian, vegan, omnivore, carnivore and ketogenic diets have been studied to identify their effects on gut microbiota. In one specific study that compared vegan and omnivore diets, it was observed that vegans had a more diverse gut microbiome [11]. A different study found that a vegetarian diet led to an increase in Bifidobacterium in rural Japanese people, while another study proposed that a plant-based diet led to an increase in Prevotella [5,12,13]. The results from these studies indicate that plant-based diets cause the gut microbiome to become highly diverse, by increasing the amounts of specific bacterial phyla. Similarly, when solely focusing on a diet consisting of cruciferous vegetables such as broccoli and cabbage, it can be seen that certain bacterial species improved metabolism. When there was a dominance of Eggerthella, improved lignan metabolism followed [5]. Furthermore, the dominance of Bacteroidetes led to the degradation of fibres and glucosinolates. Meanwhile, in a complete meat-based diet consisting of three different meats (chicken, beef, and fish), the amount of Clostridium and Bacteroides significantly increased when beef was consumed [14]. This completely differed from a vegetarian diet, in which there was no observed growth of Clostridium. Fish digestion produced fewer SCFAs such as acetic and propionic acids, contrasting with the results of fibre consumption. This study also focused on certain cooking methods and found that there was a higher Clostridium growth due to fried meat consumption when compared to boiled meats [5]. Another diet known as the ketogenic diet (high fat and low carbohydrate diet) was associated with a decrease of the phylum E. rectale, which is responsible for producing butyrate[5,15]. An additional change that occurred in children with epilepsy that consumed the ketogenic diet is the depletion of Bifidobacterium, which may be associated with a decreased production of SCFAs. The effects of the ketogenic and vegetarian diets are similar because both reduced the production of SCFAs. The depletion of Bifidobacterium in the ketogenic diet is also directly linked to the decrease in E. rectale because Bifidobacterium produces acetate which is needed for E. rectale. All in all, plant-based diets have been shown to increase gut microbiome diversity, while carnivorous diets have been observed to have increased amounts of Clostridium and Bacteroides, which could be harmful to the host, but no specific effect has been found. A diet that consists of a high amount of red or processed meats could lead to different chronic diseases. This research holds high significance today as many people have explored different diets. A push towards a vegetarian or cruciferous vegetable diet could be more beneficial as increased phylum diversity may be associated with increased metabolism. Further research studies on how certain bacterial changes result in metabolic changes, could potentially resolve the relationship between different dietary components, the gut microbiome, and human metabolism.

Infant diet

There are different variations in infant diets that have been associated with several changes in the gut microbiome. One specific study focused on three infant diets: mother’s own milk (MOM), donor pasteurized human milk (DHM), and formula milk [16]. These researchers studied the effects of these three diets on the gut microbiota of premature infants. The Acinetobacter genus was widely present in the MOM group, while the Coprococcus genus was mainly found in the DHM group [5] . The DHM and formula milk groups had lower amounts of Clostridiales, Lactobacillus, and Bacillales when compared to the MOM group of infants. Another study showed that formula fed infants had an increased richness of Clostridium difficile, which contradicts the statement made by the previous study [17]. Parra-Llorca et al. also found a substantial decrease in LPS biosynthesis as well as proteins in formula fed infants[5]. Going a step further, the formula milk not only affected the gut microbiome, it also enriched the function of sugar metabolism [16]. A study that was done on 24 healthy infants in China found that Proteobacteria was more predominant in formula fed infants [18]. By further observing faecal samples and performing pyrosequencing, it was found that Firmicutes was present in all three groups. Specifically, Firmicutes was found to be more abundant in breastfed infants when compared to the other infants. These results signify that Firmicutes is the most dominant phylum in the infant intestinal microflora. Additional research was performed in Korea, studying the effects of both formula and breast milk on the gut microbiota profile of infants [19]. Formula fed infants were found to have a more diverse gut microbiome, while breastfed infants had an increase in Bifidobacteriaceae and Lactobacillaceae. The lower bacterial richness in breastfed infants could be due to the oligosaccharides in the milk that serve as substrates to only a specific number of gut microbes [17]. The abundance in different types of gut microbiota could potentially explain how some subjects have a faster glucose metabolism than others. These research studies are highly significant today, but there is a gap in knowledge as to how infant diets could affect a human’s long-term metabolism. Researchers need to further study this topic in order to understand how different infant diets could contribute to metabolic disorders in later stages of human life.

