Improved and extended multilocus sequence typing (MLST) scheme for Streptomyces reveals complex taxonomic structure

Kiepas, Angelika and Hoskisson, Paul A and Pritchard, Leighton (2022) Improved and extended multilocus sequence typing (MLST) scheme for Streptomyces reveals complex taxonomic structure. In: Microbiology Society Annual Conference 2022, 2022-04-03 - 2022-04-07, Belfast International Conference Centre. (https://doi.org/10.6084/m9.figshare.19615869.v1)

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Abstract

Streptomyces species produce over 60% of all clinically-approved bioactive compounds. Continuing discoveries of new natural products suggest that Streptomyces genomes are a promising potential source for novel antibiotics. Comparative genomics and pangenomics are powerful tools for inferring genes involved in the synthesis of novel antibiotics from closely related genomic sequences. Current Streptomyces taxonomy is contested, making correct application of these approaches more difficult. MLST is used for genomic classification by comparing internal sequence fragments of multiple loci. The current Streptomyces MLST scheme comprises six markers and 236 sequence types (STs; only two new STs were reported since 2016). With the recent increase in sequenced Streptomyces we can now ask: (i) what resolution does MLST offer; (ii) does it reveal useful information about the structure of Streptomyces taxonomy; and (iii) does the current marker set adequately discriminate between species (or other useful groups), or could we improve it with a different set of markers? We extended the current scheme to include all available Streptomyces genomes, identifying over 600 novel STs. Using average nucleotide identity, we observed that the scheme diverged form taxonomy and nomenclature, and inadequately captures species diversity and phylogeny: (i) multiple species were found to share a single ST; (ii) multiple distinct STs were required to describe some genomic species; and (iii) some named species were split across unconnected groups of STs in the minimum spanning tree. Here we demonstrate that the extended MLST scheme provides quantitative motivation for reclassification within Streptomyces, and an improved marker scheme.

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