Industrial and agricultural chemicals quietly alter the balance of gut microbes

Industrial and agricultural chemicals quietly alter the balance of gut microbes

A large-scale laboratory study shows that widely used chemicals do more than just contaminate food and water. They can selectively suppress, promote and rewire gut bacteria, with potential consequences for microbiome balance and antimicrobial resistance.

In a study recently published in the journalnatural microbiology,Researchers observed that many agricultural and industrial chemicals exhibit antimicrobial activity against the human gut microbiota and can exert selective pressure on gut bacteriain vitro.

Synthetic chemicals have become indispensable for industry and agriculture. Industrial and agricultural chemicals enter water and food through agricultural applications, industrial processing or environmental pollution. Contamination of food and water by chemical pollutants exposes the gastrointestinal tract to xenobiotic compounds. However, little is known about the effects of these pollutants on gut bacteria under controlled laboratory conditions or how they may influence microbial fitness and competition.

Screening chemical effects on gut microbes

In the present study, researchers examined the effects of pollutants on intestinal bacteria using ain vitroScreening approach to assess bacterial growth inhibition and selection effects. They used an extensive library of 1,076 compounds that are likely to enter water and food; The library included industrial chemicals, pesticides, pesticide metabolites and compounds that target organisms such as spiders, rodents, bacteria, fungi and nematodes.

Testing growth inhibition in 22 intestinal strains

The researchers examined the influence of all compounds at 20 μM on the growth of 22 gut bacterial strains selected based on their prevalence and abundance in the healthy gut microbiota. Bacteria were grown and monitored for 24 hours; Growth was measured as the area under the growth curve. Growth inhibition hits were defined as bacterial-chemical interactions that reduced growth by more than 20%.

Chemicals with broad and narrow antimicrobial activity

The team found that 168 chemicals inhibited at least one strain. Particularly BacteroidalesParabacteroides distasoniswere the most sensitive taxa, whereasAkkermansia muciniphilaAndEscherichia coliwere the least sensitive. Fungicides, industrial chemicals, and acaricides were the chemical categories with the predominant antimicrobial activity, with approximately one-third of fungicides and industrial chemicals exhibiting inhibitory effects. While most compounds inhibited a few strains, 24 showed broad toxicity, inhibiting more than a third of strains.

Closantel (an antiparasitic for livestock), bisphenol AF (BPAF; used in plastics), tetrabromobisphenol A (TBBPA; a flame retardant), emamectin benzoate (an insecticide), fluazinam (a fungicide) and chlordecone (an insecticide) were among the compounds with broad-spectrum inhibitory activity. In addition, 150 bacterial-chemical interactions showed growth inhibition of more than 90%, indicating strong antimicrobial activity that can lead to competitive advantages or losses between intestinal microbes.

Relationships between chemical sensitivity and microbiome abundance

The number of compounds affecting a species was positively correlated with their relative abundance in the human microbiome, but not with prevalence. Therefore, chemicals with narrow or broad activity could influence the composition of the microbiome due to their effects on numerous taxa through differential growth inhibition and selection. Next, the team examined how species-level chemical effects affect bacterial communities. A synthetic, diverse community of 20 gut bacteria was challenged with TBBPA or BPAF to assess community-level responses.

Community-level responses to BPAF and TBBPA

However, BPAF-induced compositional changes were consistent with monoculture effectsEubacterium rectaleAndFusobacterium nucleatumwere protected in the community even though they were vulnerable in isolation. With TBBPA,Bacteroides thetaiotaomicrondominated the community despite being vulnerable in monocultures, demonstrating how community context can alter fitness outcomes under chemical pressure. Next, the researchers examined the interaction mechanisms in species of the order Bacteroidales due to their high sensitivity to pollutants.

Transposon mutant library for identifying tolerance genes

A transposon (Tn) mutant library fromParabacteroides merdaewhich contains Tn insertion mutants in over 3,000 non-essential genes, was used to identify genes that modulate the influence of xenobiotics on bacterial fitness. A competition test was conducted against 10 chemicals. Closantel, emamectin benzoate, fluazinam, TBBPA, imazalil sulfate, and BPAF were tested at ≤20 μM, while glyphosate, perfluorononanoic acid (PFNA), perfluorooctanoic acid, and propiconazole were tested at ≥20 μM.

Cultures inoculated with the mutant library were grown to early stationary phase, and barcoded Tn sequencing was used to quantify selection of Tn mutants under chemical stress. BPAF, closantel and TBBPA showed the strongest effects in library selection among the tested substances at ≤ 20 μM. Furthermore, 500 μM PFNA showed the most hits overall, whereas 50 μM glyphosate, 20 μM PFNA, and 20 μM perfluorooctanoic acid did not yield significant hits.

Efflux regulation and resistance mechanisms identified

Notably, the strongest selection was observed for closantel, with over 90% of Tn mutants carrying insertions across >20 different positions in the NQ542_01170 gene, which encodes a transcriptional regulator homologous to acrR, an efflux repressorBacteroides uniformis. Loss of this regulator increased tolerance to multiple pollutants and also resulted in increased resistance to the antibiotic ciprofloxacin, highlighting possible links between pollutant exposure and antibiotic resistance through shared tolerance and efflux pathways. Some transporter Tn mutants showed broad sensitivity to pollutants, suggesting common tolerance mechanisms among themP. merdae.

Conserved pollutant tolerance pathways in Bacteroidales

Further investigations into mutants ofB. thetaiotaomicronBelonging to a distant familyP. merdaerevealed common responses between the two species and supported conserved mechanisms (e.g., efflux pathways) of pollutant tolerance across the order. Additionally,P. merdaeFor most tested compounds affecting bacterial growth and metabolic performance, Tn insertion mutant gene hits were enriched in various metabolic pathways.

Pollutant-controlled selection of metabolic pathways

Twenty micromolar TBBPA selection showed significant enrichment of Tn mutants in the branched-chain amino acid (BCAA) degradation pathway. The catabolic gene cluster porA (involved in BCAA degradation into short-chain fatty acids) also showed positive selection under 20 μM TBBPA, 20 μM BPAF and 500 μM PFNA. Loss-of-function Tn insertion mutants of secondary metabolism genes, NQ542_07535–55, showed positive selection under 500 μM PFNA.

Far-reaching implications for the fitness and evolution of the microbiome

In total, the study identified 588 inhibitory interactions between 168 chemicals and human gut bacteria, most of which previously had no antibacterial properties. Industrial chemicals and fungicides had the greatest impact. Regulation of efflux pumps was a conserved mechanism between themB. thetaiotaomicronAndP. merdaeThis shapes tolerance and competitiveness under chemical stress.

Genetic selection inP. merdaewas enriched with biosynthetic and catabolic genes. Loss-of-function mutations in genes encoding enzymes involved in secondary metabolites provided a growth advantage and raised the possibility that exposure to chemical pollutants could influence the selection landscape in the gut, which could alter host-microbiome interaction pathways. However, the experiments were carried outin vitroat defined concentrations, and further in vivo and epidemiological studies are required to determine whether similar effects occur under real exposure conditions in humans and to define relevant exposure levels.

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