Human Microbiome and Autoimmunity

By Suchitra Chari, MS

human-microbiomeThe human microbiome comprises of all the microorganisms and their genes present in the human body. This totals to around a trillion in number found in site specific places like the skin, mouth, nasal cavities, gut and uterus. When we use the term “microbe” in the body we are referring to bacteria, viruses, fungi, protozoa and other one celled eukaryotes. These microbial cells outnumber the human cells 10 to 1 and their collective genome is 150 times that of humans1. The largest population of these are found in the large and small intestines primarily due to their extensive surface area. There is a symbiotic relationship between these microbes and the host that has developed over thousands of years. They help us digest carbohydrates, synthesize vitamins, provide energy for our metabolism and overwhelm infectious diseases by acting as a first line of defence against potential pathogens or so called “germs”. In turn they depend on the host for nutrients and a nice place to live. Of all these microbes, bacteria are the ones found in most abundance and thus currently the most studied species.

Gut Microbiota:

The gut or the gastrointestinal tract is an essential organ in the body. Antonie van Leeuwenhoek was the first to discover microorganisms in the gastrointestinal tract. This was in 1683. Three centuries later in the early twentieth century the Russian Nobel Prize laureate Ilya Ilyich Mechnikov first realized the positive health effects of certain microorganisms in the gut. The term dysbiosis (also known as dysbacteriosis) was coined by him to describe aberrations in the microbial communities in the gut2.

How does the gut get these microbes? The infant gut is colonised by microbes starting from the mother’s womb. From the placenta to the birth canal to the mother’s breast milk the infant gets a steady dose of the maternal microbial innoculum. The microbiome more or less stabilises itself at three years of age when it represents an adult one. But throughout life, it continues to be an ever changing microbiome. The gut microbial community in the human body is by far the largest and the densest with the large intestine alone harbouring around 1 trillion cells per millimeter. The benefits offered by the gut microbiome are aplenty. It is said that while humans have only around 20 gut enzymes to break down carbohydrates, a single gut bacterium has around 200 odd enzymes. Thus they play a major role in human metabolism and also in drug metabolism and in protecting us against pathogens.

So, what is the link between the gut microbiome and the immune system?

The newborn’s gut microbiota is known to trigger the development and maturation of its immune system. This maturing immune system then relies on the presence of some of these early microbes, to distinguish “self” from “non self”. These initial microbes are the ones that shape our immune system. Once matured and when encountering a new microbe the immune system then taps into its “memory banks” to find out whether the new microbe that enters is a friend or a foe3.

It would then either coexist with the new microbe or launch an attack against it. This process happens till a mature microbiome has developed at around three years and continues even after that. Thus these synergestic and commensal microbiota in the mucosal layer act as a competitors against pathogens by occupying binding sites, restricting pathogenic bacteria from nutrients, and producing and stimulating the synthesis of antimicrobial agents. All these various benefits help us in establishing a strong immune system. On the other side, the microbiome has also been suggested to play an important role in triggering disease development through dysbiosis (dysbiosis happens due to consumption of antibiotics or in a bacterial infection).

In general, alterations in the gut microbiome have been implicated in several health conditions like obesity, diabetes, cardiovascular diseases, rheumatoid arthritis, inflammatory bowel disease, autism and even some forms of cancer. Among these, some conditions that have been linked to dysbiosis are inflammatory bowel disease, type 2 diabetes and obesity. Since, the gut hosts a second immune system in the body known as the enteric nervous system (ENS), most of these conditions that result from dysbiosis are called autoimmune diseases.

What is an autoimmune disease?

When a pathogen attacks the body, the immune system reacts by attacking it. In an ideal situation, the immune system should return to its normal state once the so called ‘germs’ have been warded off. When this doesn’t happen and the immune system is constantly in a state of ‘high alert’ or in other words treating even beneficial microbes, proteins, its own tissues and joints as enemies, we develop what is called an ‘autoimmune disease’. There are around 80 kinds of autoimmune diseases and the most common or prominent ones are psoriasis, lupus, type 1 diabetes, inflammatory bowel disease, multiple sclerosis and rheumatoid arthritis (RA).

What are these substances that cause this microbial imbalance?

