Soil-derived Paenibacillus profundus strains showed broad-spectrum activity against MRSA and carbapenem-resistant bacteria, with genome mining revealing multiple antimicrobial peptide biosynthetic gene clusters.
Active vs MRSA + CREPaenibacillus profundus soil isolates showed broad-spectrum activity against the most dangerous drug-resistant clinical pathogens
What the researchers found
Of 29 soil isolates tested, Paenibacillus profundus strains 7.5 and M4.5 showed the most potent broad-spectrum antimicrobial activity, including significant inhibition of MRSA and carbapenem-resistant Enterobacterales (CRE).
Genome mining of three producer strains using antiSMASH revealed biosynthetic gene clusters for:
- Nonribosomal peptide synthetases (NRPSs)
- Polyketide synthases (PKSs)
- Ribosomally synthesized and post-translationally modified peptides (RiPPs)
Several clusters matched known compounds (polymyxin B, paenilan, colistin, paenibacterin), while many had no known counterparts, suggesting potential for discovering novel antimicrobial peptides.
Why it matters
Antibiotic resistance is a global health emergency, and CRE infections in particular have very few treatment options. Soil bacteria are a proven source of antibiotics (most existing antibiotics were originally discovered from soil microbes). This study identifies new producer strains with potent activity against the most dangerous drug-resistant pathogens.
How the study worked
Twenty-nine Bacillus and Paenibacillus isolates from soil samples were tested against clinically relevant multidrug-resistant pathogens using both agar and broth-based antimicrobial assays. Species were identified via 16S rRNA sequencing. Genome mining of the most active strains was performed using antiSMASH to identify biosynthetic gene clusters for antimicrobial compound production.
What this study cannot tell us
This is an early-stage discovery study — the specific antimicrobial compounds have not been purified or structurally characterized. The gene clusters suggest peptide production, but the actual molecules need to be isolated and tested. In vitro antimicrobial activity doesn't guarantee in vivo efficacy. Toxicity to human cells was not assessed.
How to read the evidence
This is an early-stage natural product discovery study combining antimicrobial screening with computational genome mining. While the antimicrobial activity is well-demonstrated, the specific compounds responsible have not been isolated or characterized.
When this study was published
Published in 2025 in MicrobiologyOpen, this is a recent contribution to the ongoing search for new antimicrobial agents from natural sources.
The bigger picture
The golden age of antibiotic discovery from soil bacteria slowed decades ago, but modern genomics tools like antiSMASH are revealing that soil microbes still harbor vast untapped chemical diversity. The finding of gene clusters with no known matches suggests these bacteria may produce antimicrobial peptides that have never been characterized — a potential treasure trove for drug development.
Questions still open
- What are the novel antimicrobial compounds produced by the gene clusters that don't match known compounds?
- Could these Paenibacillus-derived peptides be developed into new last-resort antibiotics for CRE infections?
- How do the antimicrobial peptides from these soil bacteria compare in potency and toxicity to existing polymyxins?
Common questions
Why look for antibiotics in soil bacteria?
What are NRPSs and RiPPs?
Read the original research
Various Bacillus and Paenibacillus Spp. Isolated From Soil Produce Compounds With Potent Antimicrobial Activity Against Clinically Relevant Pathogens.
MicrobiologyOpen, 14(6), e70179
Citation
Moran, Michael; Turner, Hogan; Yanchar, Joseph; Preece, Joshua; Ahlborn, Gene; Robison, Richard. (2025). Various Bacillus and Paenibacillus Spp. Isolated From Soil Produce Compounds With Potent Antimicrobial Activity Against Clinically Relevant Pathogens.. MicrobiologyOpen, 14(6), e70179. https://doi.org/10.1002/mbo3.70179