The Connection between the Human Gut Microbiota and Inflammatory Bowel Disease

/, Health and Medicine/The Connection between the Human Gut Microbiota and Inflammatory Bowel Disease

The Connection between the Human Gut Microbiota and Inflammatory Bowel Disease

2019-01-30T02:39:29-07:00 January 11th, 2019|Biology, Health and Medicine|

By Emily Villarreal, Nutrition Science (Biology Emphasis), 2018

Author’s Note: This literature review was written for a UWP 104F course. I chose this topic because the gut microbiota is something that I am deeply interested in as a student researcher. The audience for this review includes medical professionals or members of academia who are interested in the microbiota and its effects on the onset of Inflammatory Bowel Disease.

Background: Recently, disturbances in the human gut microbiota have been implicated in the causes of many gastrointestinal (GI) diseases. As the field of study grows, exciting discoveries are being made through new genome sequencing techniques. It has been found that the gut flora participates in digestion by synthesizing macromolecules, vitamins, and metabolize xenobiotics and other foreign materials for the host. Now, researchers are hypothesizing that disturbances in these functions may be the cause of many GI tract diseases, such as inflammatory bowel disease (IBD). This literature review will explore the relationship between the human GI tract microbiota and IBD.

Methods: When searching for relevant material, Medical Subject Heading (MeSH) terms were used, such as “human gut microbiota,” “gut microbiome,” “gut flora,” and “inflammatory bowel disease.” Inclusion protocol included a flexible date range and required specific subject matter.

Findings: Through the secondary analysis of multiple sources, it was found that there is a strong relationship between the human gut microbiota and the onset of IBD. Many studies allude to the idea that an imbalance of the gut microbiota, termed gut dysbiosis, is a key modulator in triggering an IBD. In addition to this phenomenon, it was also found that dysbiosis contributed two main methods of pathogenesis: altered short chain fatty acid (SCFA) metabolism and increased sulfur metabolism. Both of these pathways were shown to have individual effects on causing inflammation in the GI tract by many sources.

Relevance: Overall, this analysis provides a reason for additional research within this field. The gut microbiota serves many functions, and if these functions are properly investigated, solutions to GI tract conditions like IBD may be found. Once the overall pathogenic mechanisms are elucidated, researchers should be able to begin testing new methods for IBD control and treatment. Promising articles have already been published regarding the use of probiotics and anti-TNF-α as a method of IBD treatment, thus partially confirming the hypotheses stated above.

As NASA scientists look to the stars to discover worlds beyond our own, some scientists in the medical field are looking in the opposite direction—inward to discover the world within our own bodies. The human microbiota is an expansive environment that is entirely contained by the human body, in locations like the skin, digestive, and reproductive tracts (1). The discovery of the human microbiota has consequently led to the belief that humans do not only contain 20,000 genes in our own DNA but also at least 100,000 more, contained in the microbiota (1). Because of the discovery of an entirely new genome, along with a new perspective on what constitutes health—researchers have speculated that human diseases can be mitigated or prevented by microbial intervention. However, certain disturbances in a stable gut microbiota population can contribute to GI issues as well. Depending on a person’s microbial profile, recent publications suggest that disturbances in this population can lead to dysbiosis, or the overgrowth of commensal bacteria that can produce toxins that induce oxidative stress and inflammation. This insult is then said to trigger associated immune responses that mediate sensitive genetic pathways that lead to GI tract diseases, such as inflammatory bowel disease (IBD) (2).

Understanding the interactions between the human microbiota and GI medicine is important for the study of digestive diseases, like IBD. In order to further investigate this relationship, this literature review will discuss the characteristics of and differences between the microbiota of healthy individuals and those with IBD. Additionally, this paper will emphasize the need for advances in the treatment and management of IBD through research within the fields of microbiology and gastrointestinal medicine. Although there are many theories about the causes of this phenomenon, this discussion will also provide the context with which to evaluate the details of this disease.

