Multiple Streptomyces species with distinct secondary metabolomes have identical 16S rRNA gene sequences

Abstract

Microbial diversity studies using small subunit (SSU) rRNA gene sequences continue to advance our understanding of biological and ecological systems. Although a good predictor of overall diversity, using this gene to infer the presence of a species in a sample is more controversial. Here, we present a detailed polyphasic analysis of 10 bacterial strains isolated from three coastal lichens Lichina confinis, Lichina pygmaea and Roccella fuciformis with SSU rRNA gene sequences identical to the type strain of Streptomyces cyaneofuscatus. This analysis included phenotypic, microscopic, genetic and genomic comparisons and showed that despite their identical SSU rRNA sequences the strains had markedly different properties, and could be distinguished as 5 different species. Significantly, secondary metabolites profiles from these strains were also found to be different. It is thus clear that SSU rRNA based operational taxonomy units, even at the most stringent cut-off can represent multiple bacterial species, and that at least for the case of Streptomyces, strain de-replication based on SSU gene sequences prior to screening for bioactive molecules can miss potentially interesting novel molecules produced by this group that is notorious for the production of drug-leads.

Genome mining of biosynthetic and chemotherapeutic gene clusters in Streptomyces bacteria

“…These findings are consistent with recent reports in other genera of Actinobacteria 6,18,19 and also highlight the power of mining the genomes of closely related strains. In a recent study of ten Streptomyces strains with 16S rRNA gene sequences that are all identical to the type strain of Streptomyces cyaneofuscatus and hence are considered the same species, no two strains appear to exhibit identical secondary metabolomic profiles 32 . In another example, Streptomyces albus, a remarkable 48 BGCs were identified in a mere seven strains 33 .…”

“…BGC analyses in Actinobacteria are often done using a single strain representative of a species. A few recent studies, however, have highlighted major differences in biosynthetic diversity even among very closely related strains 32,33 , which may represent an attractive yet untapped reservoir of novel compounds. Here, we explored the extent to which members of the same species differ in the abundance and diversity of BGCs they carry.…”

Habitat fragmentation is associated with dietary shifts and microbiota variability in common vampire bats

“…A limitation of amplicon-based studies is that 16S regions often lack the sensitivity to distinguish among bacterial species and/or strains, which may have different metabolic functions despite sharing identical 16S sequences (Antony-Babu et al, 2017). Future studies using shotgun metagenomic techniques could be used to analyze how the microbiota changes on a gene-by-gene basis in response to habitat quality, which may give more detailed insight to how these changes in vampire bats impact metagenome functions related to immunity.…”

Isolation, Characterization, and Complete Genome Sequence of a Bradyrhizobium Strain Lb8 From Nodules of Peanut Utilizing Crack Entry Infection

“…For example, multiple strains in Brevundimonas alba with identical 16S rRNA sequence had different growth rate and cell yield (Jaspers and Overmann, 2014). Similarly, various species in Streptomyces that had identical 16S rRNA sequence showed different phenotypic and morphologic properties (Antony-Babu et al, 2017). In our research, the differences in the growth curve of these isolates could be explained by variations in other parts of the genome.…”