LC-MS-based metabolomics study of marine bacterial secondary metabolite and antibiotic production in Salinispora arenicola

Characterization of anthranilic acid produced by Virgibacillus salarius MML1918 and its bio-imaging application

Anthranilic acid (AA) holds significant importance in the chemical industry. It serves as a crucial building block for the amino acid tryptophan by manipulating the tryptophan biosynthesis pathway, it is possible to increase the production of anthranilic acid. In this study, we utilized metabolic engineering approaches to produce anthranilic acid from the halophilic bacterium Virgibacillus salarius MML1918. The halophilic bacteria were grown in an optimized production medium, and mass production of secondary metabolites was made in ATCC medium 1097 Proteose peptone-for halophilic bacteria and subjected to column chromatography followed by sub-column chromatography the single band for the purified compound was confirmed. Further, various spectral analyses were made for the partially purified compounds, and fluorescence microscopy for fungal cell observation was performed. The purified compound was confirmed by single crystal X-ray diffraction (XRD) analysis, and it was identified as 2-amino benzoic acid. The Fourier transform infrared Spectroscopy (FT-IR) spectrum and nuclear magnetic resonance (NMR) spectrum also confirm the structural characteristic of 2-amino benzoic acid. The UV-Vis absorption spectrum of AA shows the maximum absorption at 337.86 nm. The emission spectrum of 2-amino benzoic acid showed the maximum emission at 453 nm. The bio-imaging application of 2-amino benzoic acid was examined with fungal mycelium of Rhizoctonia solani. It was effectively bound and emitted the blue color at the concentration of 200 and 300 µg/mL. The halophilic bacterium (V. salarius), may have unique metabolic pathways and requirements compared to non-halophilic organisms, to produce AA effectively. This could have implications for industrial biotechnology, particularly in manufacturing environments where high salt concentrations are present and also it can be used as bio-imaging agent.

Reducing Mass Confusion over the Microbiome

As genetic tools continue to emerge and mature, more information is revealed about the identity and diversity of microbial community members. Genetic tools can also be used to make predictions about the chemistry that bacteria and fungi produce to function and communicate with one another and the host. Ongoing efforts to identify these products and link genetic information to microbiome chemistry rely on analytical tools. This tutorial highlights recent advancements in microbiome studies driven by techniques in mass spectrometry.

Rifamycin-Related Polyketides from a Marine-Derived Bacterium Salinispora arenicola and Their Cytotoxic Activity

Eight rifamycin-related polyketides were isolated from the culture broth of a marine-derived bacterium Salinispora arenicola, including five known (2-5 and 8) and three new derivatives (1, 6, and 7). The structures of the new compounds were determined by means of spectroscopic methods (HRESIMS and 1D, 2D NMR) and a comparison of their experimental data with those previously reported in the literature. The isolated compounds were evaluated for their cytotoxicity against one normal, six solid, and seven blood cancer cell lines and 1 showed moderate activity against all the tested cell lines with GI50 values ranging from 2.36 to 9.96 µM.

Omics technologies towards sesame improvement: a review

Genetic improvement of sesame (Sesamum indicum L.), one of the most important oilseed crops providing edible oil, proteins, minerals, and vitamins, is important to ensure a balanced diet for the growing world population. Increasing yield, seed protein, oil, minerals, and vitamins is urgently needed to meet the global demand. The production and productivity of sesame is very low due to various biotic and abiotic stresses. Therefore, various efforts have been made to combat these constraints and increase the production and productivity of sesame through conventional breeding. However, less attention has been paid to the genetic improvement of the crop through modern biotechnological methods, leaving it lagging behind other oilseed crops. Recently, however, the scenario has changed as sesame research has entered the era of "omics" and has made significant progress. Therefore, the purpose of this paper is to provide an overview of the progress made by omics research in improving sesame. This review presents a number of efforts that have been made over past decade using omics technologies to improve various traits of sesame, including seed composition, yield, and biotic and abiotic resistant varieties. It summarizes the advances in genetic improvement of sesame using omics technologies, such as germplasm development (web-based functional databases and germplasm resources), gene discovery (molecular markers and genetic linkage map construction), proteomics, transcriptomics, and metabolomics that have been carried out in the last decade. In conclusion, this review highlights future directions that may be important for omics-assisted breeding in sesame genetic improvement.

Integrated Metabolomic, Molecular Networking, and Genome Mining Analyses Uncover Novel Angucyclines From Streptomyces sp. RO-S4 Strain Isolated From Bejaia Bay, Algeria

Multi-omic approaches have recently made big strides toward the effective exploration of microorganisms, accelerating the discovery of new bioactive compounds. We combined metabolomic, molecular networking, and genomic-based approaches to investigate the metabolic potential of the Streptomyces sp. RO-S4 strain isolated from the polluted waters of Bejaia Bay in Algeria. Antagonistic assays against methicillin-resistant Staphylococcus aureus with RO-S4 organic extracts showed an inhibition zone of 20 mm by using the agar diffusion method, and its minimum inhibitory concentration was 16 μg/ml. A molecular network was created using GNPS and annotated through the comparison of MS/MS spectra against several databases. The predominant compounds in the RO-S4 extract belonged to the angucycline family. Three compounds were annotated as known metabolites, while all the others were putatively new to Science. Notably, all compounds had fridamycin-like aglycones, and several of them had a lactonized D ring analogous to that of urdamycin L. The whole genome of Streptomyces RO-S4 was sequenced to identify the biosynthetic gene cluster (BGC) linked to these angucyclines, which yielded a draft genome of 7,497,846 bp with 72.4% G+C content. Subsequently, a genome mining analysis revealed 19 putative biosynthetic gene clusters, including a grincamycin-like BGC with high similarity to that of Streptomyces sp. CZN-748, that was previously reported to also produce mostly open fridamycin-like aglycones. As the ring-opening process leading to these compounds is still not defined, we performed a comparative analysis with other angucycline BGCs and advanced some hypotheses to explain the ring-opening and lactonization, possibly linked to the uncoupling between the activity of GcnE and GcnM homologs in the RO-S4 strain. The combination of metabolomic and genomic approaches greatly improved the interpretation of the metabolic potential of the RO-S4 strain.