The human microbiota is primarily found on the skin and within the digestive and reproductive tracts. Although spread throughout the human body, the largest population of microbial symbionts are housed within the GI tract, where approximately 10-100 trillion microbes perform functions such as the metabolism of indigestible nutrients and xenobiotics, vitamin synthesis, gut epithelial cell turnover, and immune system regulation (1). The human gut microbiota is said to be a robust functioning ecosystem by the popular press, but it can also be subject to change through the influence of diet, drugs, and disease. Many studies allude to the idea that an imbalance of the gut microbiota, termed gut dysbiosis, is a key modulator in triggering different digestive system diseases, like IBD. According to recent literature, it is hypothesized that the mechanisms of IBD pathogenesis lie in the direct relationship between the effects of gut microbial dysbiosis and the intestinal immune system (3-7).

Inflammatory bowel disease is a cluster of disorders that encompasses both Crohn’s Disease (CD) and Ulcerative Colitis (UC) due to their inflammatory effects on the large intestine. Currently, the main causes of the onset of IBD are not known, but it is speculated that it is triggered through a combination of genetic mutations, environmental factors, and the gut microbiota (8). Although Crohn’s Disease and Ulcerative Colitis are two separate inflammatory conditions, they both are thought to be intensified by a disruption in the relationship between the human digestive tract and the gut microbiome. This disruption or dysbiosis is said to indirectly promote inflammation by stimulating the innate immune system. There are currently a few separate processes that are said to contribute to dysbiosis-associated inflammation: environments that support pathogen overgrowth, oxygen availability, and short-chain fatty acid (SCFA) metabolism (8). Research within this field has identified these as the most promising reasons for the promotion of IBD-associated non-functioning microbiota. However, it is recommended that further investigations be done in order to elucidate the exact mechanism of pathogenesis.

In order to gain access to a multitude of scientific journals, the UC Davis Library VPN was used to explore the Google Scholar and PubMed academic databases. Using keywords and phrases such as “human gut microbiome,” “gut flora,” and “inflammatory bowel disease” helped narrow the search process. To maintain validity and relevance, references had to fall within a recent date range If an article was written prior to 2012, it was included only if its information was considered to be a hallmark study in the field.

The Human Gastrointestinal Tract Microbiota
Recently, the human microbiota has been implicated in many functions of the digestive system (1), therefore, it can no longer be ignored when studying the functions, processes, and diseases of the human GI tract. In order to investigate these implications, many scientists agree that the core functions of the microbiota must be established. With the onset of new genetic sequencing techniques, such as 16S rRNA and shotgun genome sequencing, many research groups were able to establish the major contributions that a healthy microbiota provides to their host. For example, The Human Genome Project (HGP) and Metagenomics of the Human Intestinal Tract Project (MetaHIT) are worldwide initiatives whose mission is to investigate the impact of the microbiota on “human well-being” (1, 9). Analysis of millions of genome data sets from these projects found that the gut microbiota is primarily involved in two functions, “housekeeping” and host-specific processes (9). Housekeeping functions, such as regulating energy metabolism and DNA synthesis, were primarily found to be responsible for survival in the human GI tract. However, the host-specific gene functions were found to be related to bacterial adhesion to host cell-structures as well as the microbial breakdown of glycolipids (9). Within the host-specific functions found, there is a proposed “minimal metagenome” that contains a fraction of the roles that are commonly known within the scientific community to be vital for human digestion and GI tract health. In alignment with Qin et al.’s initial characterizations, many other research groups have continued to find that the minimal metagenome is involved with SCFA, amino acid, and vitamin synthesis, as well as the activation of T-cells and autophagy pathways (6, 9). This small subset of the metagenome and its associated functions are what have been proposed to be vital in the regulation of the human immune system, in addition to being involved in GI tract diseases (6).