The first and foremost substance that has been implied in reducing, removing or changing fundamental elements in the microbiome is antibiotics. While antibiotics have been a boon since the last century in saving millions of lives, it is being proposed that early-life use of antibiotics can cause later development of inflammatory disorders, including asthma, inflammatory bowel disease, colorectal cancer and childhood obesity. This teaches us a lesson that while we very much need these medicines, we should be cautious in using them. In developed countries, an increase in clean water and sanitation, a high rate of caesarean births and an increase in the use of antibacterial soaps have also affected the microbiome of these people. This can indirectly deplete the normal microbial innoculum that a newborn should get from its mother in these parts of the world. Thus it is believed that in developed countries generations after generations have been losing distinct colonies or species of microbes in the microbiome.

Antibiotics: Once considered a friend, now a foe? Relationship between antibiotics and autoimmune diseases:

Since its discovery, antibiotics have saved millions of people from life-threatening infections, childbirth-related maternal deaths, pre-term babies and lots of other deadly infections. An average child in the United States undergoes 10-20 courses of antibiotics till 18 years of age. A new line of thinking says that this common overuse of antibiotics actually messes with the development and healthy progression of the human microbiome. Antibiotics are consumed as medicines and as food (to animals to keep them healthy) and this routine use can lead to collateral damage to the microbial flora in 2 ways. One is by increasing global antibiotic resistance to serious infections and second by causing unintended death of non targeted bacteria.

What is antibiotic resistance? When humans do not consume the entire dose of antibiotics prescribed to them or when animals are given a sub lethal dose of antibiotics, certain bacteria tend to survive and become resistant to that particular antibiotic. Added to that is the problem that bacteria are remarkable in passing on this genetic information to other strains of bacteria thus increasing the number of antibiotic resistant bacteria. Also, antibiotics tend to kill off non targeted bacteria thus killing some good microbes in the process. All these cause antibiotic resistance.

There is a possibility that early antibiotic intervention in children leads to a disturbance in their microbiome thus causing a weak immune system. This could thus give rise to autoimmune diseases and allergies and this happens to be the case in many western countries. Current research in this field linking the human microbiome and autoimmune diseases will lead to better treatments and cures4.

Below we discuss a few of these autoimmune diseases and their connection with the human microbiome.

Gut bacteria and obesity:

New evidence thus states that gut bacteria alter the way we store fat, how we balance levels of glucose in the blood, and how we respond to hormones that make us feel hungry or full. You get the wrong mix of microbes at birth you set the stage for obesity and diabetes.

One of the first hints that gut microbes might play a role in obesity came from studies comparing intestinal bacteria of twins who were both obese and lean. The gist was that lean people have a huge variety of bacteria (in particular two dominant bacterial divisions Bacteroidetes and Firmicutes) compared to obese individuals who had a less diverse variety of bacteria. Further research was performed with so called “humanised” mice where identical baby mice were frown in a germ-free environment devoid of bacteria. Their guts were injected with bacteria from obese women and their lean twin sisters. The mice colonized with bacteria from the obese women grew fat and also had lesser microbes in their gut5. This proves that there is a definite correlation between gut bacteria and obesity.

A particular gut bacterium Akkermansia muciniphila that digests mucus is found at lower levels in obese humans and mice and those with type 2 diabetes. In fact it is 100 times lower in genetically and high-fat diet induced mice. This condition is reversed when the mice are fed either A. Muciniphila or an oligofructose prebiotic producing a dramatic increase in levels of A. Muciniphila. These mice lost weight and had a better ratio of fat to body mass, as well as reduced insulin resistance and a thicker layer of intestinal mucus. The increase in A. muciniphila led to increased intestinal levels of endocannabinoids (signalling molecules that help to control blood-glucose levels and maintain the gut’s defenses against harmful microbes). There seems to be communication between the bacterium and the cells of the intestinal lining and this aspect can put the bacterium to much use to treat disorders like obesity, diabetes and colitis in humans says Professor Patrice Cani, of the Catholic University of Leuven in Belgium who conducts this research6.

