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The Gut Microbiome and Its Role in Health and Disease

by Dr. Jaclynn Moskow

Intestinal bacteria, Gut microbiome helps control intestinal digestion and the immune system, Probiotics are beneficial bacteria used to help the growth of healthy gut flora
The gut microbiome helps control intestinal digestion and the immune system.

 

It is difficult to overstate the importance and complexity of the gut microbiome. Humans live in symbiosis with hundreds (and possibly thousands) of species of bacteria (1). Additionally, archaea, fungi, viruses, and protozoa are also present in our gut. In fact, only about 10% of the cells within our bodies are “ours” and contain human DNA. The remaining 90% of cells we carry with us are microbial. The exact makeup of the gut microbiome varies greatly from individual to individual and is influenced by variables that include diet, exercise, medication use, sleep, stress, hormonal changes, aging, and disease. Associations have been found between the composition of the microbiome and obesity, diabetes, hypertension, heart disease, autoimmune disorders, allergies, mood disorders, and more.

 

Why Do We Have a Gut Microbiome?

The bacteria in our gut participate in the digestion, absorption, and metabolism of proteins and carbohydrates and in the breakdown of endogenous intestinal mucus. They also synthesize vitamin K2 and various B group vitamins; and they influence the development of gut-associated lymphoid tissues and the development of cells of the immune system (2), and serve to limit the colonization of pathogenic bacteria. The majority of these bacteria are anaerobic. Common genera include Escherichia, Bifidobacterium, Lactobacillus, and Enterococcus.

 

The Gut Microbiome and COVID-19

A recent study examined the connection between the gut microbiome and COVID-19. Researchers found that patients hospitalized for COVID-19 had an increase in certain bacterial species and a decrease in others when compared to a control group, even after antibiotic use was accounted for (19). They found a negative correlation between disease severity and concentrations of Faecalibacterium prausnitzii and Eubacterium rectale. Patients were monitored for 30 days post-recovery, and the observed changes persisted. The researchers postulated that these changes may contribute to the persistence of symptoms and multi-system inflammation that is sometimes seen with patients who have recovered from COVID-19.

 

Gut flora vector illustration. Flat tiny gastrointestinal microbe person concept. Abstract digestive stomach living organisms for healthy life. Lactobacilli, coli and intestinal system environment.

 

The Gut Microbiome and Obesity

In recent years, many studies have examined associations between the gut microbiome and obesity. When germ-free mice are colonized with gut bacteria from obese mice, they gain weight; but when they are colonized with gut bacteria from lean mice, they do not gain weight (3). Mice also gain weight when they are colonized with bacteria from obese humans. In a discordant twin study, colonization from obese twins caused mice to gain weight while colonization from their lean siblings did not (4). Some believe the ratio of Bacteroidetes to Firmicutes may play a significant role in obesity. One study found that as obese individuals lose weight, the concentration of Bacteroidetes increases (5). Furthermore, genetically obese mice contain a higher proportion of Firmicutes than thin mice consuming the same diet, and thin mice contain more Bacteroidetes than obese mice consuming the same diet (6). When researchers employed machine learning to study this topic, they concluded that the association between the Bacteroidetes / Firmicutes ratio and obesity is relatively weak and that existing studies lack significant sample sizes (7). The science is far from settled.

 

The Gut Microbiome and Diabetes 

Studies have also investigated the link between the gut microbiome and diabetes. Some speculate that in individuals who are genetically susceptible to type 1 diabetes, it is ultimately a shift in the gut microbiome that triggers the onset (8).  The gut microbiome of children with type 1 diabetes has been found to be less diverse than that of children without the disease (9). A recent review of 42 studies that examined the gut microbiome and type 2 diabetes found Bifidobacterium, Bacteroides, Faecalibacterium, Akkermansia, and Roseburia to be negatively associated with type 2 diabetes; and Ruminococcus, Fusobacterium, and Blautia to be positively associated (10). Other work has shown that when individuals with metabolic syndrome were given fecal transplants from healthy donors, insulin-resistance improved (11).