The human gut microbiota is one of the many influential mediators of human GI tract functioning; however, when normal processes are disturbed, shifts in microbial metabolism and diversity can occur (3). The ecological balance of the microbiota of the GI tract is quite delicate. When it is subjected to any type of environmental stress, it can easily be shifted towards a distribution that promotes the overgrowth of commensal species that can be harmful in large populations. As the microbial environment becomes increasingly hostile, the human immune system will usually respond, causing the recruitment of immune system cells—thus promoting inflammation (4). In order to understand the processes behind the dysbiosis of a stressed microbiota, many research groups are using 16S rRNA gene sequencing to analyze the functional losses of IBD-associated microbial samples of either feces or intestine biopsy. For example, in 2012, an experiment investigating these effects found that the microbiota associated with IBD was strikingly different than that of healthy controls. Further analysis was able to show that dysbiosis caused increases in mucin degradation, cysteine synthesis, and the metabolism of riboflavin. The same data set also showed that dysbiosis also caused a drop in the production of SCFAs, which are an essential energy source for enterocytes (6). Similar results from other studies have also shown a characteristic decrease in SCFA production, which has been consistently hypothesized to contribute to intestinal inflammation (5-7).

Inflammatory Bowel Disease
When studying IBD, it is important to consider the onset and etiology of the disease. Although the causes are still classified as unknown, it has been speculated that IBD occurs as a result of a combination of genetic susceptibilities, environmental factors, immune system mechanisms, and gut dysbiosis (5). One major factor and common trend found in the investigation of the condition, is gut microbial dysbiosis, which has been found to be highly related to IBD in many studies (6, 7, 10). Furthermore, the shift in microbial diversity and function has been found to be different between the two divisions of IBD, Crohn’s Disease and Ulcerative Colitis (6, 7, 10). In the following sections, the gut microbiota profile of each disease will be discussed in order to examine how each profile contributes to the characteristic intestinal inflammation in IBD.

Crohn’s Disease
Crohn’s disease has taken the forefront in IBD-focused research. Historically, Crohn’s has been said to be connected to a combination of genetic susceptibility and microbial dysbiosis. In clinical settings, it is characterized by intestinal inflammation of multiple layers of the mucosa, which can occur at any part of the digestive tract. Complications of CD include bowel perforations, abscesses, malabsorption, and fistulae (11). Because of the potentially dangerous complications of CD, researchers have focused on investigating this disease alone. In an effort to elucidate the true method of pathogenesis of CD, Nagao-Kitamoto et al. used genetically modified IL-10 deficient mice in an attempt to replicate the genetic component of CD (2016). Through multivariate gene analysis and in vivo experiments, it has been confirmed that animal models barely show signs of developing CD, unless they are made to be genetically susceptible to it, as in the case of IL-10 deficiency (7).

Many researchers have also found that CD is consistently associated with the loss of specific species of bacteria, such as Faecalibacterium prausntzii and Rosburia hominis (6). It has been hypothesized that F. prausntzii has anti-inflammatory effects because they are consistently inversely correlated with levels of inflammation in the gut (10). It has also been suggested that the loss of these key bacterial species are associated with a decrease in SCFA production, and an increase in intestinal inflammation caused by enterocytes due to the lack of an energy source (6). In 2015, it was confirmed by scientists representing the American Journal of Gastroenterology that the typical microbial profile of a CD patient usually differs from that of a UC patient. In their analysis, they found that CD patients had unusually high numbers of gram-negative bacteria such as Bacteroides fragilis, Clostridium ramosum, and Eubacterium cylindroides, in addition to having the well-documented decrease in F. prausntzii (12). Overall, this bacterial phenotype has been said to be characterized by an increase in carbohydrate metabolism and a decrease in SCFA production, which has been shown to cause drastic changes in redox pathways (6). It is these changes in microbial functioning that are said to contribute to overall IBD pathogenesis, which will be discussed later.

Ulcerative Colitis
Ulcerative Colitis (UC) has remained the more elusive of the two subdivisions of IBD, likely due to the difficulty in identifying a strict origin. Like CD, it is characterized by the inflammation of the colon, which causes edema, mucosal susceptibility to pathogens, and epithelial ulceration (5). Recent literature has pointed to the hypothesis that UC is also caused or promoted by microbial dysbiosis in the gut (4), but its effects are only found in the large intestine (11). Clinical symptoms of UC include bloody diarrhea, “toxic megacolon”, and bowel perforations (11)—which follow in suit with the theory that UC-specific dysbiosis may cause an increase in mucosal permeability. This directly increases the possibility, “of bacterial translocation and endotoxemia” (4). Due to this correlation, it is believed that the onset of UC is likely caused by a severe shift in the intestinal microbiota.