Recent Advances of Marine Sponge-Associated Microorganisms as a Source of Commercially Viable Natural Products

Many industrially significant compounds have been derived from natural products in the environment. Research efforts so far have contributed to the discovery of beneficial natural products that have improved the quality of life on Earth. As one of the sources of natural products, marine sponges have been progressively recognised as microbial hotspots with reports of the sponges harbouring diverse microbial assemblages, genetic material, and metabolites with multiple industrial applications. Therefore, this paper aims at reviewing the recent literature (primarily published between 2016 and 2022) on the types and functions of natural products synthesised by sponge-associated microorganisms, thereby helping to bridge the gap between research and industrial applications. The metabolites that have been derived from sponge-associated microorganisms, mostly bacteria, fungi, and algae, have shown application prospects especially in medicine, cosmeceutical, environmental protection, and manufacturing industries. Sponge bacteria-derived natural products with medical properties harboured anticancer, antibacterial, antifungal, and antiviral functions. Efforts in re-identifying the origin of known and future sponge-sourced natural products would further clarify the roles and significance of microbes within marine sponges.

Metabolomics on the study of marine organisms

BACKGROUND

Marine ecosystems are hosts to a vast array of organisms, being among the most richly biodiverse locations on the planet. The study of these ecosystems is very important, as they are not only a significant source of food for the world but also have, in recent years, become a prolific source of compounds with therapeutic potential. Studies of aspects of marine life have involved diverse fields of marine science, and the use of metabolomics as an experimental approach has increased in recent years. As part of the "omics" technologies, metabolomics has been used to deepen the understanding of interactions between marine organisms and their environment at a metabolic level and to discover new metabolites produced by these organisms.

AIM OF REVIEW

This review provides an overview of the use of metabolomics in the study of marine organisms. It also explores the use of metabolomics tools common to other fields such as plants and human metabolomics that could potentially contribute to marine organism studies. It deals with the entire process of a metabolomic study, from sample collection considerations, metabolite extraction, analytical techniques, and data analysis. It also includes an overview of recent applications of metabolomics in fields such as marine ecology and drug discovery and future perspectives of its use in the study of marine organisms.

KEY SCIENTIFIC CONCEPTS OF REVIEW

The review covers all the steps involved in metabolomic studies of marine organisms including, collection, extraction methods, analytical tools, statistical analysis, and dereplication. It aims to provide insight into all aspects that a newcomer to the field should consider when undertaking marine metabolomics.

Recent Antimicrobial Responses of Halophilic Microbes in Clinical Pathogens

Microbial pathogens that cause severe infections and are resistant to drugs are simultaneously becoming more active. This urgently calls for novel effective antibiotics. Organisms from extreme environments are known to synthesize novel bioprospecting molecules for biomedical applications due to their peculiar characteristics of growth and physiological conditions. Antimicrobial developments from hypersaline environments, such as lagoons, estuaries, and salterns, accommodate several halophilic microbes. Salinity is a distinctive environmental factor that continuously promotes the metabolic adaptation and flexibility of halophilic microbes for their survival at minimum nutritional requirements. A genetic adaptation to extreme solar radiation, ionic strength, and desiccation makes them promising candidates for drug discovery. More microbiota identified via sequencing and ‘omics’ approaches signify the hypersaline environments where compounds are produced. Microbial genera such as Bacillus, Actinobacteria, Halorubrum and Aspergillus are producing a substantial number of antimicrobial compounds. Several strategies were applied for producing novel antimicrobials from halophiles including a consortia approach. Promising results indicate that halophilic microbes can be utilised as prolific sources of bioactive metabolites with pharmaceutical potentialto expand natural product research towards diverse phylogenetic microbial groups which inhabit salterns. The present study reviews interesting antimicrobial compounds retrieved from microbial sources of various saltern environments, with a discussion of their potency in providing novel drugs against clinically drug-resistant microbes.

Comparison of metabolome characteristics and screening of chemical markers in Chrysanthemum indicum from different habitats

Chrysanthemum indicum is a polymorphic species with many ecological, geographical or eco-geographic populations, but there are few studies on the metabolic characteristics of different populations. This study conducted widely targeted metabolomics studies on Ch. indicum from seven typical producing areas. As a result, a total of 802 metabolites were detected and identified, among which the top three categories of metabolites were flavonoids, organic acids and amino acids and derivatives. Through multivariate statistical analysis, the seven samples from different habitats could be divided into four categories, and the significantly changed metabolites between different categories were mainly concentrated in the flavonoid synthesis pathway. Through a variety of cluster analysis, it was observed that the Ch. nankingense (Nakai) Tzvel (Chinese name Juhuanao) had the largest separation degree from other samples and were clustered into a single category. Furthermore, the corresponding candidate chemical markers were screened in this study to distinguish the Juhuanao. Correlation analysis showed that climatic factors were not the main reason for the differences in the metabolic characteristics of Ch. indicum in different populations, which indicated that Ch. indicum is indeed a species with rich variation.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-022-01137-z.

