Multiple strain analysis of Streptomyces species from Philippine marine sediments reveals intraspecies heterogeneity in antibiotic activities

• Published in: Scientific reports Vol. 11; no. 1; p. 17544
• Main Authors: Tenebro, Chuckcris P., Trono, Dana Joanne Von L., Vicera, Carmela Vannette B., Sabido, Edna M., Ysulat, Jovito A., Macaspac, Aaron Joseph M., Tampus, Kimberly A., Fabrigar, Trisha Alexis P., Saludes, Jonel P., Dalisay, Doralyn S.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 02-09-2021; Nature Publishing Group; Nature Portfolio
• Subjects: 631/154; 631/158; 631/326; 631/61; 631/92; 704/829; Actinomycetes; Anti-Bacterial Agents - pharmacology; Antibacterial activity; Antibiotics; Biodiversity; DNA, Bacterial - genetics; Dominant species; E coli; Ecosystem; Genotyping; Geologic Sediments - analysis; Geologic Sediments - microbiology; Heterogeneity; Humanities and Social Sciences; Marine ecosystems; Marine sediments; Microbial Sensitivity Tests - methods; multidisciplinary; Multidrug resistance; New species; Philippines; Phylogeny; RNA, Ribosomal, 16S - genetics; RpoB protein; rRNA 16S; Science; Science (multidisciplinary); Sediments; Species diversity; Strains (organisms); Streptomyces; Streptomyces - classification; Streptomyces - drug effects; Streptomyces - genetics; Streptomyces - metabolism; Philippines
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-021-96886-4

The marine ecosystem has become the hotspot for finding antibiotic-producing actinomycetes across the globe. Although marine-derived actinomycetes display strain-level genomic and chemodiversity, it is unclear whether functional traits,
i.e
., antibiotic activity, vary in near-identical
Streptomyces
species. Here, we report culture-dependent isolation, antibiotic activity, phylogeny, biodiversity, abundance, and distribution of
Streptomyces
isolated from marine sediments across the west-central Philippines. Out of 2212 marine sediment-derived actinomycete strains isolated from 11 geographical sites, 92 strains exhibited antibacterial activities against multidrug-resistant
Staphylococcus aureus
,
Pseudomonas aeruginosa
, and
Escherichia coli
. The 16S rRNA and
rpoB
gene sequence analyses confirmed that antibiotic-producing strains belong to the genus
Streptomyces
, highlighting
Streptomyces parvulus
as the most dominant species and three possible new species. Antibiotic-producing
Streptomyces
strains were highly diverse in Southern Antique, and species diversity increase with marine sediment depth. Multiple strains with near-identical 16S rRNA and
rpoB
gene sequences displayed varying strength of antibiotic activities. The genotyping of PKS and NRPS genes revealed that closely related antibiotic-producing strains have similar BGC domains supported by their close phylogenetic proximity. These findings collectively suggest
Streptomyces
' intraspecies adaptive characteristics in distinct ecological niches that resulted in outcompeting other bacteria through differential antibiotic production.