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

Sanjay Antony-Babu,Delphine Parrot,Marcelino T Suzuki,Véronique Eparvier,Didier Stien,Sophie Tomasi

doi:10.1038/s41598-017-11363-1

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.

Highlights

It is clear that almost all eukaryotic organisms have an associated prokaryotic microflora
small subunit (SSU) rRNA gene-sequencing have played a pivotal role in solving many discrepancies in their taxonomy[17, 19, 20], regardless of the diversity observed among strains with similar SSU rRNA gene sequences[20,21,22,23,24]
MOLA1420 and MOLA1421 were isolated on marine agar they were not more halotolerant when compared to some strains isolated using actinomycetes isolation agar

Summary

Introduction

It is clear that almost all eukaryotic organisms have an associated prokaryotic microflora. Thanks to advances in massively parallel sequencing technology, accessibility to high performance computing (HPC), and the development of comparative analytical software, the number of prokaryotic microflora surveys have increased in recent years[1] These studies are mostly based on the analysis of small subunit (SSU) rRNA diversity[2] and take advantage of the correlation between the gene sequence and prokaryotic taxonomical hierarchy[3]. In this type of studies sequences are clustered together at a certain level of identity (97% in the vast majority of the cases) in what are termed Operational Taxonomic Units (OTUs)[4]. The strains were subject of morphological, phenotypical, molecular taxonomic and metabolic analyses to test whether stains with identical SSU rRNA gene sequences represented the same species, and presented similar functional traits

Methods

Results

Conclusion