Selective isolation, antimicrobial screening and phylogenetic diversity of marine actinomycetes derived from the Coast of Bejaia City (Algeria), a polluted and microbiologically unexplored environment

AIMS

The current study aimed to evaluate the occurrence of actinomycetes in the Coast of Bejaia City using selective isolation, as well as their bioactivity and phylogenitic diversity.

METHODS AND RESULTS

Different selective media and methods were used, leading to the isolation of 103 actinomycete strains. The number of strains was influenced by isolation procedures and their interactions based on a three-way ANOVA and a post hoc Tukey test, which revealed that using M2 medium, dilution of samples followed by moderate heat treatment, and sampling at 10-20 m yielded the highest numbers of actinomycetes. The isolates were screened for their antimicrobial activity against human pathogenic microorganisms using agar and well diffusion methods. Of all the isolates, ten displayed activity against at least one Gram-positive bacterium, of which P21 showed the highest activity against Staphylococcus aureus, Methicillin-resistant S. aureus and Bacillus subtilis, with a diameter of 32, 28 and 25 mm respectively. Subsequently, active isolates were assigned to Streptomyces spp. and Nocardiopsis spp. based on 16S rRNA gene sequencing, including a putative new Streptomyces species (S3). The phenotypic characteristics of the P21 strain were determined, and interesting enzymatic capacities were shown.

CONCLUSION

The recovery of actinomycetes along the Coast of Bejaia City was influenced by the isolation procedure. Ten strains displayed interesting antibacterial activity against Gram-positive bacteria, of which the P21 strain was selected as the most active strain.

SIGNIFICANCE AND IMPACT OF THE STUDY

This work provides a new insight into the occurrence of actinobacteria in the Coast of Bejaia. It suggests also that polluted environments such as Bejaia Bay could provide access to interesting actinomycetes as sources of antibiotic leads.

A comparative GC-MS analysis of bioactive secondary metabolites produced by halotolerant Bacillus spp. isolated from the Great Sebkha of Oran

The reemergence of infectious diseases and resistant pathogens represents a serious problem for human life. Hence, the screening for new or alternative antimicrobial compounds is still urgent. Unusual ecosystems such as saline habitats are considered promising environments for the purposes of isolating bacterial strains able to produce potent natural products. The aim of this study is the identification of bioactive compounds biosynthesized by three halotolerant strains isolated from the Sebkha of Oran (Algeria) using gas chromatography coupled to mass spectrometry. Primary screening investigation of antimicrobial activities were performed against reference bacterial and fungal strains and revealed a broad-spectrum activity. Secondary metabolite extraction was carried out using ethyl acetate and chloroform. Crude extracts were tested for bioactivity using the disc diffusion method and subjected to GC-MS analysis. The extracts showed an important inhibitory effect against all tested strains. Fifty-six compounds were identified; they include tert-butyl phenol compounds, fatty acid methyl esters due to the methylation procedure, hydrocarbons, aldehydes, benzoquinones, pyrrols, and terpenes. Literature reports such compounds to have wide biological and pharmaceutical applications. The molecular identification of the three isolates was achieved using the 16S-23S rRNA gene intergenic spacer region (ITS) and 16S rRNA sequencing. Partial 16S rRNA gene sequencing showed very high similarity with many species of Bacillus. This study provided insights on the potential of halotolerant Bacillus as drug research target for bioactive metabolites. The findings suggest that the Great Sebkha of Oran is a valuable source of strains exhibiting variety of beneficial attributes that can be utilized in the development of biological antibiotics.

Metabolomic study of marine Streptomyces sp.: Secondary metabolites and the production of potential anticancer compounds

Resorting to a One Strain Many Compounds (OSMAC) approach, the marine Streptomyces sp. BRB081 strain was grown in six different media settings over 1, 2, 3 or 7 days. Extractions of mycelium and broth were conducted separately for each media and cultivation period by sonication using methanol/acetone 1:1 and agitation with ethyl acetate, respectively. All methanol/acetone and ethyl acetate crude extracts were analysed by HPLC-MS/MS and data treatment was performed through GNPS platform using MZmine 2 software. In parallel, the genome was sequenced, assembled and mined to search for biosynthetic gene clusters (BGC) of secondary metabolites using the AntiSMASH 5.0 software. Spectral library search tool allowed the annotation of desferrioxamines, fatty acid amides, diketopiperazines, xanthurenic acid and, remarkably, the cyclic octapeptides surugamides. Molecular network analysis allowed the observation of the surugamides cluster, where surugamide A and the protonated molecule corresponding to the B-E isomers, as well as two potentially new analogues, were detected. Data treatment through MZmine 2 software allowed to distinguish that the largest amount of surugamides was obtained by cultivating BRB081 in SCB medium during 7 days and extraction of culture broth. Using the same data treatment, a chemical barcode was created for easy visualization and comparison of the metabolites produced overtime in all media. By genome mining of BRB081 four regions of biosynthetic gene clusters of secondary metabolites were detected supporting the metabolic data. Cytotoxic evaluation of all crude extracts using MTT assay revealed the highest bioactivity was also observed for extracts obtained in the optimal conditions as those for surugamides production, suggesting these to be the main active compounds herein. This method allowed the identification of compounds in the crude extracts and guided the selection of best conditions for production of bioactive compounds.

