“Harmless” Bacteria Cause Autoimmune Disease

“Harmless” Bacteria Cause Autoimmune Disease


Asu Erden

We all know that pathogenic bacteria can cause disease, but new research shows that commensal members of the microbiome have their own devious ways of harming their hosts. Read more…


Organs influenced by immune dynamics in the gut.(1)









Factors contributing to autoimmune disease development. (2)

The human body is the site of a flagrant yet silent invasion. We host as many foreign organisms in and on us as we have cells that make up our own body. A particular population of these colonizers has gathered much interest: the inhabitants of the gastro-intestinal tract, also known as the gut microbiome. The bacteria and fungi that colonize this space have co-evolved with humans for millions of years. Most of them are commensal, protecting us against pathogenic microorganisms and helping us carry out key metabolic functions. “They dictate our nutritional intake but also our immunological set points and whether or not we’re able to handle inflammation,” said Gregg Silverman, an immunologist from New York University.Gut microbes can make proteins or stretches of peptides very close in sequence to our own. This molecular mimicry is usually harmless, except when it causes immune cells to react against our native proteins. This can lead to a number of autoimmune disorders such as antiphospholipid syndrome (APS), a poorly studied disease characterized by blood clotting in veins and arteries as well as miscarriage and stillbirth. Patients suffering from this disorder have high levels of serum antibodies against a protein called β2 glycoprotein 1 (β2GP-1) in particular, as well as against phospholipids that make up cell membranes.

Now Martin Kriegel and William Ruff from Yale University have discovered that two commensal gut microbes, Roseburia intestinalis and Klebsiella pneumoniae, make proteins mimicking parts of β2GP-1, resulting in the breakdown of immune tolerance and contributing to APS development (1,2).

Rounding up the Unusual Suspects

“The gut is a huge reservoir of antigens that can lead to various cross-reactive responses not only in APS but we believe maybe in rheumatoid arthritis, multiple sclerosis, type 1 diabetes, and lupus,” said Ruff.

While a popular idea in the microbiome field, the mechanism of molecular mimicry as a cause for immune cross-reactivity remains poorly characterized. The best-known example is that of Guillain-Barré syndrome, an autoimmune disease leading to paralysis. A decade ago, researchers discovered thatCampylobacter jejuni molecules drive immune cross-reactivity with lipids (i.e., gangliosides) in the brain, eventually causing the disease (3).

So far, the role of molecular mimicry in driving other autoimmune diseases remains largely hypothetical. “What [Kriegel] is talking about is actually the next level where it isn’t necessarily purely pathogenic bacteria that trigger these responses,” said Silverman, who was not involved in the new study.

“I think that [this idea] is a potential paradigm shift! If we can show that commensal cross-reactivity is not only occurring but that it’s actually driving a physiological response, that’s a completely new way of thinking about host–microbiome interactions,” said Ruff.

Two High-maintenance Culprits

To look for a possible role for gut bacteria in APS etiology, Kriegel’s group selectively depleted bacteria in the gut using antibiotics such as neomycin, vancomycin, metronidazole, and ampicillin in a mouse model of APS (1,4). They found that vancomycin and metronidazole prevented disease development, indicating that Gram-positive bacteria are possible culprits in APS (2,4).

APS development requires auto-antibodies against a specific region of β2GP-1 called domain 1, so Kriegel’s team next searched for gut bacterial proteins with stretches of sequence mimicking this domain. Using BLAST alignment tools, Ruff found several proteins from both Gram-negative and Gram-positive bacteria living in the gut with homology to domain 1 of β2GP-1. To narrow down the candidates, he selected proteins that can be recognized by B and T cells, suggesting a potential for autoimmunity. In the end, “it came down to a common lower intestinal or colon mucosal resident called Roseburia intestinalisand a pathobiont, Klebsiella pneumoniae,” said Ruff. 16S ribosomal RNA sequencing of bacteria isolated from fecal samples confirmed the presence of both R. intestinalis and K. pneumoniae in APS patients.

