Skip to main content
ARS Home » Midwest Area » Peoria, Illinois » National Center for Agricultural Utilization Research » Mycotoxin Prevention and Applied Microbiology Research » Research » Publications at this Location » Publication #325104
Title: Taxonomic evaluation of unidentified Streptomyces isolates in the ARS Culture Collection (NRRL) using multi-locus sequence analysis

Author
item Labeda, David
item DOROGHAZI, JAMES - University Of Illinois
item JU, KU-SAN - University Of Illinois
item METCALF, WILLIAM - University Of Illinois

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 6/20/2016
Publication Date: 6/20/2016
Citation: Labeda, D.P., Doroghazi, J.R., Ju, K., Metcalf, W.W. 2016. Taxonomic evaluation of unidentified Streptomyces isolates in the ARS Culture Collection (NRRL) using multi-locus sequence analysis [abstract].

Interpretive Summary:

Technical Abstract: The ARS Culture Collection (NRRL) currently contains 7569 strains within the family Streptomycetaceae but 4368 of them have not been characterized to the species level. A gene sequence database using the Bacterial Isolate Genomic Sequence Database package (BIGSdb) (Jolley & Maiden, 2010) is available on the ARS Microbial Genomic Sequence Database website (http://199.133.98.43) and contains partial sequences of five house-keeping genes atpD, gyrB, recA, rpoB and trpB used for the identification of Streptomyces species. A set of 243 uncharacterized Streptomyces strains were selected for evaluation by multi-locus sequence analysis based on their reported production of blue- or green-colored spores, representing a manageable strain set for evaluation. Other strains that had draft genome sequences available from prior screening of the collection for production of phosphonate-containing compounds were also included in the study. Sequences of the house-keeping loci were concatenated head-to-tail in frame during export by the BIGSdb package and subsequently aligned using MAFFT (Katoh &Standley, 2013). Phylogenetic relationships were constructed with MEGA 6.0 (Tamura et al., 2013) using Maximum Likelihood (ML) based on the General Time Reversible model (Nei & Kumar, 2000) using Gamma distribution among sites, including invariant sites (G+I), and 11 rate categories, previously determined to be the optimal model for these data using jModelTest2 (Darriba et al., 2012). The MLSA distance was also calculated for all strain pairs in MEGA6. On the basis of phylogenetic position in the ML tree and an MLSA distance of = 0.007 it was possible to conclusively identify 74 of the 243 strains as representatives of described Streptomyces species. The remaining strains represent t at least 115 potentially new Streptomyces species.