Bioactive natural products from the genus Salinospora: a review

Actinomycetes are an important source for bioactive secondary metabolites. Among them, the genus Salinispora is one of the first salt obligatory marine species worldwide and is typically found in various types of substrates in tropical and subtropical marine environments including sediments and marine organisms. This genus produces a wide range of chemical scaffolds and bioactive compounds such as lomaiviticins, cyclomarins, rifamycins, salinaphthoquinones, and salinosporamides. This review arranged Salinispora derived secondary metabolites according to the three species that comprise the genus. Moreover, muta- and semi-synthesis analogs derived from salinosporamide were also described in this review.

Evaluation of microalgae and cyanobacteria as potential sources of antimicrobial compounds

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Three microalgal extracts show antimicrobial activity against gram-positive bacteria.

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Different purification techniques were used to reveal the bioactive compounds.

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Linoleic acid, oleic acid, DHA and EPA inhibited the growth of gram-positive bacteria.

In recent decades, marine microorganisms have become known for their ability to produce a wide variety of secondary bioactive metabolites. Several compounds have been isolated from marine microorganisms for the development of novel bioactives for the food and pharmaceutical industries. In this study, a number of microalgae were evaluated for their antimicrobial activity against gram-positive and gram-negative bacteria, including food and plant pathogens, using various extraction techniques and antimicrobial assays. Disc diffusion and spot-on-lawn assays were conducted to confirm the antimicrobial activity. To measure the potency of the extracts, minimum inhibition concentrations (MIultCs) were measured. Three microalgae, namely Isochrysis galbana, Scenedesmus sp. NT8c, and Chlorella sp. FN1, showed strong inhibitory activity preferentially against gram-positive bacteria. These microalgal species were then selected for further purification and analysis, leading to compound identification. By using a mixture of different chromatography techniques gas chromatography–mass spectrometry (GC–MS) and high-performance liquid chromatography (HPLC) and ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF-MS), we were able to separate and identify the dominant compounds that are responsible for the inhibitory activity. Additionally, nuclear magnetic resonance (NMR) was used to confirm the presence of these compounds. The dominant compounds that were identified and purified in the extracts are linoleic acid, oleic acid, docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA). These compounds are the potential candidates that inhibit the growth of gram-positive bacteria. This indicates the potential use of microalgae and their antimicrobial compounds as biocontrol agents against food and plant pathogens.

The unexplored bacterial lifestyle on leaf surface

Social interactions impact microbial communities and these relationships are mediated by small molecules. The chemical ecology of bacteria on the phylloplane environment is still little explored. The harsh environmental conditions found on leaf surface require high metabolic performances of the bacteria in order to survive. That is interesting both for scientific fields of prospecting natural molecules and for the ecological studies. Important queries about the bacterial lifestyle on leaf surface remain not fully comprehended. Does the hostility of the environment increase the populations' cellular altruism by the production of molecules, which can benefit the whole community? Or does the reverse occur and the production of molecules related to competition between species is increased? Does the phylogenetic distance between the bacterial populations influence the chemical profile during social interactions? Do phylogenetically related bacteria tend to cooperate more than the distant ones? The phylloplane contains high levels of yet uncultivated microorganisms, and understanding the molecular basis of the social networks on this habitat is crucial to gain new insights on the ecology of the mysterious community members due to interspecies molecular dependence. Here, we review and discuss what is known about bacterial social interactions and their chemical lifestyle on leaf surface.

Metabolomic tools used in marine natural product drug discovery

Introduction: The marine environment is a very promising resource for natural product research, with many of these reaching the market as new drugs, especially in the field of cancer therapy as well as the drug discovery pipeline for new antimicrobials. Exploitation for bioactive marine compounds with unique structures and novel bioactivity such as the isoquinoline alkaloid; trabectedin, the polyether macrolide; halichondrin B, and the peptide; dolastatin 10, requires the use of analytical techniques, which can generate unbiased, quantitative, and qualitative data to benefit the biodiscovery process. Metabolomics has shown to bridge this understanding and facilitate the development of new potential drugs from marine sources and particularly their microbial symbionts.Areas covered: In this review, articles on applied secondary metabolomics ranging from 1990-2018 as well as to the last quarter of 2019 were probed to investigate the impact of metabolomics on drug discovery for new antibiotics and cancer treatment.Expert opinion: The current literature review highlighted the effectiveness of metabolomics in the study of targeting biologically active secondary metabolites from marine sources for optimized discovery of potential new natural products to be made accessible to a R&D pipeline.

Halophiles and Their Biomolecules: Recent Advances and Future Applications in Biomedicine

The organisms thriving under extreme conditions better than any other organism living on Earth, fascinate by their hostile growing parameters, physiological features, and their production of valuable bioactive metabolites. This is the case of microorganisms (bacteria, archaea, and fungi) that grow optimally at high salinities and are able to produce biomolecules of pharmaceutical interest for therapeutic applications. As along as the microbiota is being approached by massive sequencing, novel insights are revealing the environmental conditions on which the compounds are produced in the microbial community without more stress than sharing the same substratum with their peers, the salt. In this review are reported the molecules described and produced by halophilic microorganisms with a spectrum of action in vitro: antimicrobial and anticancer. The action mechanisms of these molecules, the urgent need to introduce alternative lead compounds and the current aspects on the exploitation and its limitations are discussed.