Probiotics

Looking forward, researchers have proposed that probiotics could be a solution to counteract detrimental changes that occur in gut flora. These dietary strategies are now being used to alter the gut bacteria to help the body fight against diabetes and obesity [20]. Probiotics, which can also be found in foods such as yogurt, are dietary substitutions that help alter energy homeostasis. Addition of probiotics to the diet could activate the immune system by helping it produce more antibodies to fight infections and tumours [21]. Additionally, probiotics have the ability to block certain receptor sites for toxins, which may protect against disorders such as IBD. An increase in consumption of probiotics can also result in the production of SCFAs, which may improve insulin resistance. Some strains of probiotics have also been found to have anti-inflammatory effects which signifies that through future applications, probiotics may be used to prevent IBD. Although probiotics have their advantages, there are also several consequences associated with using them in our daily diets. In patients with IBD, it is possible that the probiotic species could translocate across the gut and cause systemic sepsis, which could be very harmful to the host. Moreover, increased mortality rates have been observed for patients with acute pancreatitis when treated with probiotics. Early supplementation of probiotics in an infant’s diet has not yet been proposed, so recommendations have not been made on this topic as yet [22].

In addition to altering our gut microbiome using probiotics, our bacteria can also be modified by changing our diets. In the future, a high fibre diet may be prescribed to fight against metabolic disorders. Exclusive trials must be conducted in order to examine the effects of probiotics on digestive disorders, along with investigations in the laboratory to analyze the in-depth mechanisms of probiotics in the gut. Potential research on this topic could resolve the relationship between the effects of probiotics and diet on the gut microbiome and its relationship with metabolism.

Results

Research on bacterial changes due to several dietary differences has suggested how these alterations affect a human’s metabolism. All of these alterations and their significant effects on the host’s health have been specified in table one[5]. Although some gut microbial phyla have not been specified to have any significant effect on the host, most species such as Bacteroides, Clostridia, and Firmicutes have been observed to greatly impact the gut microbiome. An increase in dietary fibres leads to an increase in Prevotella and Bacteroides, which has downstream effects on metabolism [6,7]. Additionally, a change from a more varied diet to a vegetarian, omnivore, carnivore, or ketogenic diet, could also lead to a number of modifications to our gut microbiome such as changes in certain bacterial phyla. For example, a vegetarian diet leads to an increase in Bifidobacteria and Prevotella, while a carnivorous diet results in an increase in Clostridium growth, which has not been found to have a positive nor a negative effect on the gut microbiome [12,13,14]. Another research focus has been differences in infant diets and changes in the gut microbiome. The Acinetobacter genus was mostly found in the MOM group, the Coprococcus genus was abundant in the DHM group, and Clostridium difficile predominated in the formula fed infants.

Conclusion

Overall, these various bacterial changes that occur due to different dietary components are greatly affecting the human gut microbiome, and research studies have shown insight on how these alterations would affect human metabolism. In regard to future medicine, it has been shown that probiotics could be used to improve our metabolism and more research needs to be performed to further analyze the positive effects of probiotics on our gut microbiome. To conclude, our understanding of the world of gut microbiota has just begun, and much more is to be learned before manipulating it for our therapeutic use.

Acknowledgments

I would like to thank Dr. Sarah Singer for helping me throughout every step of this process and for providing me with valuable feedback on my research paper. I couldn’t have done it without your support. I would also like to say thank you to Dr. Kartik Angara for taking the time out of his busy schedule to peer review my paper and give me wonderful comments.

A close up of text on a white background

Description automatically generated

Figure 1: Relationship between Diet and the Gut Microbiome

This image represents the step by step process of how different dietary components affect the gut microbiome. The different diets that are ingested, the effects of these dietary components, diseases that could occur, and the altered gut microbiome as a result, is shown in this diagram.