 

The Gut Microbiome, Hypertension, and Cardiovascular Disease

The ratio of Bacteroidetes to Firmicutes has also been implicated in hypertension. Consuming milk fermented with Lactobacilli can lower blood pressure in some cases, and Lactobacilli produce peptides that can inhibit ACE1 (12).  The same bacterial species found within the atherosclerotic lesions of individuals with cardiovascular disease are found in their gut (13). Additionally, Akkermansia muciniphila may have a cardioprotective effect. Researchers observed that when mice were fed a Western diet, they experienced a decrease in Akkermansia muciniphila and an increase in atherosclerotic lesions. When these same mice were recolonized with Akkermansia muciniphila, a reversal in atherosclerotic lesions was observed (14). 

 

The Gut Microbiome, Autoimmune Disorders, and Allergies

Components of the gut microbiome may be involved in eliciting or quelling immune responses that lead to the development of autoimmune disorders and allergies. Antibodies directed against a yeast species, Saccharomyces cerevisiae,  have been found in patients with rheumatoid arthritis, systemic lupus erythematosus, antiphospholipid syndrome, and Crohn’s Disease (15). Individuals with these conditions show an increase in the numbers of certain bacterial species and a decrease in other species –  as do individuals with multiple sclerosis, Sjögren’s syndrome, and celiac disease. The ratio of Clostridium difficile to Bifidobacterium in infants has been associated with food and aero-allergies, and high levels of fecal Escherichia coli in infants are associated with IgE-mediated eczema (16).

 

The Gut Microbiome and Neuropsychiatric Disorders

The central nervous system and enteric nervous system (together known as the gut-brain axis) are both influenced by the gut microbiome. Bacteria in the gut can directly secrete neurotransmitters, including serotonin, dopamine, norepinephrine, GABA, and histamine. Several studies have shown that patients with bipolar and major depressive disorder have an increase in Actinobacteria and Enterobacteriaceae, and a decrease in Faecalibacterium (17). Mice treated with Lactobacillus rhamnosus have reduced anxiety/depression-like behavior and altered expression of GABA receptors (18). Differences in microbiome composition have also been noted in patients with schizophrenia, Parkinson’s disease, and an autism spectrum disorder.

 

Fecal microbiota transplant (FMT) stool transferring bacteria microbes
Fecal microbiota transplantation (FMT)

 

Fecal Microbiota Transplantation and Clostridium Difficile Colitis

Fecal microbiota transplantation (FMT) is currently being used as a treatment for Clostridium difficile colitis. In fact, FMT is more effective than vancomycin at treating recurrent Clostridium difficile colitis. Most commonly, FMT is performed via colonoscopy. Nasoduodenal tubes, nasogastric tubes, and enemas can also be used. FMT made headlines in 2019 when a transplant recipient died, and several others became seriously ill, after becoming colonized with multi-drug resistant Escherichia coli. This led the FDA to recommend new safety measures for FMTs, including screening donors for risk factors associated with carrying multi-drug-resistant organisms and testing all donor stools for such organisms.

 

Optimizing the Microbiome

In many regards, studying the gut microbiome often leads to more questions than answers. When a change in bacterial levels is observed in a disease state, it is sometimes difficult to know whether that change contributed to the disease state or merely resulted from it. Anyone who seeks to convince you that they know the perfect solution to optimizing gut health is misleading you. While a host of food products and health supplements are touted to enhance the gut microbiome, in most cases the details of this “enhancement” are not defined. As additional studies are conducted, we will gain a better understanding of this vast topic and will likely see an increase in the utilization of fecal transplants in treating various diseases.

 

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References

(1) Almeida A, Mitchell AL, Boland M, et al. A new genomic blueprint of the human gut microbiota. Nature. 2019 Apr;568(7753):499-504. Available: 10.1038/s41586-019-0965-1.

