Mining the Biosynthetic Potential for Specialized Metabolism of a Streptomyces Soil Community

Abstract

The diversity and distribution of specialized metabolite gene clusters within a community of bacteria living in the same soil habitat are poorly documented. Here we analyzed the genomes of 8 Streptomyces isolated at micro-scale from a forest soil that belong to the same species or to different species. The results reveal high levels of diversity, with a total of 261 biosynthesis gene clusters (BGCs) encoding metabolites such as terpenes, polyketides (PKs), non-ribosomal peptides (NRPs) and ribosomally synthesized and post-translationally modified peptides (RiPPs) with potential bioactivities. A significant part of these BGCs (n = 53) were unique to only one strain when only 5 were common to all strains. The metabolites belong to very diverse chemical families and revealed that a large diversity of metabolites can potentially be produced in the community. Although that analysis of the global metabolome using GC-MS revealed that most of the metabolites were shared between the strains, they exhibited a specific metabolic pattern. We also observed that the presence of these accessory pathways might result from frequent loss and gain of genes (horizontal transfer), showing that the potential of metabolite production is a dynamic phenomenon in the community. Sampling Streptomyces at the community level constitutes a good frame to discover new biosynthetic pathways and it appears as a promising reservoir for the discovery of new bioactive compounds.

The Isolation of a Novel Streptomyces sp. CJ13 from a Traditional Irish Folk Medicine Alkaline Grassland Soil that Inhibits Multiresistant Pathogens and Yeasts

“…In order to predict the potential synthesis of antibiotics by Streptomyces sp., CJ13, we analysed its whole genome sequence using antiSMASH (antibiotics and secondary metabolite analysis shell), which predicts the potential for synthesis of secondary metabolite clusters [29]. Some of the secondary metabolites that we identified are common to many species of Streptomyces, including: spore pigment, melanin, siderophores, alkylresorcinol (phenolic lipid, also contact allergen) and hopene (condenses membranes and decreases permeability) [34][35][36].…”

Elicitation of Antimicrobial Active Compounds by Streptomyces-Fungus Co-Cultures

“…To set up bacterial–fungal co-cultures, we used two collections of the soil dwelling bacterium Streptomyces and of forest basidiomycetes available in our laboratories ( Figure 1 ). On the one hand, the bacterial collection was made up of eight Streptomyces isolated from the same forest soil micro-habitats and belonging to identical or different species as previously described by Nicault et al [ 8 ]. Their genome sequences were determined and showed a great diversity of their specialized metabolite BGCs, with 261 identified for the eight strains [ 8 ].…”

“…On the one hand, the bacterial collection was made up of eight Streptomyces isolated from the same forest soil micro-habitats and belonging to identical or different species as previously described by Nicault et al [ 8 ]. Their genome sequences were determined and showed a great diversity of their specialized metabolite BGCs, with 261 identified for the eight strains [ 8 ]. On the other hand, the fungal collection was made up of wood-decaying basidiomycetes.…”

“…It also represents a good interaction model with Streptomyces , as it was shown to restore hyphal formation-deficient phenotypes in some strains [ 51 ]. S1D4-11 and S1D4-23 are closely related but different species of Streptomyces and each were previously predicted to harbor 36 BGCs with 25 in common and 11 specific ones [ 8 ]. It can be noticed that the two other Streptomyces RLB1-33 and RLB1-9 that showed no anti- B. subtilis activity in mono-culture ( Figure 1 B) had no induced capacity in their SFI zones with S. commune .…”

“…In that respect, fungi and bacteria of the genus Streptomyces are of special interest, as they provide alone 42% and 32% of the natural products used in the human and veterinary medicine, respectively [ 6 ]. For Streptomyces , genomic analyses have shown that they possess between 20 and 50 biosynthesis gene clusters (BGCs) predicted to produce SMs [ 7 , 8 ]. Yet, Streptomyces strains are generally used for the production of a single or a few compounds.…”