Gut bacteria and Type 1 Diabetes (T1D):

T1D is an autoimmune disease where the antibodies destroy the host’s insulin-producing beta cells of the pancreas thus causing insulin deficiency and increase in blood sugar. It is usually diagnosed in childhood or adolescence. Three main reasons have been proposed for the onset of type 1 diabetes. The first is dysbiotic gut microbiota, followed by genetic abnormalities in the regulation of mucosal immunity and increased impairment of the mucosal barrier (leaky gut). A leaky gut has its tight junctions between epithelial cells disrupted, thereby spilling some proteins into the blood stream. This in turn leads to an overstimulation of the immune system and potentially leading to auto immune destruction of islet cells. Studies done in healthy and patients with T1D revealed that children with T1D had a smaller amount of beneficial gut bacteria that was less stable and diverse compared to healthy children. This change was reversed when the blood sugar levels came back to normal clearly indicating a connection between the microbiome and T1D.

A very recent study was done in 33 infants who genetically predisposed to T1D to examine the relationship between the human gut microbiome and T1D7. Four of these infants developed the disease by the age of 3 and they also showed a decline in good bacteria one year before the onset of the disease. More research has to be done in this area to establish clear conclusions.

Gut bacteria and Rheumatoid Arthritis (RA):

Rheumatoid arthritis is an autoimmune disease in which the body’s immune system attacks its own joints considering them to be foreign objects. It typically strikes in young and middle-aged adults. It causes painfully stiff, swollen joints in the hands and feet and can also destroy bone and cartilage and damage organs like the heart, lungs and kidneys. The genetic association with this disease is even lesser than that of T1D. A connection between the gut bacteria and RA has been implicated for a long time now. Recent studies have revealed a remarkable association of a particular bacterium called Prevotella copri and RA8. Fecal samples of 114 residents of the New York City area were tested (this was a mixed population of healthy, patients who had just been diagnosed with RA but not treated yet for it (Group A) and those living with RA for a few years (Group B). The bacterium was present in 75% of the patients’ intestines in the group A compared to Group B (37% of patients had the bacterium) and in healthy patients (only 21% similar to the number found in developed countries). Later findings tested that this bacterium P.copri when present in the intestines trains the immune system to produce a type of cell called the Th17 cells that release molecules that cause inflammation and bone damage in arthritis. Although there is evidence that this bacterium and the disease occur together, other factors also influence RA like genetics and other environmental factors like smoking, hormones, aging and infections. To further elucidate this, one has to study the microbiomes of healthy individuals and monitor the course of change of gut bacteria and see who develops RA. Current RA drugs have a lot of serious side effects. Attacking the bacterium with probiotics full of good bacteria is a future possibility. There is also a link between the bacteria present in patients with peridontal disease and RA.

Gut bacteria in Inflammatory Bowel Disease (IBD):

There are two types of IBD, one is known as Crohn’s disease and the other is ulcerative colitis. The symptoms are diarrhoea, abdominal cramping and intestinal ulcers. Apart from genes that appear to predispose for IBD, scientists have also looked for environmental factors like diet and antibiotic use. One of the findings connects our very own gut microbiome to the disease. Let us look at Crohn’s disease in particular. Microbial dysbiosis is a characteristic of Crohn’s disease. Antibiotics given to patients for a gut infection (before being diagnosed with IBD) have a huge impact on the microbial population. This change can cause an inflammation of gut cells. Whether, it is this shift in microbial species that causes IBD or vice versa is still to be determined.

A couple of studies that correlate the gut microbiome and IBD are presented here.

A group headed by Ramnik Xavier, a gastroenterologist at Harvard Medical school in Boston has done a study with kids diagnosed with Crohn’s disease and those without the disease but having noninflammatory abdominal symptoms, such as bloating and diarrhoea9. Fecal samples and biopsies of the lower part of the small intestine and rectum revealed that harmful microbial species were more abundant in patients with the disease and beneficial bacteria like Bacteroidales and Clostridiales were lower.

Dan Knights and his international team of researchers at the University of Minnesota have shown that people who inherit certain genes are predisposed to have an imbalanced intestinal bacteria, which in turn causes IBD10. Samples of DNA taken from each human subject with IBD and their intestinal bacteria for a two year period revealed a connection between the two DNAs. They had more harmful bacteria and less beneficial ones. There are other factors like age, gender and medication that could affect this population. Antibiotic use worsened this microbial imbalance.

