Open Access Highly Accessed Research article

Complete genome sequence of Saccharothrix espanaensis DSM 44229T and comparison to the other completely sequenced Pseudonocardiaceae

Tina Strobel1, Arwa Al-Dilaimi2, Jochen Blom3, Arne Gessner1, Jörn Kalinowski2, Marta Luzhetska1, Alfred Pühler4, Rafael Szczepanowski2, Andreas Bechthold1* and Christian Rückert2

Author affiliations

1 Department of Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, Freiburg, 79104, Germany

2 Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, 33615, Germany

3 Bioinformatics Resource Facility, CeBiTec, Bielefeld University, Bielefeld, 33615, Germany

4 Senior Research Group in Genome Research of Industrial Microorganisms, CeBiTec, Bielefeld University, Bielefeld, 33615, Germany

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Citation and License

BMC Genomics 2012, 13:465  doi:10.1186/1471-2164-13-465

Published: 9 September 2012



The genus Saccharothrix is a representative of the family Pseudonocardiaceae, known to include producer strains of a wide variety of potent antibiotics. Saccharothrix espanaensis produces both saccharomicins A and B of the promising new class of heptadecaglycoside antibiotics, active against both bacteria and yeast.


To better assess its capabilities, the complete genome sequence of S. espanaensis was established. With a size of 9,360,653 bp, coding for 8,501 genes, it stands alongside other Pseudonocardiaceae with large genomes. Besides a predicted core genome of 810 genes shared in the family, S. espanaensis has a large number of accessory genes: 2,967 singletons when compared to the family, of which 1,292 have no clear orthologs in the RefSeq database. The genome analysis revealed the presence of 26 biosynthetic gene clusters potentially encoding secondary metabolites. Among them, the cluster coding for the saccharomicins could be identified.


S. espanaensis is the first completely sequenced species of the genus Saccharothrix. The genome discloses the cluster responsible for the biosynthesis of the saccharomicins, the largest oligosaccharide antibiotic currently identified. Moreover, the genome revealed 25 additional putative secondary metabolite gene clusters further suggesting the strain’s potential for natural product synthesis.