The microbes inside our bodies not only help break down food but also impact our health. Yet their precise influence is not always understood, especially in the presence of prescription drugs. Researchers at Princeton University Department of Chemistry have now reported how one of the most abundant gut bacteria, Bacteroides dorei, responds to tetracyclines, a class of commonly prescribed antibiotics.
Using a technology known as UPLC-MS-guided high-throughput elicitor screening (HiTES), Mohammad R. Seyedsayamdost, PhD, and colleagues, examined how the metabolome of this commensal bacterium responds to hundreds of FDA-approved drug molecules. The team’s findings indicate how newly characterized signals released by the bacterium in response to tetracycline antibiotics could aid the host’s immune response, inhibit pathogens, and restructure the gut microbiome.
“We previously showed that exogenous molecules can trigger production of otherwise ‘hidden’ metabolites in marine- and soil-dwelling microbes,” commented Seyedsayamdost, who is corresponding author of the researchers’ study in ACS Central Science. “Our goal here was to extend this analysis to human microbiota and examine their responses to FDA-approved drugs.” Reporting on their results in a paper titled “Tetracycline Antibiotics Induce Biosynthesis of Pro-Inflammatory Metabolites in the Immunobiotic Bacteroides dorei,” the investigators stated, “Our results show that low-dose antibiotics can perturb the secondary metabolome of gut bacteria, and that these induced metabolites can exert immunomodulatory effects and restructure the microbiome.”
The human gut microbiome consists of a “… diverse and dynamic community of microorganisms that shapes host health,” the authors wrote. “Among the multitude of microbial inhabitants, Bacteroides comprise 25% of human gut microbiota and represent one of the most abundant anaerobes.” These gram-negative bacteria have been of interest for their multifunctional roles, including regulation of metabolism and immunomodulatory activities.
Every day, medical professionals across the country prescribe drug treatments for a variety of ailments. Although these drugs may have their desired effect, there is also the possibility that they impact the microbes that keep us healthy. Antibiotics, for example, often inactivate not only offending microbes but also beneficial gut bacteria. Scientists have proposed the idea that consuming pharmaceuticals could also alter microbial metabolism, changing the compounds that bacteria release into the body and impacting human health.
To study this, Seyedsayamdost and colleagues employed a technique known as HiTES that can allow the discovery of novel metabolites that are not seen under standard laboratory conditions. “In HiTES, a microorganism is subjected to a library of small molecules and the secondary metabolome is then examined using a variety of read-outs, including genetic reporters, biological activity, or mass spectrometry (MS)-based methods,” the authors explained.
For their reported study the team exposed separate cultures of the prominent gut microbe Bacteroides dorei to hundreds of FDA-approved drugs—such as antihistamines, hypertension drugs, anticancer agents and antibiotics—and looked for metabolic changes compared to untreated bacterial cultures.
After incubating B. dorei with and without pharmaceuticals, the researchers isolated and identified compounds the bacterium secreted. They found that among the various drugs tested, low doses of tetracycline antibiotics had the strongest effect on bacterial cultures, inducing the microbes to produce two types of new compounds: a series of serine-glycine dipeptide lipids, which they called doreamides, and 6-N-acyladenosines.
Further testing showed that both compounds trigger human immune cells to produce pro-inflammatory cytokines, which can help respond to infections. “Investigations into their biological functions revealed induction of pro-inflammatory cytokines in macrophages, notably tumor necrosis factor (TNFα), interleukin (IL)-1β, IL-6, and IL-10,” the team wrote. The doreamides also induced production of the host-derived cathelicidin antimicrobial peptide (CAMP) that inhibited the growth of several bacterial strains, including pathogenic ones, but not the growth of B. dorei.
“Additionally and importantly, the doreamides elicited production of cathelicidin, a host-derived antimicrobial peptide that inhibited the growth of several gut bacteria tested but did not affect B. dorei,” the scientist stated. “It is conceivable that this sequence, initiated by tetracyclines, mediated by doreamides, and culminating in the production of CAMP and inflammatory cytokines, leads to local reshaping of bacterial composition.” The investigators suggest that their findings set the stage for animal studies to explore possible therapeutic properties of the doreamides.
They also noted that while it is established that antibiotics can “prune or restructure” the local microbiome through their activity on bacteria, their newly reported findings “… suggest that there is another mechanism by which antibiotics can alter bacterial composition, one that occurs through cryptic metabolites that are elicited by low-dose antibiotics in gut bacteria.” Of particular interest, they pointed out, the doreamides and N-acyladenosines are produced by genes or gene clusters that are not captured by typical genome mining tools, which indicates the potential strength of chemistry-first approaches for discovering what they call “the metabolomic potential” of gut bacteria. “This type of chemistry-first discovery approach is poised to unearth more natural products, thousands of which are predicted from the human microbiome, thus enabling insights into the roles that small molecules play in human health and disease.”