Gut Microbiome and Multiple Sclerosis:

Another very serious autoimmune disease is one called Multiple Sclerosis or MS. The body’s immune system attacks the myelin sheath that insulates the nerve fibres as well as the nerve fibres themselves, thus damaging it. This damaged myelin forms scar tissues (sclerosis) thus impeding nerve impulses travelling to and from the brain and spinal cord. The exact protein that the immune system targets is still a mystery and hence the disease is treated more like an immune-mediated one rather that an autoimmune disease. Factors that have been connected with MS are geographical location, vitamin D, smoking, increased salt intake, certain viruses and genetics. We are here to talk about the connection between the microbiome and MS.

A coalition of four U.S. research centers called the MS Microbiome Consortium has recently been formed to investigate the role of gut microbes in the disease. Many presentations have been made so far with up to date information about this research.

A study from Brigham and Women’s Hospital (BWH), reported a single-celled organism called methanobrevibacteriaceae that activates the immune system is enriched in the gastrointestinal tracts of MS patients whereas bacteria that suppress immune activity are depleted11. A collaboration of 10 academic researcher centers across the U.S. and Canada reported significantly altered gut flora in pediatric MS patients.

Sushrut Jangi, a staff physician at Beth Israel Deaconess Medical Center in Boston who co-authored the BWH study, thinks that regional dietary influences might even be at play. “The biomes of people living in different areas and who consume Western versus non-Western diets are demonstratively different,” he says. “People who emigrate from non-Western countries, including India, where MS rates are low, consequently develop a high risk of disease in the U.S. One idea to explain this is that the biome may shift from an Indian biome to an American biome,” although there is not yet data to support this theory.

An MS drug, glatiramer acetate altered the gut microbiota in MS patients compared to untreated subjects. Does it alter gut flora thus suppressing abnormal immune activity and hence MS activity? Can the microbiome be manipulated to benefit MS patients? These and many other questions exist. In any case, the gut flora is definitely a big research area going forward in the MS field and it is important to keep going.

Microbiome-based applications to promote human health and treat disease:

The microbiome is a dynamic, ever changing community. It is this aspect of it that can be taken advantage of while developing treatments for diseases. These treatments can affect the microbial community found in a diseased individual to one that is found in a healthy one by altering the content or number of microbes in a particular site.

One very important microbiome-based application is something known as bacteriotherapy or fecal transplant. These have been done for patients affected by the bacterium Clostridium difficile which causes severe diarrhoea and dehydration of the patients. This transplant flushes out the harmful bacteria and replaces the gut with the good ones. This healthy microbiome can now resist attack by the same bacterium.

The other application is in the field of cancer. Doctors are collecting and storing cancer patients’ gut microbiomes in the form of stool before they undergo radiation and chemotherapy. These standard cancer treatments tend to destroy a lot of good cells and microbes along with the cancerous ones. Re-inoculating the patient with the stored microbiome will help lessen recovery time.

Other methods where the changeable properties of the microbiome are taken advantage of, is in vaccine development, pharmaceuticals and in dietary supplements like probiotics and prebiotics. Probiotics are “live microorganisms which when administered in adequate amount confer a health benefit on the host” (as defined by the UN’s Food and Agriculture Organization). A prebiotic is “a selectively fermented ingredient which results in specific changes in the composition and/or activity of the gastrointestinal microbiota, thus conferring health benefits to the host” (defined by the International Scientific Association for Probiotics and Prebiotics). Science based studies on probiotics and prebiotics is on the rise. Treatments using the microbiome seem to be the solution going forward at least in autoimmune diseases, and hopefully we will cure if not alleviate the symptoms of these patients.


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6. Amandine Everard, Clara Belzer, Lucie Geurts, Janneke P. Ouwerkerk, Céline Druart, Laure B. Bindels, Yves Guiot, Muriel Derrien, Giulio G. Muccioli, Nathalie M. Delzenne, Willem M. de Vos, and Patrice D. Cani Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity. Proceedings of the National Academy of Sciences 110 (22), 9066-9071)

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11. Sushrut Jhangi, Roopali Gandhi, Bonnie Glanz, Sandra Cook, Parham Nejad, Doyle Ward, Ning Li, Georg Gerber, Lynn Bry and Howard Weiner Increased Archaea Species and Changes with Therapy in Gut Microbiome of Multiple Sclerosis Subjects Neurology April 8, 2014 vol. 82 no. 10 Supplement S24.001

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