(2) Wu HJ, Wu E. The role of gut microbiota in immune homeostasis and autoimmunity. Gut Microbes. 2012 Jan-Feb;3(1):4-14. Available: 10.4161/gmic.19320.

(3) Turnbaugh PJ, Ley RE, Mahowald MA, et al. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 2006 Dec 21;444(7122):1027-31. Available: 10.1038/nature05414. 

(4) Ridaura VK, Faith JJ, Rey FE, et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science. 2013 Sep 6;341(6150):1241214. Available: 10.1126/science.1241214.

(5) Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Microbial ecology: human gut microbes associated with obesity. Nature. 2006 Dec 21;444(7122):1022-3. Available: 10.1038/4441022a.

(6) Ley RE, Bäckhed F, Turnbaugh P, et al. Obesity alters gut microbial ecology. Proc Natl Acad Sci U S A. 2005 Aug 2;102(31):11070-5. Available: 10.1073/pnas.0504978102.

(7) Sze MA, Schloss PD. Looking for a Signal in the Noise: Revisiting Obesity and the Microbiome. mBio. 2016 Aug 23;7(4):e01018-16. Available: 10.1128/mBio.01018-16.

(8) Zheng P, Li Z, Zhou Z. Gut microbiome in type 1 diabetes: A comprehensive review. Diabetes Metab Res Rev. 2018 Oct;34(7):e3043. Available: 10.1002/dmrr.3043.

(9) Giongo A, Gano KA, Crabb DB, et al. Toward defining the autoimmune microbiome for type 1 diabetes. ISME J. 2011 Jan;5(1):82-91. Available: 10.1038/ismej.2010.92.

(10) Gurung M, Li Z, You H, et al. Role of gut microbiota in type 2 diabetes pathophysiology. EBioMedicine. 2020 Jan;51:102590. Available: 10.1016/j.ebiom.2019.11.051.

(11) Vrieze A, Van Nood E, Holleman F, et al. Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome. Gastroenterology. 2012 Oct;143(4):913-6.e7. Available: 10.1053/j.gastro.2012.06.031.

(12) Jose PA, Raj D. Gut microbiota in hypertension. Curr Opin Nephrol Hypertens. 2015 Sep;24(5):403-9. Available: 10.1097/MNH.0000000000000149.

(13) Tang WH, Kitai T, Hazen SL. Gut Microbiota in Cardiovascular Health and Disease. Circ Res. 2017 Mar 31;120(7):1183-1196. Available: 10.1161/CIRCRESAHA.117.309715.

(14) Li J, Lin S, Vanhoutte PM, et al. Akkermansia Muciniphila Protects Against Atherosclerosis by Preventing Metabolic Endotoxemia-Induced Inflammation in Apoe-/- Mice. Circulation. 2016 Jun 14;133(24):2434-46. Available: 10.1161/CIRCULATIONAHA.115.019645.

(15) De Luca F, Shoenfeld Y. The microbiome in autoimmune diseases. Clin Exp Immunol. 2019 Jan;195(1):74-85. Available: 10.1111/cei.13158.

(16) Pascal M, Perez-Gordo M, Caballero T, et al. Microbiome and Allergic Diseases. Front Immunol. 2018 Jul 17;9:1584. Available: 10.3389/fimmu.2018.01584.

(17) Huang TT, Lai JB, Du YL, et al. Current Understanding of Gut Microbiota in Mood Disorders: An Update of Human Studies. Front Genet. 2019 Feb 19;10:98. Available: 10.3389/fgene.2019.00098.

(18) Bravo JA, Forsythe P, Chew MV, et al. Ingestion of Lactobacillus strain regulates emotional behavior and central GABA receptor expression in a mouse via the vagus nerve. Proc Natl Acad Sci U S A. 2011 Sep 20;108(38):16050-5. Available: 10.1073/pnas.1102999108.

(19) Yeoh YK, Zuo T, Lui GC, et al. Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19. Gut. 2021 Jan 11:gutjnl-2020-323020. Available: 10.1136/gutjnl-2020-323020.

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