Dietary component Bacterial Changes Result
Dietary Fibres Increase in Prevotella and Bacteroides Higher production of SCFAs
Vegetarian Diet Increase in Prevotella and Bifidobacteria -no observed effect-
Cruciferous Vegetable Diet Increase in Eggerthella and Bacteroidetes Improved lignan metabolism and degradation of fibres and glucosinolates
Ketogenic Diet Decrease in E. rectale and Bifidobacteria Decrease in the amount of butyrate
Carnivorous Diet Increase in Clostridium (fried meat) -no observed effect-
MOM Infant Diet Increase in Acinetobacter, Bifidobacteriaceae and Lactobacillaceae -no observed effect-
DHM Infant Diet Increase in Coprococcus

Decrease in Clostridiales, Lactobacillus, and Bacillales

-no observed effect-
Formula Milk Infant Diet Increase in Clostridium Difficile and proteobacteria

Decrease in Clostridiales, Lactobacillus, and Bacillales

Reduction in LPS and protein biosynthesis

Faster sugar metabolism

Table 1: Bacterial Changes Due to Different Dietary Components

This table shows the bacterial changes that occur in the gut microbiome as a result of the ingestion of different diets. The changes that occur in the body due to these bacterial changes are also represented in the table above.

References

[1] Jandhyala, Sai Manasa. 2015. “Role of The Normal Gut Microbiota”. World Journal Of Gastroenterology 21 (29): 8787. https://doi.org/10.3748/wjg.v21.i29.8787.

[2] M M. Quigley, Eamonn. 2020. “Gut Bacteria In Health And Disease”. Gastroenterology And Hepatology 9 (9): 560-569.

[3] Zhang, Yu-Jie, Sha Li, Ren-You Gan, Tong Zhou, Dong-Ping Xu, and Hua-Bin Li. 2015. “Impacts Of Gut Bacteria On Human Health And Diseases”. International Journal Of Molecular Sciences 16 (12): 7493-7519. https;//doi.org/10.3390/ijms16047493.

[4] Ramakrishnan, Akshaya. “Relationship between Diet and the Gut Microbiome”. Case Western Reserve University.2020

[5] Ramakrishnan, Akshaya. “Bacterial Changes Due to Different Dietary Components”. Case Western Reserve University.2020

[6] Gray, Lawrence E. K., Martin O’Hely, Sarath Ranganathan, Peter David Sly, and Peter Vuillermin. 2017. “The Maternal Diet, Gut Bacteria, And Bacterial Metabolites During Pregnancy Influence Offspring Asthma”. Frontiers In Immunology 8. https://doi.org/10.3389/fimmu.2017.00365.

[7] Kovatcheva-Datchary, Petia, Anne Nilsson, Rozita Akrami, Ying Shiuan Lee, Filipe De Vadder, Tulika Arora, Anna Hallen, Eric Martens, Inger Björck, and Fredrik Bäckhed. 2015. “Dietary Fiber-Induced Improvement In Glucose Metabolism Is Associated With Increased Abundance Of Prevotella”. Cell Metabolism 22 (6): 971-982. https://doi.org/10.1016/j.cmet.2015.10.001.

[8] Zhao, Liping, et al. 2018. “Gut Bacteria Selectively Promoted By Dietary Fibers Alleviate Type 2 Diabetes”. Science 359 (6380): 1151-1156. https://doi.org/10.1126/science.aao5774.

[9] Soverini, Matteo, Silvia Turroni, Elena Biagi, Sara Quercia, Patrizia Brigidi, Marco Candela, and Simone Rampelli. 2017. “Variation Of Carbohydrate-Active Enzyme Patterns In The Gut Microbiota Of Italian Healthy Subjects And Type 2 Diabetes Patients”. Frontiers In Microbiology 8. https://doi.org/10.3389/fmicb.2017.02079.

[10] Salonen, Anne, Leo Lahti, Jarkko Salojärvi, Grietje Holtrop, Katri Korpela, Sylvia H Duncan, and Priya Date et al. 2014. “Impact Of Diet And Individual Variation On Intestinal Microbiota Composition And Fermentation Products In Obese Men”. The ISME Journal 8 (11): 2218-2230. https://doi.org/10.1038/ismej.2014.63.

[11] Wu, Gary D, Charlene Compher, Eric Z Chen, Sarah A Smith, Rachana D Shah, Kyle Bittinger, and Christel Chehoud et al. 2014. “Comparative Metabolomics In Vegans And Omnivores Reveal Constraints On Diet-Dependent Gut Microbiota Metabolite Production”. Gut 65 (1): 63-72. https://doi.org/10.1136/gutjnl-2014-308209.

