Production of a new thiopeptide antibiotic, TP-1161, by a marine Nocardiopsis species

Biosynthetic gene clusters with biotechnological applications in novel Antarctic isolates from Actinomycetota

Actinomycetota have been widely described as valuable sources for the acquisition of secondary metabolites. Most microbial metabolites are produced via metabolic pathways encoded by biosynthetic gene clusters (BGCs). Although many secondary metabolites are not essential for the survival of bacteria, they play an important role in their adaptation and interactions within microbial communities. This is how bacteria isolated from extreme environments such as Antarctica could facilitate the discovery of new BGCs with biotechnological potential. This study aimed to isolate rare Actinomycetota strains from Antarctic soil and sediment samples and identify their metabolic potential based on genome mining and exploration of biosynthetic gene clusters. To this end, the strains were sequenced using Illumina and Oxford Nanopore Technologies platforms. The assemblies were annotated and subjected to phylogenetic analysis. Finally, the BGCs present in each genome were identified using the antiSMASH tool, and the biosynthetic diversity of the Micrococcaceae family was evaluated. Taxonomic annotation revealed that seven strains were new and two were previously reported in the NCBI database. Additionally, BGCs encoding type III polyketide synthases (T3PKS), beta-lactones, siderophores, and non-ribosomal peptide synthetases (NRPS) have been identified, among others. In addition, the sequence similarity network showed a predominant type of BGCs in the family Micrococcaceae, and some genera were distinctly grouped. The BGCs identified in the isolated strains could be associated with applications such as antimicrobials, anticancer agents, and plant growth promoters, among others, positioning them as excellent candidates for future biotechnological applications and innovations. KEY POINTS: • Novel Antarctic rare Actinomycetota strains were isolated from soil and sediments • Genome-based taxonomic affiliation revealed seven potentially novel species • Genome mining showed metabolic potential for novel natural products.

Phylogenomics, phenotypic, and functional traits of five novel (Earth-derived) bacterial species isolated from the International Space Station and their prevalence in metagenomes

With the advent of long-term human habitation in space and on the moon, understanding how the built environment microbiome of space habitats differs from Earth habitats, and how microbes survive, proliferate and spread in space conditions, is becoming more important. The microbial tracking mission series has been monitoring the microbiome of the International Space Station (ISS) for almost a decade. During this mission series, six unique strains of Gram-stain-positive bacteria, including two spore-forming and three non-spore-forming species, were isolated from the environmental surfaces of the ISS. The analysis of their 16S rRNA gene sequences revealed > 99% similarities with previously described bacterial species. To further explore their phylogenetic affiliation, whole genome sequencing was undertaken. For all strains, the gyrB gene exhibited < 93% similarity with closely related species, which proved effective in categorizing these ISS strains as novel species. Average nucleotide identity and digital DNA-DNA hybridization values, when compared to any known bacterial species, were < 94% and <50% respectively for all species described here. Traditional biochemical tests, fatty acid profiling, polar lipid, and cell wall composition analyses were performed to generate phenotypic characterization of these ISS strains. A study of the shotgun metagenomic reads from the ISS samples, from which the novel species were isolated, showed that only 0.1% of the total reads mapped to the novel species, supporting the idea that these novel species are rare in the ISS environments. In-depth annotation of the genomes unveiled a variety of genes linked to amino acid and derivative synthesis, carbohydrate metabolism, cofactors, vitamins, prosthetic groups, pigments, and protein metabolism. Further analysis of these ISS-isolated organisms revealed that, on average, they contain 46 genes associated with virulence, disease, and defense. The main predicted functions of these genes are: conferring resistance to antibiotics and toxic compounds, and enabling invasion and intracellular resistance. After conducting antiSMASH analysis, it was found that there are roughly 16 cluster types across the six strains, including β-lactone and type III polyketide synthase (T3PKS) clusters. Based on these multi-faceted taxonomic methods, it was concluded that these six ISS strains represent five novel species, which we propose to name as follows: Arthrobacter burdickii IIF3SC-B10T (= NRRL B-65660T = DSM 115933T), Leifsonia virtsii F6_8S_P_1AT (= NRRL B-65661T = DSM 115931T), Leifsonia williamsii F6_8S_P_1BT (= NRRL B-65662T = DSM 115932T), Paenibacillus vandeheii F6_3S_P_1CT (= NRRL B-65663T = DSM 115940T), and Sporosarcina highlanderae F6_3S_P_2T (= NRRL B-65664T = DSM 115943T). Identifying and characterizing the genomes and phenotypes of novel microbes found in space habitats, like those explored in this study, is integral for expanding our genomic databases of space-relevant microbes. This approach offers the only reliable method to determine species composition, track microbial dispersion, and anticipate potential threats to human health from monitoring microbes on the surfaces and equipment within space habitats. By unraveling these microbial mysteries, we take a crucial step towards ensuring the safety and success of future space missions.

