Antimicrobial biosynthetic potential and diversity of culturable soil actinobacteria from forest ecosystems of Northeast India

Abstract

Actinobacteria is a goldmine for the discovery of abundant secondary metabolites with diverse biological activities. this study explores antimicrobial biosynthetic potential and diversity of actinobacteria from Pobitora Wildlife Sanctuary and Kaziranga National Park of Assam, India, lying in the Indo-Burma mega-biodiversity hotspot. A total of 107 actinobacteria were isolated, of which 77 exhibited significant antagonistic activity. 24 isolates tested positive for at least one of the polyketide synthase type I, polyketide synthase type II or non-ribosomal peptide synthase genes within their genome. their secondary metabolite pathway products were predicted to be involved in the production of ansamycin, benzoisochromanequinone, streptogramin using DoBISCUIT database. Molecular identification indicated that these actinobacteria predominantly belonged to genus Streptomyces, followed by Nocardia and Kribbella. 4 strains, viz. Streptomyces sp. PB-79 (GenBank accession no. KU901725; 1313 bp), Streptomyces sp. Kz-28 (GenBank accession no. KY000534; 1378 bp), Streptomyces sp. Kz-32 (GenBank accession no. KY000536; 1377 bp) and Streptomyces sp. Kz-67 (GenBank accession no. KY000540; 1383 bp) showed ~89.5% similarity to the nearest type strain in EzTaxon database and may be considered novel. Streptomyces sp. Kz-24 (GenBank accession no. KY000533; 1367 bp) showed only 96.2% sequence similarity to S. malaysiensis and exhibited minimum inhibitory concentration of 0.024 µg/mL against methicilin resistant Staphylococcus aureus ATCC 43300 and Candida albicans MTCC 227. This study establishes that actinobacteria isolated from the poorly explored Indo-Burma megabiodiversity hotspot may be an extremely rich reservoir for production of biologically active compounds for human welfare. Since ancient times, mankind has been exploring nature for bioactive organisms to treat different ailments. More than 100000 natural products have been identified in the last 150 years, which include highly assorted chemical classes such as polyketides, alkaloids, non-ribosomal peptides, isoprenoids or phenylpropanoids 1,2. Microbial biodiversity can provide us with the richest and the most versatile reservoir of potentially active natural products. A large portion of genomes from beneficial microbes are dedicated to the production of these valuable natural products. A single microbe is capable of making 30-50 natural product compounds 3. There are approximately 1 million natural products out of which about 25% are biologically active showing either positive activity or toxicity. Among the prospective sources of natural products, bacteria are prolific sources and a vast majority of these products are produced by a phylum of Gram-positive bacteria known as the "Actinobacteria" 4-6. Actinobacteria are diverse group of bacteria with high content of guanosine-cytosine (65-75%) ranging from 2.5-9.7 Mb genome size 7. Among actinobacteria, about 75% of antibiotics such as ivermectin, streptomycin, nystatin and tetracycline are produced by the microbial world's...

Antimicrobial and antinematicidal metabolites from Streptomyces cuspidosporus strain SA4 against selected pathogenic bacteria, fungi and nematode

“…The peak area is directly proportional to magnitude of the bioactive compounds existing in the partially purified composites. GCMS analysis showed the presence of 17 compounds, most of which were earlier documented for its antibacterial, antifungal, antitumor, anticancer and antioxidant activities ( Al-Dhabi et al, 2014 , Tan et al, 2015 , Law et al, 2019 , Priyanka and Debajit, 2020 ; Sholkamy et al, 2020 ).…”

Comparative Genomics Reveals Prophylactic and Catabolic Capabilities of Actinobacteria within the Fungus-Farming Termite Symbiosis

“…Second, the genomes contain genes for enzymes targeting all plant and fungal substrates identified in fungus-growing termite gut community-level analyses (20). Lastly, although Actinobacteria represent a very small set of the complex microbiomes present within termite guts and fungus combs, their large enzymatic potential is consistent with their well-established roles in natural ecosystems as efficient biomass degraders (16,20,(44)(45)(46)(47) and prolific producers of antimicrobial compounds (5,43). In line with this, the closely related free-living Actinobacteria show similar metabolic and enzymatic potential, thus making horizontal acquisition highly likely.…”

Tapping Into Actinobacterial Genomes for Natural Product Discovery

“…The products formed by the combination of clusters can be crucial and might counter the problem of infections caused by resistant microbes by providing novel bioactive molecules. The production of virginiamycin and oxazolomycin has been reported recently, resulting from PKS/NRPS hybrid (Sharma and Thakur, 2020).…”

“…Practically, γ-butyrolactones can be used as chemical elicitors for the production of antibiotics like virginiamycin, showdomycins in actinobacteria. Using ribosomal engineering, S. coelicolor A3(2) yielded 1.63 g/L of actinorhodin which is 180-fold higher than wild type strain (Sharma and Thakur, 2020).…”