Marine metagenomics, a valuable tool for enzymes and bioactive compounds discovery

Barone, Rosalba; Santi, Concetta De; Esposito, Fortunato Palma; Tedesco, Pietro; Galati, Federica; Visone, Marco; Scala, Alessia; Pascale, Donatella de

doi:10.3389/fmars.2014.00038

Cited by 48 publications

(29 citation statements)

References 70 publications

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“…Metagenomics studies from extreme environments led to the discovery of biocatalysts, secondary metabolites and bioactive compounds (Wong 2010; Barone et al 2014). For example sulphur-cycling genes from sulphidic deep sea hydrothermal vent communities (Cao et al 2014), H 2 oxidation genes from H 2 -rich serpentinite hydrothermal vent communities (Brazelton et al 2011), lipid oxidation genes in DSHV communities (He et al 2013) and genes for ammonia- oxidation (amoA) in the Guaymas Basin (Baker et al 2012) were identified by community metagenome analysis.…”

Section: Introductionmentioning

confidence: 99%

Bacterial and archeal community composition in hot springs from Indo-Burma region, North-east India

et al. 2016

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Bacterial and archaeal diversity of two alkaline Indian hot springs, Jakrem (Meghalaya) and Yumthang (Sikkim), were studied. Thirteen major bacterial phyla were identified of which Firmicutes, Chloroflexi and Thermi were dominant in Jakrem and Proteobacteria in Yumthang. The dominant genera were Clostridium, Chloroflexus and Meiothermus at Jakrem (water temperature 46 °C, pH 9) and Thiobacillus, Sulfuritalea at Yumthang (water temperature 39 °C, pH 8) hot springs. The four Euryarchaeota taxa that were observed in both the hot springs were Methanoculleus, Methanosaeta, Methanosarcina and Methanocorposculum. Elstera litoralis, Thiovirga sp., Turneriella sp. were observed for the first time in association with hot springs along with Tepidibacter sp., Ignavibacterium sp., Teribacillus sp. and Dechloromonas sp. Individual bacterial phyla were found to be specifically correlated with certain physico-chemical factors such as temperature, dissolved SiO2, elemental S, total sulphide, calcium concentrations in hot spring water. Bacterial reads involved in sulfur cycle were identified in both16S rRNA gene library and sulfur metabolism may play key physiological functions in this hot spring. Members within Desulfobacterales and Thermodesulfovibrionaceae were identified and hypothesized their role in regulating sulfur cycle. The presence of many taxonomically unsolved sequences in the 16S rRNA gene tag datasets from these hot springs could be a sign of novel microbe richness in these less known hot water bodies of Northeastern India.Electronic supplementary materialThe online version of this article (doi:10.1186/s13568-016-0284-y) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Bacterial and archeal community composition in hot springs from Indo-Burma region, North-east India

et al. 2016

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“…Compound dereplication is one of the big hurdles in the discovery of MNPs. To achieve a simpler, faster, and more effective compound dereplication, the collected data in these databases include computational data from bioinformatics, compound curation and compilation, and experimental data from UV spectroscopy, mass spectroscopy, and nuclear magnetic resonance (NMR) . These databases deliver crucial information to the scientific community to discover new MNPs.…”

Section: Available Databases Of Mnpsmentioning

confidence: 99%

Free Marine Natural Products Databases for Biotechnology and Bioengineering

Barbosa

Roque

2019

Biotechnology Journal

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Marine organisms and micro‐organisms are a source of natural compounds with unique chemical features. These chemical properties are useful for the discovery of new functions and applications of marine natural products (MNPs). To extensively exploit the potential implementations of MNPs, they are gathered in chemical databases that allow their study and screening for applications of biotechnological interest. However, the classification of MNPs is currently poor in generic chemical databases. The present availability of free‐access‐focused MNP databases is scarce and the molecular diversity of these databases is still very low when compared to the paid‐access ones. In this review paper, the current scenario of free‐access MNP databases is presented as well as the hindrances involved in their development, mainly compound dereplication. Examples and opportunities for using freely accessible MNP databases in several important areas of biotechnology are also assessed. The scope of this paper is, as well, to notify the latent potential of these information sources for the discovery and development of new MNPs in biotechnology, and push future efforts to develop a public domain MNP database freely available for the scientific community.

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“…For example, inferences concerning the metabolic pathways for nitrogen and carbon cycling, respiration mechanisms and the degradation of particular toxic compounds can be based on the relative abundance or even the presence and absence of the relevant genes (Barone et al 2014;Narihiro et al 2014). With the constantly improved methods for sequence generation and bioinformatic analysis, near complete genome assembly is slowly becoming a standard method (Hug et al 2016).…”

Section: Genomes From Metagenomesmentioning

confidence: 99%

The multi-omics promise in context: from sequence to microbial isolate

Gutleben

Mares

Elsas

et al. 2017

Critical Reviews in Microbiology

170

107

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The numbers and diversity of microbes in ecosystems within and around us is unmatched, yet most of these microorganisms remain recalcitrant to in vitro cultivation. Various high-throughput molecular techniques, collectively termed multi-omics, provide insights into the genomic structure and metabolic potential as well as activity of complex microbial communities. Nonetheless, pure or defined cultures are needed to (1) decipher microbial physiology and thus test multiomics-based ecological hypotheses, (2) curate and improve database annotations and (3) realize novel applications in biotechnology. Cultivation thus provides context. In turn, we here argue that multi-omics information awaits integration into the development of novel cultivation strategies. This can build the foundation for a new era of omics information-guided microbial cultivation technology and reduce the inherent trial-and-error search space. This review discusses how information that can be extracted from multi-omics data can be applied for the cultivation of hitherto uncultured microorganisms. Furthermore, we summarize groundbreaking studies that successfully translated information derived from multi-omics into specific media formulations, screening techniques and selective enrichments in order to obtain novel targeted microbial isolates. By integrating these examples, we conclude with a proposed workflow to facilitate future omics-aided cultivation strategies that are inspired by the microbial complexity of the environment. ARTICLE HISTORY

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Marine metagenomics, a valuable tool for enzymes and bioactive compounds discovery

Cited by 48 publications

References 70 publications

Bacterial and archeal community composition in hot springs from Indo-Burma region, North-east India

Bacterial and archeal community composition in hot springs from Indo-Burma region, North-east India

Free Marine Natural Products Databases for Biotechnology and Bioengineering

The multi-omics promise in context: from sequence to microbial isolate

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