Diversity, Ecology, and Prevalence of Antimicrobials in Nature

Microorganisms possess a variety of survival mechanisms, including the production of antimicrobials that function to kill and/or inhibit the growth of competing microorganisms. Studies of antimicrobial production have largely been driven by the medical community in response to the rise in antibiotic-resistant microorganisms and have involved isolated pure cultures under artificial laboratory conditions neglecting the important ecological roles of these compounds. The search for new natural products has extended to biofilms, soil, oceans, coral reefs, and shallow coastal sediments; however, the marine deep subsurface biosphere may be an untapped repository for novel antimicrobial discovery. Uniquely, prokaryotic survival in energy-limited extreme environments force microbial populations to either adapt their metabolism to outcompete or produce novel antimicrobials that inhibit competition. For example, subsurface sediments could yield novel antimicrobial genes, while at the same time answering important ecological questions about the microbial community.

Widely Targeted Metabolomics Analysis Reveals the Effect of Flooding Stress on the Synthesis of Flavonoids in Chrysanthemum morifolium

Chrysanthemum morifolium. cv "Hangju" is an important medicinal material with many functions in China. Flavonoids as the main secondary metabolites are a major class of medicinal components in "Hangju" and its composition and content can change significantly after flooding. This study mimicked the flooding stress of "Hangju" during flower bud differentiation and detected its metabolites in different growth stages. From widely targeted metabolomics data, 661 metabolites were detected, of which 46 differential metabolites exist simultaneously in the different growth stages of "Hangju". The top three types of the 46 differential metabolites were flavone C-glycosides, flavonol and flavone. Our results demonstrated that the accumulation of flavonoids in different growth stages of "Hangju" was different; however, quercetin, eriodictyol and most of the flavone C-glycosides were significantly enhanced in the two stages after flooding stress. The expression of key enzyme genes in the flavonoid synthesis pathway were determined using RT-qPCR, which verified the consistency of the expression levels of CHI, F3H, DFR and ANS with the content of the corresponding flavonoids. A regulatory network of flavonoid biosynthesis was established to illustrate that flooding stress can change the accumulation of flavonoids by affecting the expression of the corresponding key enzymes in the flavonoid synthesis pathway.

Genome Mining Coupled with OSMAC-Based Cultivation Reveal Differential Production of Surugamide A by the Marine Sponge Isolate Streptomyces sp. SM17 When Compared to Its Terrestrial Relative S. albidoflavus J1074

Much recent interest has arisen in investigating Streptomyces isolates derived from the marine environment in the search for new bioactive compounds, particularly those found in association with marine invertebrates, such as sponges. Among these new compounds recently identified from marine Streptomyces isolates are the octapeptidic surugamides, which have been shown to possess anticancer and antifungal activities. By employing genome mining followed by an one strain many compounds (OSMAC)-based approach, we have identified the previously unreported capability of a marine sponge-derived isolate, namely Streptomyces sp. SM17, to produce surugamide A. Phylogenomics analyses provided novel insights on the distribution and conservation of the surugamides biosynthetic gene cluster (sur BGC) and suggested a closer relatedness between marine-derived sur BGCs than their terrestrially derived counterparts. Subsequent analysis showed differential production of surugamide A when comparing the closely related marine and terrestrial isolates, namely Streptomyces sp. SM17 and Streptomyces albidoflavus J1074. SM17 produced higher levels of surugamide A than S. albidoflavus J1074 under all conditions tested, and in particular producing >13-fold higher levels when grown in YD and 3-fold higher levels in SYP-NaCl medium. In addition, surugamide A production was repressed in TSB and YD medium, suggesting that carbon catabolite repression (CCR) may influence the production of surugamides in these strains.

Marine Natural Products: A Source of Novel Anticancer Drugs

Cancer remains one of the most lethal diseases worldwide. There is an urgent need for new drugs with novel modes of action and thus considerable research has been conducted for new anticancer drugs from natural sources, especially plants, microbes and marine organisms. Marine populations represent reservoirs of novel bioactive metabolites with diverse groups of chemical structures. This review highlights the impact of marine organisms, with particular emphasis on marine plants, algae, bacteria, actinomycetes, fungi, sponges and soft corals. Anti-cancer effects of marine natural products in in vitro and in vivo studies were first introduced; their activity in the prevention of tumor formation and the related compound-induced apoptosis and cytotoxicities were tackled. The possible molecular mechanisms behind the biological effects are also presented. The review highlights the diversity of marine organisms, novel chemical structures, and chemical property space. Finally, therapeutic strategies and the present use of marine-derived components, its future direction and limitations are discussed.

Marine Natural Products: A Source of Novel Anticancer Drugs

Cancer remains one of the most lethal diseases worldwide. There is an urgent need for new drugs with novel modes of action and thus considerable research has been conducted for new anticancer drugs from natural sources, especially plants, microbes and marine organisms. Marine populations represent reservoirs of novel bioactive metabolites with diverse groups of chemical structures. This review highlights the impact of marine organisms, with particular emphasis on marine plants, algae, bacteria, actinomycetes, fungi, sponges and soft corals. Anti-cancer effects of marine natural products in in vitro and in vivo studies were first introduced; their activity in the prevention of tumor formation and the related compound-induced apoptosis and cytotoxicities were tackled. The possible molecular mechanisms behind the biological effects are also presented. The review highlights the diversity of marine organisms, novel chemical structures, and chemical property space. Finally, therapeutic strategies and the present use of marine-derived components, its future direction and limitations are discussed.

