Gene Sequence Based Clustering Assists in Dereplication of Pseudoalteromonas luteoviolacea Strains with Identical Inhibitory Activity and Antibiotic Production

Abstract

Some microbial species are chemically homogenous, and the same secondary metabolites are found in all strains. In contrast, we previously found that five strains of P. luteoviolacea were closely related by 16S rRNA gene sequence but produced two different antibiotic profiles. The purpose of the present study was to determine whether such bioactivity differences could be linked to genotypes allowing methods from phylogenetic analysis to aid in selection of strains for biodiscovery. Thirteen P. luteoviolacea strains divided into three chemotypes based on production of known antibiotics and four antibacterial profiles based on inhibition assays against Vibrio anguillarum and Staphylococcus aureus. To determine whether chemotype and inhibition profile are reflected by phylogenetic clustering we sequenced 16S rRNA, gyrB and recA genes. Clustering based on 16S rRNA gene sequences alone showed little correlation to chemotypes and inhibition profiles, while clustering based on concatenated 16S rRNA, gyrB, and recA gene sequences resulted in three clusters, two of which uniformly consisted of strains of identical chemotype and inhibition profile. A major time sink in natural products discovery is the effort spent rediscovering known compounds, and this study indicates that phylogeny clustering of bioactive species has the potential to be a useful dereplication tool in biodiscovery efforts.

Diversity and distribution of the bmp gene cluster and its Polybrominated products in the genus Pseudoalteromonas

“…The 25th strain (HI1) was not available for testing. H33 and H33‐S are the only strains in clade 2 that are missing the entire bmp gene cluster and, as expected, no BNPs were detected (Vynne et al ., ). We also failed to detect brominated compounds from the strains that possess bmp version C (NCIMB 1942 and NCIMB 2035).…”

“…Subsequently, pentabromopseudilin has been reported from multiple Pseudoalteromonas spp. (Isnansetyo and Kamei, 2003;Fehér et al, 2010;Vynne et al, 2011;Vynne et al, 2012;Whalen et al, 2015;El Gamal et al, 2016a, 2016bAgarwal et al, 2017) and a single strain (MMB-1) of Marinomonas mediterranea (Agarwal et al, 2014). These two genera of Gammaproteobacteria belong to different Orders, raising the possibility that the associated biosynthetic gene cluster (BGC) was exchanged by horizontal gene transfer.…”

Genome mining reveals unlocked bioactive potential of marine Gram-negative bacteria

“…However, also several known antibiotic compounds were re-discovered, for instance, S2753 produces holomycin [ 28 ], an antibiotic previously only isolated from terrestrial streptomycetes, and Vibrio coralliilyticus S2052 produces andrimid [ 28 ]. Also, in pigmented Pseudoalteromonas , we have re-identified a range of antibiotic compounds (indolmycin, pentabromopseudilin, prodigiosin) [ 44 , 45 ].…”

“…During the last five years, we have demonstrated that marine Gram-negative bacteria produce an array of antibiotic and anti-virulence compounds [ 19 , 28 , 29 , 40 , 41 , 43 - 45 ] and here, we ask the question if the classical bioprospecting approach had fully revealed the potential of these bacteria. We present an in silico study of different marine bacterial genomes, which were analyzed using several of the prediction tools developed for the identification of secondary metabolism pathways, namely antiSMASH, NapDos, Np.search, and BAGEL3 [ 37 , 46 , 47 ].…”

Isolation of Bioactive Compounds from Indonesian Marine Sponge Clathria sp., Xestopongia muta, and Endectyon delaubenfelsi as Antibacterial Escherichia coli

“…Escherichia coli incubated at 37°C on Middlebrook 7H10 added with 10% Middlebrook OADC and 0,5% gliserol, or Middlebrook 7H9 lsolution with 10% Middlebrook OADC, 0,2% gliserol, and 0,05% Tween 80 [8][9][10][11].…”