There has been overwhelming support in the scientific community for the idea that UC is caused by microbial dysbiosis (3-7). Many studies have confirmed that UC also has a distinct microbial profile, which is hypothesized to contribute to the effects of the condition. Broad-spectrum genetic analysis has revealed that patients who have UC typically have an overgrowth of Escherichia coli, Akkermansia, and Desulfvibrio, in addition to phyla related to Clostridium difficile (4, 12). These commensal pathogens have been said to exist in environments that are high in oxygen, suggesting that UC-associated dysbiosis is related to high levels of reactive oxygen species (ROS). To further this argument, it was found that these species have been known to use sulfur as a source of redox potential, thus promoting the production of ROS and host secretion of homocysteine, an inflammatory amino acid derivative from sulfur metabolism (4, 6). These pathogenic mechanisms are said to be major contributors to the inflammation caused by UC and are connected to overall microbiota-IBD related complications.

The Mechanisms behind the Gut Microbiota and Irritable Bowel Disease Pathogenesis
As previously stated, the scientific community has established that one of the primary mechanisms of IBD-pathogenesis lies behind microbial dysbiosis in the intestines. In this section, the following potential mechanisms will be evaluated across all references: changes in SCFA and sulfur metabolism.

Changes in Short-Chain Fatty Acid Metabolism
Many publications established that both CD and UC have microbial compositions that decrease SCFA production (6, 7, 10). This is caused by the decrease in genera like Faecalibacterium, likely induced by an overgrowth of other commensal bacteria. This genus is said to be among the group of gut microbiota that participates in the digestion of complex polysaccharides, such as mucin and N-acetyl glucosamine, producing SCFAs as a byproduct (6). SCFAs, like butyrate, then stimulate intestinal enterocyte turnover and can influence the host response to inflammatory cytokines, which is vital for the prevention of inflammation in the gut. The fact that SCFAs can mediate host response to inflammatory chemicals, is the foundation on which the theory about SCFAs exists. Through cell-culture and animal studies, it has been found that SCFAs function by inhibiting pro-inflammatory cytokine production like TNF-α and the NF-kB pathway, which are both instrumental in causing the widespread inflammation in all bodily tissues (13, 14).

Changes in Sulfur Metabolism
Some researchers also believe that increases in sulfur metabolism may be a factor in the onset of inflammation in IBD. As the IBD-associated microbial population shifts towards dysbiosis, some bacteria switch to using sulfur as a source of redox potential. In an article by Morgan et al., this phenomenon was observed (2012). The researchers hypothesized that the microbiota increased in metabolizing sulfur-containing amino acids in order to achieve either of the following: homocysteine conversion to methionine as a method of maintaining redox balance or using cysteine to convert to pyruvate for energy (6). This observation was also recorded in a few other studies as well (4, 5, 10). The mechanism by which this phenomenon causes inflammation likely stems from the idea that high sulfur metabolism creates hydrogen sulfide as a byproduct, which suppresses fermentation in the gut, thus creating a marked decrease in SCFA production (5). Because this occurrence was found in many studies, it is safe to say that sulfur-metabolism likely serves an important role in IBD pathogenesis.

Concluding Remarks
Overall, the comprehensive analysis of multiple sources point to the conclusion that the human gut microbiota is highly instrumental in mediating host responses to diseases. Results from the respective studies analyzed throughout this review show that gut microbial dysbiosis is likely a root cause of IBD. Additionally, it is important to mention that the proposed mechanisms of IBD pathogenesis were also found globally, rather than in a singular study. Because of the widespread nature of the results, future research on the proposed mechanisms of IBD should be promising. Further research on treatments for IBD should definitely consider the impact of the gut microbiota towards the onset of each of the diseases (CD and UC). Currently, there are a few studies investigating the use of probiotics and other anti-pro-inflammatory cytokine drugs for the treatment of IBD, with the ultimate goal of remission (12, 15). In addition to using these findings to propose new, high efficacy methods of treatment, further research needs to be done in order to confirm their effectiveness.


