Related Experiment Video
Updated: Nov 13, 2025
Antimicrobial Peptides Produced by Selective Pressure Incorporation of Non-canonical Amino Acids
Published on: May 4, 2018
Selective Isolation of Multidrug-Resistant Pedobacter spp., Producers of Novel Antibacterial Peptides
Joakim Bjerketorp1,2, Jolanta J Levenfors1,2, Christina Nord1
1Department of Molecular Sciences, Uppsala BioCentrum, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Abstract:
Twenty-eight multidrug-resistant bacterial strains closely related or identical to Pedobacter cryoconitis, Pedobacter lusitanus and Pedobacter steynii were isolated from soil samples by selection for multidrug-resistance. Approximately 3-30% of the selected isolates were identified as Pedobacter, whereas isolation without antibiotics did not yield any isolates of this genus. Next generation sequencing data showed Pedobacter to be on 69th place among the bacterial genera (0.32% of bacterial sequences). The Pedobacter isolates produced a wide array of novel compounds when screened by UHPLC-MS/MSMS, and hierarchical cluster analysis resulted in several distinct clusters of compounds produced by specific isolates of Pedobacter, and most of these compounds were found to be peptides. The Pedobacter strain UP508 produced isopedopeptins, whereas another set of strains produced pedopeptins, which both are known cyclic lipodepsipeptides produced by Pedobacter sp. Other Pedobacter strains produced analogous peptides with a sequence variation. Further strains of Pedobacter produced additional novel antibacterial cyclic lipopeptides (ca 800 or 1400 Da in size) and/or linear lipopeptides (ca 700-960 Da in size). A 16S rRNA phylogenetic tree for the Pedobacter isolates revealed several distinct clades and subclades of isolates. One of the subclades comprised isolates producing isopedopeptin analogs, but the isopedopeptin producing isolate UP508 was clearly placed on a separate branch. We suggest that the non-ribosomal peptide synthases producing pedopeptins, isopedopeptins, and the analogous peptides, may derive from a common ancestral non-ribosomal peptide synthase gene cluster, which may have been subjected to a mutation leading to changed specificity in one of the modules and then to a modular rearrangement leading to the changed sequence found in the isopedopeptins produced by isolate UP508.
Insights
Multidrug-resistant bacteria, including Pedobacter species, were isolated from soil. These bacteria produce novel cyclic lipopeptides, suggesting a common ancestral gene cluster for peptide synthesis.
Area of Science:
- Microbiology
- Natural Product Chemistry
- Genomics
Background:
- Multidrug-resistant bacterial strains, particularly Pedobacter species, are challenging to isolate using traditional methods.
- Soil environments harbor diverse bacterial communities with potential for novel compound discovery.
Purpose of the Study:
- To isolate and characterize multidrug-resistant Pedobacter strains from soil samples.
- To investigate the novel secondary metabolites, specifically peptides, produced by these isolates.
- To analyze the phylogenetic relationships and potential evolutionary origins of peptide biosynthesis in Pedobacter.
Main Methods:
- Isolation of multidrug-resistant bacteria from soil samples using antibiotic selection.
- Identification of bacterial isolates using next-generation sequencing and 16S rRNA gene sequencing.
- Screening for novel compounds using ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS).
- Hierarchical cluster analysis of compound profiles and phylogenetic analysis of isolates.
Main Results:
- Twenty-eight multidrug-resistant bacterial strains, closely related to Pedobacter species, were successfully isolated via antibiotic selection.
- Pedobacter isolates produced a diverse array of novel cyclic and linear lipopeptides, including isopedopeptins and pedopeptins.
- Phylogenetic analysis revealed distinct clades of Pedobacter isolates, with variations in lipopeptide production linked to specific clades and isolate UP508.
- Next-generation sequencing indicated Pedobacter constituted a small fraction of the total soil bacterial community.
Conclusions:
- Antibiotic selection is crucial for isolating specific multidrug-resistant bacterial genera like Pedobacter from soil.
- Pedobacter species are a rich source of novel lipopeptides with potential pharmaceutical applications.
- The observed variations in lipopeptide structures suggest an evolutionary pathway involving mutations and rearrangements in non-ribosomal peptide synthetase gene clusters.
More Related Videos
06:05Using the Overlay Assay to Qualitatively Measure Bacterial Production of and Sensitivity to Pneumococcal Bacteriocins
Published on: September 30, 2014
08:58Isolation and Identification of Waterborne Antibiotic-Resistant Bacteria and Molecular Characterization of their Antibiotic Resistance Genes
Published on: March 3, 2023
Related Concept Videos
00:57Antibiotic Selection
01:30Development of Antibiotic Resistance
01:23Antimicrobial Proteins
Interferons
Interferons (IFNs) are proteins produced by lymphocytes, macrophages, and fibroblasts infected with viruses. While IFNs cannot prevent viruses from entering and...