Toluene degradation via a unique metabolic route in indigenous bacterial species

Tanneries are the primary source of toluene pollution in the environment and toluene due to its hazardous effects has been categorized as persistent organic pollutant. Present study was initiated to trace out metabolic fingerprints of three toluene-degrading bacteria isolated from tannery effluents of Southern Punjab. Using selective enrichment and serial dilution methods followed by biochemical, molecular and antibiotic resistance analysis, isolated bacteria were subjected to metabolomics analysis. GC-MS/LC-MS analysis of bacterial metabolites helped to identify toluene transformation products and underlying pathways. Three toluene-metabolizing bacteria identified as Bacillus paralicheniformis strain KJ-16 (IUBT4 and IUBT24) and Brevibacillus agri strain NBRC 15538 (IUBT19) were found tolerant to toluene and capable of degrading toluene. Toluene-degrading potential of these isolates was detected to be IUBT4 (10.35 ± 0.084 mg/h), IUBT19 (14.07 ± 3.14 mg/h) and IUBT24 (11.1 ± 0.282 mg/h). Results of GC-MS analysis revealed that biotransformation of toluene is accomplished not only through known metabolic routes such as toluene 3-monooxygenase (T3MO), toluene 2-monooxygenase (T2MO), toluene 4-monooxygenase (T4MO), toluene methyl monooxygenase (TOL), toluene dioxygenase (Tod), meta- and ortho-ring fission pathways. But additionally, confirmed existence of a unique metabolic pathway that involved conversion of toluene into intermediates such as cyclohexene, cyclohexane, cyclohexanone and cyclohexanol. LC-MS analysis indicated the presence of fatty acid amides, stigmine, emmotin A and 2, 2-dinitropropanol in supernatants of bacterial cultures. As the isolated bacteria transformed toluene into relatively less toxic molecules and thus can be preferably exploited for the eco-friendly remediation of toluene.

Extending the "One Strain Many Compounds" (OSMAC) Principle to Marine Microorganisms

Genomic data often highlights an inconsistency between the number of gene clusters identified using bioinformatic approaches as potentially producing secondary metabolites and the actual number of chemically characterized secondary metabolites produced by any given microorganism. Such gene clusters are generally considered as “silent”, meaning that they are not expressed under laboratory conditions. Triggering expression of these “silent” clusters could result in unlocking the chemical diversity they control, allowing the discovery of novel molecules of both medical and biotechnological interest. Therefore, both genetic and cultivation-based techniques have been developed aimed at stimulating expression of these “silent” genes. The principles behind the cultivation based approaches have been conceptualized in the “one strain many compounds” (OSMAC) framework, which underlines how a single strain can produce different molecules when grown under different environmental conditions. Parameters such as, nutrient content, temperature, and rate of aeration can be easily changed, altering the global physiology of a microbial strain and in turn significantly affecting its secondary metabolism. As a direct extension of such approaches, co-cultivation strategies and the addition of chemical elicitors have also been used as cues to activate “silent” clusters. In this review, we aim to provide a focused and comprehensive overview of these strategies as they pertain to marine microbes. Moreover, we underline how changes in some parameters which have provided important results in terrestrial microbes, but which have rarely been considered in marine microorganisms, may represent additional strategies to awaken “silent” gene clusters in marine microbes. Unfortunately, the empirical nature of the OSMAC approach forces scientists to perform extensive laboratory experiments. Nevertheless, we believe that some computation and experimental based techniques which are used in other disciplines, and which we discuss; could be effectively employed to help streamline the OSMAC based approaches. We believe that natural products discovery in marine microorganisms would be greatly aided through the integration of basic microbiological approaches, computational methods, and technological innovations, thereby helping unearth much of the as yet untapped potential of these microorganisms.

Identification of Nutritional Components in Black Sesame Determined by Widely Targeted Metabolomics and Traditional Chinese Medicines

Chemical composition of secondary metabolites is of great importance for quality control of agricultural products. Black sesame seeds are significantly more expensive than white sesame seeds, because it is thought that black sesame seeds are more beneficial to human health than white sesame seeds. However, the differences in nutrient composition between black sesame seeds and white sesame seeds are still unknown. The current study examined the levels of different metabolites in black and white sesame seeds via the use of a novel metabolomics strategy. Using widely targeted metabolomics data, we obtained the structure and content of 557 metabolites, out of which 217 metabolites were identified, and discovered 30 metabolic pathways activated by the secondary metabolites in both black and white sesame seeds. Our results demonstrated that the main pathways that were differentially activated included: phenylpropanoid biosynthesis, tyrosine metabolism, and riboflavin metabolism. More importantly, the biomarkers that were significantly different between black seeds and white sesame seeds are highly related to the functions recorded in traditional Chinese medicine. The results of this study may serve as a new theoretical reference for breeding experts to promote the genetic improvement of sesame seeds, and therefore the cultivation of higher quality sesame varieties.