[12] Hayashi, Hidenori, Mitsuo Sakamoto, and Yoshimi Benno. 2002. “Fecal Microbial Diversity In A Strict Vegetarian As Determined By Molecular Analysis And Cultivation”. Microbiology And Immunology 46 (12): 819-831. https://doi.org/10.1111/j.1348-0421.2002.tb02769.x.

[13] Losasso, Carmen, Ester M. Eckert, Eleonora Mastrorilli, Jorg Villiger, Marzia Mancin, Ilaria Patuzzi, and Andrea Di Cesare et al. 2018. “Assessing The Influence Of Vegan, Vegetarian And Omnivore Oriented Westernized Dietary Styles On Human Gut Microbiota: A Cross Sectional Study”. Frontiers In Microbiology9. https://doi.org/10.3389/fmicb.2018.00317.

[14] Shen, Qing, Yin An Chen, and Kieran M. Tuohy. 2010. “A Comparative In Vitro Investigation Into The Effects Of Cooked Meats On The Human Faecal Microbiota”. Anaerobe 16 (6): 572-577. https://doi.org/10.1016/j.anaerobe.2010.09.007.

[15] Lindefeldt, Marie, Alexander Eng, Hamid Darban, Annelie Bjerkner, Cecilia K Zetterström, Tobias Allander, Björn Andersson, Elhanan Borenstein, Maria Dahlin, and Stefanie Prast-Nielsen. 2019. “The Ketogenic Diet Influences Taxonomic And Functional Composition Of The Gut Microbiota In Children With Severe Epilepsy”. Npj Biofilms And Microbiomes 5 (1). https://doi.org/10.1038/s41522-018-0073-2.

[16] Parra-Llorca, Anna, María Gormaz, Cristina Alcántara, María Cernada, Antonio Nuñez-Ramiro, Máximo Vento, and Maria C. Collado. 2018. “Preterm Gut Microbiome Depending On Feeding Type: Significance Of Donor Human Milk”. Frontiers In Microbiology 9. https://doi.org/10.3389/fmicb.2018.01376.

[17] Azad, M. B., T. Konya, H. Maughan, D. S. Guttman, C. J. Field, R. S. Chari, M. R. Sears, A. B. Becker, J. A. Scott, and A. L. Kozyrskyj. 2013. “Gut Microbiota Of Healthy Canadian Infants: Profiles By Mode Of Delivery And Infant Diet At 4 Months”. Canadian Medical Association Journal 185 (5): 385-394. https://doi.org/10.1503/cmaj.121189.

[18] Fan, Wenguang, Guicheng Huo, Xiaomin Li, Lijie Yang, and Cuicui Duan. 2014. “Impact Of Diet In Shaping Gut Microbiota Revealed By A Comparative Study In Infants During The Six Months Of Life”. Journal Of Microbiology And Biotechnology 24 (2): 133-143. https://doi.org/10.4014/jmb.1309.09029.

[19] Lee, Sang A, Ji Ye Lim, Bong-Soo Kim, Su Jin Cho, Nak Yon Kim, Ok Bin Kim, and Yuri Kim. 2015. “Comparison Of The Gut Microbiota Profile In Breast-Fed And Formula-Fed Korean Infants Using Pyrosequencing”. Nutrition Research And Practice 9 (3): 242. https://doi.org/10.4162/nrp.2015.9.3.242.

[20] Wang, Peng-Xu, Xin-Ru Deng, Chen-Hong Zhang, and Hui-Juan Yuan. 2020. “Gut Microbiota And Metabolic Syndrome”. Chinese Medical Journal 133 (7): 808-816. https://doi.org/10.1097/cm9.0000000000000696.

[21] Fooks, Laura J., Roy Fuller, and Glenn R. Gibson. 1999. “Prebiotics, Probiotics And Human Gut Microbiology”. International Dairy Journal 9 (1): 53-61. https://doi.org/10.1016/s0958-6946(99)00044-8.

[22] Quigley, Eamonn MM. 2011. “Gut Microbiota And The Role Of Probiotics In Therapy”. Current Opinion In Pharmacology 11 (6): 593-603. https://doi.org/10.1016/j.coph.2011.09.010.

Biography

Akshaya Ramakrishnan is an incoming freshman at Case Western Reserve
University and will major in Nutritional Biochemistry and Metabolism. She hopes to continue her research on the relationship between nutrition and metabolism throughout her undergraduate years and eventually pursue a career in medicine.

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