Background: Actinobacteria are famous for the production of unique secondary metabolites that help in controlling the continuously emerging drug resistance all over the globe. This study aimed at the investigation of an extreme environment the Cholistan desert, located in southern Punjab, Pakistan, for actinobacterial diversity and their activity against methicillin resistant Staphylococcus aureus (MRSA). The Cholistan desert is a sub-tropical and arid ecosystem with harsh environment, limited rainfall and low humidity. The 20 soil and sand samples were collected from different locations in the desert and the actinobacterial strains were selectively isolated. The isolated strains were identified using a polyphasic taxonomic approach including morphological, biochemical, physiological characterization, scanning electron microscopy (SEM) and by 16S rRNA gene sequencing.

Results: A total of 110 desert actinobacterial strains were recovered, which were found to be belonging to 3 different families of the order Actinomycetales, including the family Streptomycetaceae, family Pseudonocardiaceae and the family Micrococcaceae. The most frequently isolated genus was Streptomyces along with the genera Pseudonocardia and Arthrobacter. The isolated strains exhibited promising antimicrobial activity against methicillin resistant Staphylococcus aureus (MRSA) with zone of inhibition in the range of 9–32 mm in antimicrobial screening assays. The chemical profiling by thin layer chromatography, HPLC-UV/Vis and LC-MS analysis depicted the presence of different structural classes of antibiotics.

Conclusion: The study revealed that Cholistan desert harbors immense actinobacterial diversity and most of the strains produce structurally diverse bioactive secondary metabolites, which are a promising source of novel antimicrobial drug candidates.

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Published in BMC Microbiology, v. 19, article no. 49, p. 1-17.

© The Author(s). 2019

This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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This work was supported by the grant from Higher Education Commission (HEC) Pakistan (Grant No. PIN: 112–31652-2BM1–172, and HEC-NRPU Project 2121). This work was also supported by National Institutes of Health grant R24 OD21479 (JST), The University of Kentucky, College of Pharmacy and the National Center for Advancing Translational Sciences (UL1TR001998 and UL1TR000117). The grants PIN: 112–31652-2BM1–172, and HEC-NRPU Project 2121, provided the support in terms of student’s stipend and experimental design, travel cost for sample collection, research supplies, reagents, DNA sequencing cost, data analysis and writing the paper. Grants R24 OD21479 (JST), UL1TR001998 and UL1TR000117 supported, in part, personnel and reagents associated with chemical screening, analytical methods and data analysis.

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Additional file 1: Isolation media used for the Actinobacterial Diversity.

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