Use of a mixed culture strategy to isolate halophilic bacteria with antibacterial and cytotoxic activity from the Manaure solar saltern in Colombia

Background

Water evaporation in solar salterns creates salinity gradients that promote the adaptation of microbial species to different salinities. This competitive habitat challenges the metabolic capabilities of microorganisms and promotes alterations in their production of secondary metabolites. Thus, solar salterns are a potentially important source of new natural products. In Colombia, the most important and representative solar saltern is located in Manaure (La Guajira) in the north of Colombia. The aim of this study was to develop an alternative screening strategy to select halophilic bacteria as producers of bioactive compounds from mixed microbial cultures rather than individual environmental isolates. Brine and sediment samples from different ponds (across a salinity gradient) were inoculated in seven different culture media to grow bacteria and archaea, allowing for a total of 40 different mixed cultures. An organic extract from each mixed culture was obtained and tested against multidrug resistant pathogens, including Klebsiella pneumoniae, vancomycin-resistant Enterococcus faecium, methicillin-resistant Staphylococcus aureus and Bacillus subtilis. In addition, the extracts were tested against two human cancer cell lines, cervical adenocarcinoma (SiHa) and lung carcinoma (A-549).

Results

Twenty-four of the forty extracts from mixed cultures obtained from brine and sediment samples from the Manaure solar saltern showed antibacterial activity against Bacillus subtilis. Two extracts, referred to as A1SM3–29 and A1SM3–36, were also active against a methicillin-resistant Staphylococcus aureus, with the latter extract also showing slight cytotoxic activity against the assayed human lung cancer cell line. From this mixed culture, nine isolates were cultivated, and their extracts were tested against the same pathogens, resulting in the identification of a Vibrio sp. strain (A1SM3–36-8) with antimicrobial activity that was similar to that observed for the mixed culture extract. The extract of this strain was subjected to a bioautography assay, and 3 different fractions exhibited antibacterial activity against methicillin-resistant Staphylococcus aureus. Based on the amount obtained for each fraction, F3 was selected to isolate and identify its metabolites. The major compound was identified by NMR and HRMS as 13-cis-docosenamide, an amide that has been previously reported to be an antimicrobial and cytotoxic compound.

Conclusions

Our results shows the utility of our strategy in detecting bioactive molecules in initial mixed cultures by biological assays, resulting in the isolation and characterization of Vibrio sp. A1SM3–36-8, a halophilic strain with great antibacterial and cytotoxic potential.

Electronic supplementary material

The online version of this article (10.1186/s12866-017-1136-x) contains supplementary material, which is available to authorized users.

Evidence for a Saponin Biosynthesis Pathway in the Body Wall of the Commercially Significant Sea Cucumber Holothuria scabra

The sea cucumber (phylum Echinodermata) body wall is the first line of defense and is well known for its production of secondary metabolites; including vitamins and triterpenoid glycoside saponins that have important ecological functions and potential benefits to human health. The genes involved in the various biosynthetic pathways are unknown. To gain insight into these pathways in an echinoderm, we performed a comparative transcriptome analysis and functional annotation of the body wall and the radial nerve of the sea cucumber Holothuria scabra; to define genes associated with body wall metabolic functioning and secondary metabolite biosynthesis. We show that genes related to signal transduction mechanisms were more highly represented in the H. scabra body wall, including genes encoding enzymes involved in energy production. Eight of the core triterpenoid biosynthesis enzymes were found, however, the identity of the saponin specific biosynthetic pathway enzymes remains unknown. We confirm the body wall release of at least three different triterpenoid saponins using solid phase extraction followed by ultra-high-pressure liquid chromatography-quadrupole time of flight-mass spectrometry. The resource we have established will help to guide future research to explore secondary metabolite biosynthesis in the sea cucumber.

Diversity Analysis and Bioresource Characterization of Halophilic Bacteria Isolated from a South African Saltpan

Though intensive research has been channeled towards the biotechnological applications of halophiles and other extremophilic microbes, these studies have not been, by any means, exhaustive. Saline environments still offer a vast diversity of microbes with potential to produce an array of natural products which can only be unlocked by concerted research efforts. In this study, a combination of culture and molecular approaches were employed to characterize halophilic bacteria from saltpan water samples and profile their potential biotechnological applications. Physicochemical analysis of the water samples showed that pH was alkaline (pH 8.8), with a salinity of 12.8%. 16S rRNA gene targeted amplicon analysis produced 10 bacterial phyla constituting of Bacteroidetes (30.57%), Proteobacteria (15.27%), Actinobacteria (9.05%), Planctomycetes (5.52%) and Cyanobacteria (3.18%). Eighteen strains were identified using sequencing analysis of the culturable bacterial strains. From these, the strains SP7 and SP9 were positive for cellulase production while the strains SP4, SP8 and SP22 were positive for lipase production. Quantitative enzyme assays showed moderate extracellular cellulase activity (1.95 U/mL) and lipase activity (3.71 U/mL) by the isolate SP9 and SP4 respectively. Further, of the six isolates, the isolate SP9 exhibited exploitable potential in the bioremediation of hydrocarbon pollution as demonstrated by its fairly high activity against benzanthracene (70% DCPIP reduction). Elucidation of the isolates secondary metabolites showed the production of the molecules 2,3-butanediol, hexahydro-3-(2-methylpropyl)pyrrole[1,2a]pyrazine-1,4-dione, aziridine, dimethylamine and ethyl acetate (GC-MS) and oxypurinol and 5-hydroxydecanoic acid (LC-MS), particularly by the isolate Salinivibrio sp. SP9. Overall, the study showed that the isolated halophiles can produce secondary metabolites with potential industrial and pharmaceutical application.

