Microbes Need Care in the ICU

Guest BloggerMicrobiome Environment


While often life-saving, hospitals can be dangerous to your health. Exposed to infections, lack of sleep and poor nutrition, patients may spiral down into the intensive care unit (ICU) where two critical illnesses are common: sepsis and acute respiratory failure.

A role for microbes

Microbes are emerging as key players in the genesis, advance and ultimately, the aftermath of critical hospital illnesses. A healthy microbiome is easily and rapidly disturbed in the ICU.

Blame for this dysbiosis is shared:

Antibiotics (routine in hospitals), poor nutrition, drugs, new portals created by catheters and tubes, and pathogens spread from workers and surfaces are all at fault in the ICU.

All too quickly, dysbiosis can lead to life-threatening conditions including sepsis and acute respiratory disorders (ARDS).

One prime and prevalent example is the Clostridium difficile pathogen. Once contracted, patients are at 70% increased risk for re-hospitalization with sepsis. Fecal microbial transplantation is highly effective in treating C. Difficile infection.

Many studies show clinical benefit for probiotic and synbiotic use. Strengthening and nourishing the gut epithelial barrier as well as boosting immune function are the modes of action. Gut microbes ferment dietary fiber into short-chain fatty acids (SCFA); one of these called butyrate preserves gut integrity. But during dysbiosis, these benefits are lost and pathogens cause dysregulated inflammatory responses, immune exhaustion, end-organ damage, and can invade the critically-ill patient to cause sepsis.

Unfortunately, current technique for isolating cultures can take 3 days to identify the pathogen. Broad spectrum antibiotics are often used leading to unnecessary toxicity and antibiotic resistance. Maybe worse, these antibiotics kill indiscriminately, wiping out colonies of good bacteria. Newer DNA sequencing should make targeted treatment more likely.

A new paper reviewed 51 studies in animal models and pediatric and adult critically-ill patients. Data show that probiotics are generally safe and even effective in several critical care settings.

Microbiome therapies

Therapies include fecal microbiota transplantation, genetic engineering of modified strains to outcompete pathogens, selective nutrient or prebiotic administration, and engineered bacteriophages. These may alter the course of the illness. Potential solutions include targeted inhibition of enzymes, use of bacteriocins as antibiotics and analogs to emulate beneficial actions of microbiota.

The comprehensive paper summarizes support for microbiome studies in sepsis and ARDS.


“…available research highlights a pattern of intestinal diversity loss with abundance of pathogens in septic adults, indicates different mechanisms of dysbiosis for sepsis subtypes in neonates, and provides a concerning signal for the effects of early life antibiotics. “


“…available evidence highlights… progressive diversity reduction in the airspace, and nutrient-related bacterial proliferation and propagation of inflammation.”

The authors consider challenges and opportunities as well as a roadmap for future microbiome research in critical care. They are optimistic.

“We can envision a time in the not-too-distant future when the microbiome will be viewed as yet another organ system of the critically-ill patient, requiring special attention and plan of care during our daily ICU rounds.”