Complete Genome Sequence of Two Deep-Sea Streptomyces Isolates from Madeira Archipelago and Evaluation of Their Biosynthetic Potential

Abstract

The deep-sea constitutes a true unexplored frontier and a potential source of innovative drug scaffolds. Here, we present the genome sequence of two novel marine actinobacterial strains, MA3_2.13 and S07_1.15, isolated from deep-sea samples (sediments and sponge) and collected at Madeira archipelago (NE Atlantic Ocean; Portugal). The de novo assembly of both genomes was achieved using a hybrid strategy that combines short-reads (Illumina) and long-reads (PacBio) sequencing data. Phylogenetic analyses showed that strain MA3_2.13 is a new species of the Streptomyces genus, whereas strain S07_1.15 is closely related to the type strain of Streptomyces xinghaiensis. In silico analysis revealed that the total length of predicted biosynthetic gene clusters (BGCs) accounted for a high percentage of the MA3_2.13 genome, with several potential new metabolites identified. Strain S07_1.15 had, with a few exceptions, a predicted metabolic profile similar to S. xinghaiensis. In this work, we implemented a straightforward approach for generating high-quality genomes of new bacterial isolates and analyse in silico their potential to produce novel NPs. The inclusion of these in silico dereplication steps allows to minimize the rediscovery rates of traditional natural products screening methodologies and expedite the drug discovery process.

Actinobacteria from Arctic and Atlantic deep-sea sediments—Biodiversity and bioactive potential

“…Taxonomic analysis of some of the retrieved isolates indicate that they may constitute new species, in the light of the similarity threshold for a new species of 98.7% ( Supplementary Table S1 ; Stackebrandt, 2006 ). Of these, Streptomyces strain MA3_2.13 was already proven to be a new species ( Albuquerque et al, 2021 ).…”

“…The E.Z.N.A. Bacterial DNA kit (Omega Bio-Tek, GA, United States) was used for DNA extraction, following the instructions of the manufacturer, with a few modification steps described by Albuquerque et al (2021) . 16S rRNA gene was amplified by Polymerase Chain Reaction (PCR) using the universal primers 1492R (5’-GGTTACCTTGTTACGACTT-3′) and 27F (5’-GAGTTTGATCCTGGCTCAG-3′) as described by Ribeiro et al (2020) .…”

Streptomyces profundus sp. nov., a novel marine actinobacterium isolated from deep-sea sediment of Madeira Archipelago, Portugal

“…The isolation process was performed as described by Albuquerque et al . [12]. Briefly, 1 g sediment was suspended in 1 ml sterile seawater and subjected to a pre-treatment consisting in the incubation of the suspension in a water bath at 57 °C, for 15 min.…”

“…For whole-genome sequencing, genomic DNA of strain MA3_2.13 T was isolated as previously described [12]. In brief, genomic DNA was obtained from cells grown in tryptic soy broth (30 °C, at 220 r.p.m., for 48 h) and extracted using the GeneJET Genomic DNA Purification Kit (Thermo Fisher Scientific).…”

“…The genome was screened for the presence of secondary metabolite biosynthetic gene clusters (BGCs) using antiSMASH [32] with a strict detection setting and manually curated. The analysis predicted the presence of 32 BGC including two siderophore-encoding clusters, four terpenes and 16 polyketide synthase containing clusters [12]. The metabolic potential of strain MA3_2.13 T for producing novel metabolites is reflected in the low similarities (<50 %) or no similarity displayed to known clusters of 23 out of the 32 BGC identified in strain MA3_2.13 T [12].…”