Discrimination of Four Marine Biofilm-Forming Bacteria by LC-MS Metabolomics and Influence of Culture Parameters

Most marine bacteria can form biofilms, and they are the main components of biofilms observed on marine surfaces. Biofilms constitute a widespread life strategy, as growing in such structures offers many important biological benefits. The molecular compounds expressed in biofilms and, more generally, the metabolomes of marine bacteria remain poorly studied. In this context, a nontargeted LC-MS metabolomics approach of marine biofilm-forming bacterial strains was developed. Four marine bacteria, Persicivirga (Nonlabens) mediterranea TC4 and TC7, Pseudoalteromonas lipolytica TC8, and Shewanella sp. TC11, were used as model organisms. The main objective was to search for some strain-specific bacterial metabolites and to determine how culture parameters (culture medium, growth phase, and mode of culture) may affect the cellular metabolism of each strain and thus the global interstrain metabolic discrimination. LC-MS profiling and statistical partial least-squares discriminant analyses showed that the four strains could be differentiated at the species level whatever the medium, the growth phase, or the mode of culture (planktonic vs biofilm). A MS/MS molecular network was subsequently built and allowed the identification of putative bacterial biomarkers. TC8 was discriminated by a series of ornithine lipids, while the P. mediterranea strains produced hydroxylated ornithine and glycine lipids. Among the P. mediterranea strains, TC7 extracts were distinguished by the occurrence of diamine derivatives, such as putrescine amides.

Natural Products Diversity of Marine Ascidians (Tunicates; Ascidiacea) and Successful Drugs in Clinical Development

This present study reviewed the chemical diversity of marine ascidians and their pharmacological applications, challenges and recent developments in marine drug discovery reported during 1994-2014, highlighting the structural activity of compounds produced by these specimens. Till date only 5% of living ascidian species were studied from <3000 species, this study represented from family didemnidae (32%), polyclinidae (22%), styelidae and polycitoridae (11-12%) exhibiting the highest number of promising MNPs. Close to 580 compound structures are here discussed in terms of their occurrence, structural type and reported biological activity. Anti-cancer drugs are the main area of interest in the screening of MNPs from ascidians (64%), followed by anti-malarial (6%) and remaining others. FDA approved ascidian compounds mechanism of action along with other compounds status of clinical trials (phase 1 to phase 3) are discussed here in. This review highlights recent developments in the area of natural products chemistry and biotechnological approaches are emphasized.

Sample preparation procedures utilized in microbial metabolomics: An overview

Bacteria are remarkably diverse in terms of their size, structure and biochemical properties. Due to this fact, it is hard to develop a universal method for handling bacteria cultures during metabolomic analysis. The choice of suitable processing methods constitutes a key element in any analysis, because only appropriate selection of procedures may provide accurate results, leading to reliable conclusions. Because of that, every analytical experiment concerning bacteria requires individually and very carefully planned research methodology. Although every study varies in terms of sample preparation, there are few general steps to follow while planning experiment, like sampling, separation of cells from growth medium, stopping their metabolism and extraction. As a result of extraction, all intracellular metabolites should be washed out from cell environment. What is more, extraction method utilized cannot cause any chemical decomposition or degradation of the metabolome. Furthermore, chosen extraction method should correlate with analytical technique, so it will not disturb or prolong following sample preparation steps. For those reasons, we observe a need to summarize sample preparation procedures currently utilized in microbial metabolomic studies. In the presented overview, papers concerning analysis of extra- and intracellular metabolites, published over the last decade, have been discussed. Presented work gives some basic guidelines that might be useful while planning experiments in microbial metabolomics.

Suppression of charcoal rot in soybean by moderately halotolerant Pseudomonas aeruginosa GS-33 under saline conditions

Charcoal rot severely limits the soybean crop yield under saline conditions. The present studies focus on biocontrol and plant growth promoting potential of phenazine producing moderately halotolerant Pseudomonas aeruginosa (GS-33) in soybean under saline soil conditions. A marine isolate; GS-33 was identified as P. aeruginosa based on polyphasic characterization. This strain showed potent in vitro biocontrol activity against charcoal rot causing fungus Macrophomina phaseolina. It was capable of producing phenazine-1-carboxylic acid even at elevated salt concentrations. Moreover, GS-33 possessed other biocontrol traits like production of siderophores, HCN and protease under saline conditions. Multiple traits for plant growth promotion such as synthesis of IAA, NH3 , and solubilization of phosphate were also exhibited by GS-33. Plant growth promoting and biocontrol control potentials of GS-33 were evaluated by pot assay under saline soil conditions. Higher biomass and chlorophyll content were observed in GS-33 treated seedlings. A greater reduction in charcoal rot caused by fungal pathogens under both normal and saline soil conditions in GS-33 treated seedlings was observed. In a nut shell, phenazine producing halotolerant strain GS-33 could mitigate saline soil conditions (abiotic stress) and infestation of M. phaseolina (biotic stress) in soybean.

The marine actinomycete genus Salinispora: a model organism for secondary metabolite discovery

This review covers the initial discovery of the marine actinomycete genus Salinispora through its development as a model for natural product research. A focus is placed on the novel chemical structures reported with reference to their biological activities and the synthetic and biosynthetic studies they have inspired. The time line of discoveries progresses from more traditional bioassay-guided approaches through the application of genome mining and genetic engineering techniques that target the products of specific biosynthetic gene clusters. This overview exemplifies the extraordinary biosynthetic diversity that can emanate from a narrowly defined genus and supports future efforts to explore marine taxa in the search for novel natural products.