Pathobionts: The tale of an opportunist

By Brooke Napier

Our gastrointestinal (GI) tract harbors a rich ecological niche of an extraordinary amount and variety of microbes. Most of these microbes we keep around because they provide us nutritional, metabolic, or immunological benefits. How our body keeps in constant communication with these microbes to “keep-it-down-in-there” is relatively unknown, however we do know that sometimes these microbes can turn to the dark side.Two-face, yall. Get it?

When the rough gets going in your GI tract, silent microbes can turn virulent and cause disease. These 2-faced-microbial species are known as pathobionts (patho-, disease causing; biont-, living organism).

But how do pathobionts know when it’s a good time to flourish, and when it’s a good time to stay quiet?

The key is homeostasis. The dysregulation of your immune system can lead to multiple inflammatory human diseases such as autoimmunity, allergy, and cancer – so what happens when there is dysregulation in your GI tract?

As mentioned, the GI tract is the interface between you and your microbiome, this junction between host and microbe is highly regulated by your immune system and by the microorganisms that are colonizing your gut. You can imagine there is constant contact between the two sides – like Russia and America during the Cold War, there is a very delicate invisible boundary that either side cannot cross or there could be massive destruction.

Interestingly, a survival strategy for your healthy microbiome is to suppress, or constrain, pathobionts. Your microbiome cannot thrive in an environment of destruction, it cannot afford for its environment to become obliterated; therefore, in effort to maintain homeostasis with the GI tract, your microbiota will communicate with the pathobionts and tell them to keep quiet and under control.

Side note: Relatively little is known about the communication between healthy microbiota and pathobionts, for an interesting (but not free) review go here.

Luckily the wonders of science have provided insight into this very testy relationship. Recently, it’s been seen that when there is disruption of the healthy microbiota, pathobionts can cause disease. I use “disruption”, a very non-specific word, on purpose because there are many causes of dysregulation in the GI tract, however in the lab (and sometimes in humans) you can induce “disruption” by the addition of antibiotics. Antibiotics can clear out the microbiota, no longer providing the proper control over pathobionts, and allowing pathobionts to cause disease.  

What disease is caused by pathobionts, and why are we so worried about this?

Ayres et al. found that disruption of the microbiota by antibiotics induces a lethal sepsis-like disease upon intestinal injury that they found was caused by an increase of multi-drug resistant E. coli, a pathobiont!

Break-it-down:

What is their model?

1) Treat mice with antibiotics (AVNM – ampicillin, vancomycin, neomycin & metronidazole).

2) Next, induce intestinal injury with the addition of dextran sulfate sodium (DSS). If you add DSS to the drinking water of mice you can induce acute colitis within the mouse GI tract. 

Mouse small intestines, 4 days after treatment.

3) Look to see if antibiotic-induced disruption of the microbiota influences the DSS-induced disease in the mice.

What did they see?

Mice with DSS + antibiotics died faster than mice treated with DSS alone or antibiotics alone. They looked and found that the mice treated with DSS, which usually causes colitis-like disease alone, plus the antibiotics did not have signs of colitis – rather they had signs of sepsis (bleeding in small intestine, organ damage & hypothermia).

Fire, yall.

Sepsis is usually in response to an elevated level of microbes in the blood stream, urine, lungs, skin, or other tissues. Generally, it is an over-reaction of the immune system to a pathogen that causes a whole-body inflammatory state (remember septic-shock?) = not pleasant.

And you guessed it; it was the expansion of the multi-drug resistant E. coli pathobiont in the extraintestinal tissues of mice that caused sepsis. In fact, this E. coli was isolated from the liver, lung, spleen, and kidney of mice treated with antibiotics and DSS.

Like most pathobionts, this E. coli species was found in untreated mice as well, but in very low doses because itwas unable to overcome the silencing of the microbiome.

What mediates this switch from silent to pathogenic in this E. coli strain?

A key component of the immune response happens to be this lab’s specialty, the inflammasome. Inflammasomes are multiprotein complexes that detect infection in the cytosol (intracellular milieu of host cells, or cytoplasm) and activate proinflammatory cytokines (IL-1B and IL-18) to induce an inflammatory response to infection. To clear infection you need to mount a healthy inflammatory response, therefore these multiprotein complexes are very important in protecting against disease.

However, recent publications have suggested that inflammasomes serve a protective role in regulating the composition of the microbiome. Additionally, excessive activation of the inflammasome = excessive inflammation = bad.  

Ah HA! So, could inflammasome activation be involved in response to disruption in the microbiome of the GI tract? And could this mediate the sepsis-like disease caused by an influx of pathogenic E. coli?

Indeed! They found the Naip5-Nlrc4 inflammasome was critical for mediation of the sepsis-like disease. When they treated Nlrc4/Naip5 knock-out mice with antibiotics and then DSS there was no longer massive signs of sepsis.

A) Survival of mice treated with antibiotics and DSS with and without the Nlrc4/Naip4 inflammasome, B) Colon pictures, and C) more intestine pictures.

Naip5-Nlrc4 inflammasome detects bacterial flagellin and the E. coli strain responsible for causing disease encodes a functional flagellin. Therefore, if you delete the flagellin encoding gene than the E. coli cannot make it, the inflammasome cannot detect it, and it should not cause disease – in spite of there being a high number of E. coli.

They were right! The flagellin was the key to Mordor. And if you made it this far in the post, you were treated with my allusion to the Lord of the Rings.

Ok, so how does this influence human medicine?

Good question, this model of treating with antibiotics plus DSS (or a colitis-inducing toxin) resembles the problem in human patients undergoing combination therapies involving antibiotics and cytotoxic treatments that damage the gut epithelium (chemotherapy, for example).

A key to this study was that a very specific multi-drug resistant E. coli pathobiont exists in the normal flora, but expands dramatically under these conditions inducing a highly inflammatory sepsis-like disease.

In attempt to circumvent the further disruption of the microbiome, the authors suggest that the inflammasome may be a good therapeutic target for patients showing pathology from antibiotic resistant pathobionts.

Anyone interested in funding my anti-inflammasome drug start up company?

I’ll give you 5%. 

Ayres JS, Trinidad NJ, & Vance RE (2012). Lethal inflammasome activation by a multidrug-resistant pathobiont upon antibiotic disruption of the microbiota. Nature medicine, 18 (5), 799-806 PMID: 22522562

Round JL, & Mazmanian SK (2009). The gut microbiota shapes intestinal immune responses during health and disease. Nature reviews. Immunology, 9 (5), 313-23 PMID: 19343057

Comments

[Sarah]

"if you delete the flagellin encoding gene than the E. coli cannot make it, the inflammasome cannot detect it, and it should not cause disease – in spite of there being a high number of E. coli." --> that's amazing!

Is there any idea about how our bodies developed in such a way that they could take advantage of that in "the gut"?

[Sisu]

Allusion/Illusion
(You can delete this comment)

Great post, though, and a fascinating subject; I'd love to see hwo this ties in to allergy.

[Brooke]

Sarah - sorry, I don't understand. Take advantage of what in the gut?

Sisu - thank you! and thank you for reading the whole article :)