Natural compounds continue to serve as the most fruitful source of new antimicrobials. Analysis of bacterial genomes have revealed that the biosynthetic potential of antibiotic producers by far exceeds the number of already discovered structures. However, due to the repeated discovery of known substances, it has become necessary to change both approaches to the search for antibiotics and the sources of producer strains. The pressure of natural selection and the diversity of interactions in symbiotic communities make animal microbiomes promising sources of novel substances. Here, microorganisms associated with various animals were examined in terms of their antimicrobial agents. The application of alternative cultivation techniques, ultrahigh-throughput screening, and genomic analysis facilitated the investigation of compounds produced by unique representatives of the animal microbiota. We believe that new strategies of antipathogen defense will be discovered by precisely studying cell–cell and host–microbe interactions in microbiomes in the wild.

Soil is a classical source of beneficial microorganisms. Soil microbiomes provided the overwhelming majority of antibiotic-producing strains, biocontrol agents, probiotics, and plant-protecting bacteria. The functionality of strains isolated from various soil samples is predetermined by the biosynthetic potential encoded in their genomes. Here, we describe a novel Peribacillus simplex d27.3 strain isolated from the soil sample of a pine forest in the Republic of Dagestan, Russia. P. simplex d27.3 displayed antibiotic activity against gram-positive bacteria and fungi while being inactive against the model hypersensitive gram-negative strain E. coli ΔlptD. Metabolomic analysis revealed that antimicrobial activity was partially mediated by the fengycin lipopetides (C-16 fengycin A, C-17 fengycin A, and C-16 fengycin B). In addition, the P. simplex d27.3 strain was found to produce other hydrophilic and more hydrophobic antimicrobials yet to be described. Thus, the P. simplex d27.3 strain is a producer of useful antimicrobial compounds with a high potential for application in biotechnology and agriculture.