Microbial diversity of a Himalayan forest and characterization of rare actinomycetes for antimicrobial compounds

Abstract

The slow pace of discovery of new effective drugs against multi-drug resistant pathogens and largely unsuccessful combinatorial chemistry has resulted in shifting the focus back to natural products as sources of lead molecules for antimicrobial drugs, mainly due to their structural diversity. Investigation of under-explored habitats for potentially novel microorganisms provides for wider chemodiversity. In this study, four actinomycetes, namely UK-274, UK-281, UK-282 and UK-285, which showed broad-spectrum antibacterial and antifungal activities, were isolated from Timli forest range of the biodiversity-rich Himalayan region. 16S rRNA gene sequence analysis showed that the nearest neighbours of the isolates were Actinomadura nitrigenes, Streptomyces niveiscabiei, and Kitasatospora psammotica with similarity values ranging between 97 and 98% suggesting their potential as new isolates. Further morphological and phenotypic characterization strengthened this assumption. Isolate UK-282, of the rare actinomycetes Kitasatospora group, was found to produce antimicrobial activity. Metabolite fingerprinting of ethyl acetate fraction of isolate UK-282 by GC-MS and 1H NMR analysis showed the presence of three novel compounds. The study underlines that a combination approach of bioprospecting of under-studied habitats and focus on rare actinomycetes may result in the identification of novel chemodiversity.

Keywords: Actinomycete; Antimicrobial; Forest; Metabolite fingerprinting; Multi-drug resistant; Natural products.

Fig. 1

Antimicrobial activity of the isolates from the Timli forest range

Fig. 2

Antimicrobial activity of selected isolates (UK-274, UK-281, UK-282 and UK-285) from the Timli forest range

Fig. 3

Neighbour-joining phylogenetic tree based on 16S rDNA sequence showing relationship between isolates UK-274, UK-281, UK-282 and UK-285 with related type strains of Actinomadura sp., Streptomyces sp. and Kitasatospora sp. Bootstrap values at the nodes indicate collated values based on 1000 resampled datasets; only values above > 95% are given. Bar 0.005 indicates substitutions per nucleotide. *And # at nodes indicate branches that were also recovered using the maximum-likelihood and maximum-parsimony algorithms. A Actinomadura, K Kitasatospora, S Streptomyces, NBRC NITE Biological Resource Centre, DSM DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, JCM Japan Collection of Microorganisms, NRRL Agriculture Research Service Culture Collection, ATCC American Type Culture Collection