Infections by pathogenic Staphylococcus aureus bacteria cause many tens of thousands of deaths every year, and the threat of antibiotic-resistant strains, including methicillin-resistant S. aureus (MRSA) is escalating. New research by National Institutes of Health (NIH) scientists now suggests how probiotic Bacillus bacteria can eliminate the reservoir of these potentially harmful bacteria that we can harbor in our noses and gut systems, by secreting a compound that blocks a key S. aureus signaling system known as quorum sensing.

“Probiotics frequently are recommended as dietary supplements to improve digestive health,” says  Anthony S. Fauci, M.D., director of the National Institutes of Allergy and Infectious Diseases (NIAID). “This is one of the first studies to describe precisely how they may work to provide health benefits. The possibility that oral Bacillus might be an effective alternative to antibiotic treatment for some conditions is scientifically intriguing and definitely worthy of further exploration.”

The NIH team, headed by Michael Otto, Ph.D., and working with scientists in Thailand at the Faculty of Medicine, Siriraj Hospital Mahidol University, and at Rajamangala University of Technology Srivijaya, report their research in Nature, in a paper titled, “Pathogen elimination by probiotic Bacillus via signaling interference.”

Probiotics are commonly claimed to have health benefits, and in particular, oral probiotics taken with food are thought to help prevent harmful bacteria from colonizing the gut. However, the NIH authors acknowledge, the mechanisms that might underpin these benefits are not well understood. “The mechanisms that have been implicated in this beneficial function of probiotic bacteria are mostly indirect, and include modulation of the immune system, enhancement of the intestinal epithelial barrier, or competition with pathogens for nutrient,” they write. “Whether there is direct interference between probiotic and pathogenic bacteria is less clear.” And while some probiotic strains can produce bacteriocin proteins that can kill related pathogenic bacteria in mice, this hasn’t been demonstrated in humans.

S. aureus is a common skin-colonizing bacterium, which can also live in the nose or gut without causing harm. However, when the skin barrier is broken or the immune system is compromised the organism can cause infections ranging from moderately severe skin infections, to fatal pneumonia and sepsis, the authors continue. One strategy to prevent these infections is to block S. aureus colonization, but some existing approaches to this inhibition are controversial because of the amount of antibiotics used, and because they only target the nose, and not the reservoir of bacteria in the gut. “Possibly, intestinal S. aureus colonization explains the failure of previous topical decolonization efforts aimed solely at the nose,” the researchers comment.

The NIH team hypothesized that the human gut microbiota might directly affect gut colonization by S. aureus. They focused on species of the bacterium Bacillus, which is commonly used as a constituent of probiotic formulae, and which is thought to reduce pathogen colonization. Bacillus species are commonly found in the soil, and generate spores that we eat with vegetables, and which develop into cells that can colonize the gut.  

For their study, the researchers first analyzed fecal samples from 200 volunteers in rural Thailand, for S. aureus and Bacillus species. This population of people was selected to rule out, as far as possible, the use of food sterilization procedures or antibiotics, which might otherwise influence the composition of probiotic bacteria in the gastrointestinal tracts of the participants.

The team found that 12.5% of the human subjects carried S. aureus in their intestines, and 13% had the bacteria in the nasal passages. The overall frequency of S. aureus colonization was far lower than the 20% (gut) and 40% (nasal), frequencies that are commonly recorded in adults in urban areas. Most “strikingly”, however, the team notes, while about 50% of people carried Bacillus species (most commonly B. subtilis, and primarily in the gut), when Bacillus was present, S. aureus was always absent, both in the gut and nose. “S. aureus was never detected in fecal samples when Bacillus species were present,” the authors write.

Hypothesizing that the Bacillus bacteria might produce a substance that directly and specifically inhibits intestinal colonization by S. aureus, the researchers turned to a mouse model to investigate further. Prompted by their previous findings on the S. aureus accessory gene regulator (Agr) quorum-sensing system, the team reasoned that Bacillus might secrete a substance that interferes with quorum-sensing signaling in S. aureus, and so prevent gut colonization. Quorum sensing is a bacterial signaling mechanism that senses the density of a bacterial population (the ‘quorum’) and controls cell adaptations to match. Different species of bacteria have different quorum-sensing signals and sensors, so it’s possible that a substance that inhibits quorum sensing in one bacterium may not affect another.

The team first demonstrated that Agr-based quorum sensing is essential for S. aureus intestinal colonization in a mouse model. They next isolated from different fecal Bacillus strains a secreted, enzyme-resistant cyclic lipopeptide, fengycin B, which directly inhibited S.aureus Agr and so blocked quorum sensing.  All of the more than 100 Bacillus isolates recovered from human feces efficiently inhibited the quorum-sensing system.

Encouragingly, feeding mice with B. subtilis spores to mirror probiotic consumption completely wiped out all S. aureus strains in the animals’ feces and intestines, whether or not the mice had been pretreated with antibiotics to eliminate existing microbiota. In contrast, feeding the animals with fengycin-deficient Bacillus had no inhibitory effect on S. aureus colonization. The team concluded that fengycin-mediated inhibition of quorum sensing was likely responsible for blocking S. aureus colonization in the Thai human volunteers.

“By demonstrating that quorum sensing is indispensable for S. aureus to colonize the intestine, and discovering that secreted Bacillus fengycin lipopeptides function as quorum-sensing blockers to achieve complete eradication of intestinal S. aureus, we provide evidence that strongly suggests that this pathogen-exclusion effect in humans is due to a widespread and efficient probiotic-mediated mechanism that inhibits pathogen quorum-sensing signaling,”  the authors conclude. “ … “In particular, our data underscore the often-debated probiotic value of B. subtilis.”

They suggest that the study results highlight new approaches to fighting antibiotic-resistant S. aureus. One possibility is that quorum-quenching fengycins—“which previously had only been known for their antifungal activity,” —could potentially be developed as a new, quorum-blocking strategy against the pathogenic S. aureus. Bacillus-containing probiotics could also be used as part of “simple and safe S. aureus decolonization strategies” that eradicate S. aureus from the nose and gastrointestinal tract. The team says this strategy has advantages over current approaches that rely on antibiotics, and which can only decolonize S. aureus in the nose. 

The NIH and Thai scientists plan to test whether a probiotic product that contains only B. subtilis can eliminate S. aureus in humans. “Ultimately, we hope to determine if a simple probiotic regimen can be used to reduce MRSA infection rates in hospitals,” Dr. Otto says.

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