R. intestinalis and K. pneumoniae are anaerobic bacteria, making them inherently difficult to culture. With the help of Andrew Goodman from Yale University, who specializes in microbial pathogenesis, Kriegel’s team developed a system of anaerobic chambers with atmosphere control and glove-free handling in the lab. As a result, Ruff was able to grow these high-maintenance microbes and isolate proteins that potentially mimic domain 1 of β2GP-1. He is currently testing whether host antibodies can bind these bacterial proteins, using blood and fecal samples from APS patients.

To uncover the mechanism for creating auto-antibodies against these protein mimics, the researchers decided to characterize the T cells of APS patients. They started by gathering information about the dominant epitopes the T cell receptors bind. “This is not an easy task,” said Kriegel.

According to Ruff, the key is to sort out antigen-specific single cells and determine their immunological profiles. Building on prior work (5), the team is now developing a functional tetramer—a construct comprising multiple molecules that can bind specific antigens—that binds to one of the dominant antigens in APS patients. “We are close, but validation studies are ongoing,” said Ruff. Developing this tetramer will allow the team to Identify T cells that are specific to R. intestinalis andK. pneumoniae in APS patient samples and provide the first mechanistic proof that molecular mimicry by commensal bacteria can lead to APS development.

“Being able to have such a clear paradigm and study a relatively simple molecular mechanism can be very informative not only for patients but also for the field in general,” said Silverman.

Beyond the Microbiome

In addition to uncovering the mechanisms responsible for cross-reactivity, Kriegel’s team is also interested in how host genetics can influence the microbial niche in our gut. “There is a certain autoimmune single nucleotide polymorphism (SNP) in an important gene called PTPN22,” said Kriegel. “Certain Clostridium species are depleted in subjects carrying this SNP. And this research is evolving! But that’s what we are also excited about, how this autoimmune SNP may alter the microbiota and then immune function.”

The team is also looking at the effect of diet—resistant starches that escape digestion in particular—on curtailing breaks in tolerance. They believe that altering the diet may limit the inflammation seen in the guts of mice with APS. Resistant starches increase short chain fatty acids, which have anti-inflammatory properties, so Kriegel’s team plans to assess the effect of diets with different starch profiles on disease outcome.

Beyond the gut lies a universe of bacteria colonizing every surface of the human body, all with the potential to induce breaks in tolerance through molecular mimicry. “We believe that there are roles for all of these niches in immunomodulation,” noted Ruff.

Disclaimer: Asu Erden is currently an immunology PhD student at Yale University.


1 Kriegel, MA. “Self or non-self? The multifaceted role of the microbiota in immune- mediated diseases.” Clin Immunol. 2015 Aug;159(2):119-21. doi: 10.1016/j.clim.2015.05.010.

2 Ruff, WE & Kriegel, MA. “Autoimmune host-microbiota interactions at barrier sites and beyond.” Trends Mol Med. 2015 Apr;21(4):233-44. doi: 10.1016/j.molmed.2015.02.006.

3 Goodyear, CS et al. “Monoclonal antibodies raised against Guillain-Barré syndrome– associated Campylobacter jejuni lipopolysaccharides react with neuronal gangliosides and paralyze muscle-nerve preparations.” J Clin Invest. 1999 Sep;104(6):697-708

4 Ruff WE, Vieira SM, Kriegel MA. “The role of the gut microbiota in the pathogenesis of antiphospholipid syndrome.” Curr Rheumatol Rep. 2015 Jan;17(1):472. doi: 10.1007/s11926-014-0472-1

5 Cao, Y et al. “Functional inflammatory profiles distinguish myelin-reactive T cells from patients with multiple sclerosis.”Sci Transl Med. 2015 May 13;7(287):287ra74. doi: 10.1126/scitranslmed.aaa8038

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