Biotechnological Potential of Bacteria Isolated from the Sea Cucumber Holothuria leucospilota and Stichopus vastus from Lampung, Indonesia

Abstract

In order to minimize re-discovery of already known anti-infective compounds, we focused our screening approach on understudied, almost untapped marine environments including marine invertebrates and their associated bacteria. Therefore, two sea cucumber species, Holothuria leucospilota and Stichopus vastus, were collected from Lampung (Indonesia), and 127 bacterial strains were identified by partial 16S rRNA-gene sequencing analysis and compared with the NCBI database. In addition, the overall bacterial diversity from tissue samples of the sea cucumbers H. leucospilota and S. vastus was analyzed using the cultivation-independent Illumina MiSEQ analysis. Selected bacterial isolates were grown to high densities and the extracted biomass was tested against a selection of bacteria and fungi as well as the hepatitis C virus (HCV). Identification of putative bioactive bacterial-derived compounds were performed by analyzing the accurate mass of the precursor/parent ions (MS1) as well as product/daughter ions (MS2) using high resolution mass spectrometry (HRMS) analysis of all active fractions. With this attempt we were able to identify 23 putatively known and two previously unidentified precursor ions. Moreover, through 16S rRNA-gene sequencing we were able to identify putatively novel bacterial species from the phyla Actinobacteria, Proteobacteria and also Firmicutes. Our findings suggest that sea cucumbers like H. leucospilota and S. vastus are promising sources for the isolation of novel bacterial species that produce compounds with potentially high biotechnological potential.

Anti-Infective and Antiviral Activity of Valinomycin and Its Analogues from a Sea Cucumber-Associated Bacterium, Streptomyces sp. SV 21

“…It showed 100% similarity sequence to Streptomyces cavourensis with the type strain accession number NR_043851.1. Further information on bacterial isolation can be found in [ 5 ]. After successful isolation, the bacterium was grown from the glycerol stock on Marine Agar that was made from Marine Broth (MB, Carl Roth, Karlsruhe, Germany) according to manufacturer’s instruction, with addition of 9 g/L agar (Agar-agar Bacteriological, Carl Roth, Karlsruhe, Germany).…”

“…For structure verification purposes, we analyzed the MS 2 data by using MASST GNPS to identify the likely fragments of the target compounds or its analogues with the set parameters described in [ 5 ]. In addition, we also measured the NMR spectra on a Bruker 700 MHz cryo NMR spectrometer (Avance III HD) with Topspin 3.6.2 for analysis.…”

“…The anti-HCV assay was performed as mentioned in [ 5 ]. In brief, Huh7.5 cells stably expressing Firefly luciferase (Huh7.5 Fluc) were cultured in Dulbecco’s modified minimum essential medium (DMEM, Gibco, Thermo Fisher Scientific, Schwerte, Germany) and maintained in a 37 °C environment with 5% CO 2 supply.…”

“…Recently, the isolation and fast identification of putatively new bioactive compounds from sea cucumber-associated bacteria have been reported in [ 5 ]. Extracts of Streptomyces sp.…”

Culturable Microorganisms Associated with Sea Cucumbers and Microbial Natural Products

“…More than 80% of the sampling sites are located on the west coast of the Pacific Ocean. However, a small number of sampling sites are also located in the Atlantic, Indian, and Antarctic Oceans [ 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 ] ( Figure 1 and Table S1 ). Sea cucumber samples are typically collected from the coast at a depth of less than 20 m [ 17 , 18 , 19 , 20 , 21 ].…”