  1. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. The Human Microbiome Project. Nature 2007;449:804. doi: 10.1038/nature06244.
  2. Cario E. Microbiota and innate immunity in intestinal inflammation and neoplasia. Current Opinion in Gastroenterology 2013;29(1):85-91. doi: 10.1097/MOG.0b013e32835a670e.
  3.  Gevers D, Kugathasan S, Denson Lee A, Vázquez-Baeza Y, Van Treuren W, Ren B, Schwager E, Knights D, Song Se J, Yassour M, et al. The Treatment-Naive Microbiome in New-Onset Crohn’s Disease. Cell Host & Microbe 2014;15(3):382-92. doi:
  4.  Håkansson Å, Tormo-Badia N, Baridi A, Xu J, Molin G, Hagslätt M-L, Karlsson C, Jeppsson B, Cilio CM, Ahrné S. Immunological alteration and changes of gut microbiota after dextran sulfate sodium (DSS) administration in mice. Clinical and Experimental Medicine 2015;15(1):107-20. doi: 10.1007/s10238-013-0270-5.
  5.  Hudcovic T, Štěpánková R, Cebra J, Tlaskalová-Hogenová H. The role of microflora in the development of intestinal inflammation: Acute and chronic colitis induced by dextran sulfate in germ-free and conventionally reared immunocompetent and immunodeficient mice. Folia Microbiologica 2001;46(6):565-72. doi: 10.1007/bf02818004.
  6.  Morgan XC, Tickle TL, Sokol H, Gevers D, Devaney KL, Ward DV, Reyes JA, Shah SA, LeLeiko N, Snapper SB, et al. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biology 2012;13(9):R79. doi: 10.1186/gb-2012-13-9-r79.
  7.  Nagao-Kitamoto H, Shreiner AB, Gillilland MG, III, Kitamoto S, Ishii C, Hirayama A, Kuffa P, El-Zaatari M, Grasberger H, Seekatz AM, et al. Functional Characterization of Inflammatory Bowel Disease–Associated Gut Dysbiosis in Gnotobiotic Mice. Cellular and Molecular Gastroenterology and Hepatology 2016;2(4):468-81. doi: 10.1016/j.jcmgh.2016.02.003.
  8.  Zechner EL. Inflammatory disease caused by intestinal pathobionts. Current Opinion in Microbiology 2017;35:64-9. doi:
  9.  Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010;464:59. doi: 10.1038/nature08821.
  10.  Machiels K, Joossens M, Sabino J, De Preter V, Arijs I, Eeckhaut V, Ballet V, Claes K, Van Immerseel F, Verbeke K, et al. A decrease of the butyrate-producing species <em>Roseburia hominis</em> and <em>Faecalibacterium prausnitzii</em> defines dysbiosis in patients with ulcerative colitis. Gut 2014;63(8):1275.
  11.  The Facts About Inflammatory Bowel Diseases. New York, NY: Crohn’s and Colitis Foundation of America, 2014.
  12.  Kolho K-L, Korpela K, Jaakkola T, Pichai MVA, Zoetendal EG, Salonen A, de Vos WM. Fecal Microbiota in Pediatric Inflammatory Bowel Disease and Its Relation to Inflammation. The American Journal Of Gastroenterology 2015;110:921. doi: 10.1038/ajg.2015.149.
  13.  F. W, J. L, T. W, K. S, Z. C, Y. Y, Q. H, G. W, Z. L, S. J. The Inflammation Induced by Lipopolysaccharide can be Mitigated by Short‐chain Fatty Acid, Butyrate, through Upregulation of IL‐10 in Septic Shock. Scandinavian Journal of Immunology 2017;85(4):258-63. doi: doi:10.1111/sji.12515.
  14. Tedelind S, Westberg F, Kjerrulf M, Vidal A. Anti-inflammatory properties of the short-chain fatty acids acetate and propionate: A study with relevance to inflammatory bowel disease. World Journal of Gastroenterology : WJG 2007;13(20):2826-32. doi: 10.3748/wjg.v13.i20.2826.
  15. Kim I, Hans H. Role of probiotic therapy in IBD. Inflammatory Bowel Diseases 2008;14(11):1597-605. doi: doi:10.1002/ibd.20465.