Vol.:(0123456789) 1 3 Current Microbiology https://doi.org/10.1007/s00284-019-01698-5 REVIEW ARTICLE Metagenomics Approaches in Discovery and Development of New Bioactive Compounds from Marine Actinomycetes Gyana Prakash Mahapatra 1  · Surabhi Raman 1  · Suman Nayak 2  · Sushanto Gouda 3  · Gitishree Das 4  · Jayanta Kumar Patra 4 Received: 4 March 2019 / Accepted: 26 April 2019 © Springer Science+Business Media, LLC, part of Springer Nature 2019 Abstract Marine actinomycetes are prolific sources of marine drug discovery system contributing for several bioactive compounds of biomedical prominence. Metagenomics, a culture-independent technique through its sequence- and function-based screen- ing has led to the discovery and synthesis of numerous biologically significant compounds like polyketide synthase, Non- ribosomal peptide synthetase, antibiotics, and biocatalyst. While metagenomics offers different advantages over conventional sequencing techniques, they also have certain limitations including bias classification, non-availability of quality DNA sam- ples, heterologous expression, and host selection. The assimilation of advanced amplification and screening methods such as φ29 DNA polymerase, Next-Generation Sequencing, Cosmids, and recent bioinformatics tools like automated genome mining, anti-SMASH have shown promising results to overcome these constrains. Consequently, functional genomics and bioinformatics along with synthetic biology will be crucial for the success of the metagenomic approach and indeed for exploring new possibilities among the microbial consortia for the future drug discovery process. Introduction Marine Ecosystem Marine environments constitute for over 70% of the earth’s surface, comprising the sub-zero condition of Arctic and glacial Antarctic region, to the temperate aquatic ecosystem in the tropics, representing an untapped source of natural resources and novel drugs [1–3]. The marine ecosystem is formed mostly by the five oceans on Earth and their biotic components of plants, mammals, fishes, and profound micro- bial consortia of protozoans, phytoplankton, bacteria, fungi, micro, and macro algae, viruses, etc. Marine microbes can be found inhabiting the deep ocean sediments with depths of 11,000 m and pressures exceeding 100 MPa and temperature between − 10 and 100 °C [4]. Extreme environmental con- ditions along with varying temperatures, elevated pressure, and limited sources of light in the oceanic ecosystem work as ideal conditions for synthesis of secondary metabolites [5]. The instinct for survival and thrive for the limited avail- able energy among different marine organisms can also be credited for their diverse amount of derivatives. Microorgan- isms form about 98% of the marine primary productivity, either as free-living organisms or by forming a synergetic relationship with other microbes, thereby posing a range of bioactive complex either through their own metabolic sys- tem or in association with others [6, 7]. Till date, over 23,000 compounds of medicinal impor- tance had been contributed by marine microorganisms including that of peptides, fatty acids, terpenes, enzymes, alkaloids, polyketides, phenols, etc. [8, 9]. Of this, approxi- mately 70% is extracted from actinomycetes, 20% by fungi, 7% from Bacillus spp., and 1–2% by other microbes [10]. Marine microbes like sponges, bryozoans, algae (Chloro- phyta, Rhodophyta), cyanobacteria (BGA), and soft corals have also led their contribution in the discovery of drugs like Pyranonigrin [9], Rubrumazine [11], Echinulin [12], Dehy- droechinulin [13], Variecolorin [14], and Cristatumin [15]. * Jayanta Kumar Patra jkpatra.cet@gmail.com 1 Centre for Advanced Study in Marine Biology, Annamalai University, Parangipettai, Tamilnadu, India 2 Department of Biotechnology and Biomedical Engineering, National Institute of Technology, Rourkela, Odisha, India 3 Amity Institute of Forestry and Wildlife, Amity University, Noida, Uttar Pradesh, India 4 Research Institute of Biotechnology & Medical Converged Science, Dongguk University-Seoul, Goyang, Republic of Korea