Phylogenetic affiliations and genomic characterization of novel bacterial species and their abundance in the International Space Station

Background

With the advent of long-term human habitation in space and on the moon, understanding how the built environment microbiome of space habitats differs from Earth habits, and how microbes survive, proliferate and spread in space conditions, is coming more and more important. The Microbial Tracking mission series has been monitoring the microbiome of the International Space Station (ISS) for almost a decade. During this mission series, six unique strains of Gram-positive bacteria, including two spore-forming and three non-spore-forming species, were isolated from the environmental surfaces of the International Space Station (ISS).

Results

The analysis of their 16S rRNA gene sequences revealed <99% similarities with previously described bacterial species. To further explore their phylogenetic affiliation, whole genome sequencing (WGS) was undertaken. For all strains, the gyrB gene exhibited <93% similarity with closely related species, which proved effective in categorizing these ISS strains as novel species. Average ucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values, when compared to any known bacterial species, were less than <94% and 50% respectively for all species described here. Traditional biochemical tests, fatty acid profiling, polar lipid, and cell wall composition analyses were performed to generate phenotypic characterization of these ISS strains. A study of the shotgun metagenomic reads from the ISS samples, from which the novel species were isolated, showed that only 0.1% of the total reads mapped to the novel species, supporting the idea that these novel species are rare in the ISS environments. In-depth annotation of the genomes unveiled a variety of genes linked to amino acid and derivative synthesis, carbohydrate metabolism, cofactors, vitamins, prosthetic groups, pigments, and protein metabolism. Further analysis of these ISS-isolated organisms revealed that, on average, they contain 46 genes associated with virulence, disease, and defense. The main predicted functions of these genes are: conferring resistance to antibiotics and toxic compounds, and enabling invasion and intracellular resistance. After conducting antiSMASH analysis, it was found that there are roughly 16 cluster types across the six strains, including β-lactone and type III polyketide synthase (T3PKS) clusters.

Conclusions

Based on these multi-faceted taxonomic methods, it was concluded that these six ISS strains represent five novel species, which we propose to name as follows: Arthrobacter burdickii IIF3SC-B10T (=NRRL B-65660T), Leifsonia virtsii, F6_8S_P_1AT (=NRRL B-65661T), Leifsonia williamsii, F6_8S_P_1BT (=NRRL B- 65662T and DSMZ 115932T), Paenibacillus vandeheii, F6_3S_P_1CT(=NRRL B-65663T and DSMZ 115940T), and Sporosarcina highlanderae F6_3S_P_2 T(=NRRL B-65664T and DSMZ 115943T). Identifying and characterizing the genomes and phenotypes of novel microbes found in space habitats, like those explored in this study, is integral for expanding our genomic databases of space-relevant microbes. This approach offers the only reliable method to determine species composition, track microbial dispersion, and anticipate potential threats to human health from monitoring microbes on the surfaces and equipment within space habitats. By unraveling these microbial mysteries, we take a crucial step towards ensuring the safety and success of future space missions.

Rare Halophilic Nocardiopsis from Algerian Saharan Soils as Tools for Biotechnological Processes in Pharmaceutical Industry

The Sahara Desert, one of the most extreme ecosystems in the planet, constitutes an unexplored source of microorganisms such as mycelial bacteria. In this study, we investigated the diversity of halophilic actinobacteria in soils collected from five regions of the Algerian Sahara. A total of 23 halophilic actinobacterial strains were isolated by using a humic-vitamin agar medium supplemented with 10% NaCl. The isolated halophilic strains were subjected to taxonomic analysis using a polyphasic approach, which included morphological, chemotaxonomic, physiological (numerical taxonomy), and phylogenetic analyses. The isolates showed abundant growth in CMA (complex medium agar) and TSA (tryptic soy agar) media containing 10% NaCl, and chemotaxonomic characteristics were consistent with their assignment to the genus Nocardiopsis. Analysis of the 16S rRNA sequence of 23 isolates showed five distinct clusters and a similarity level ranging between 98.4% and 99.8% within the Nocardiopsis species. Comparison of their physiological characteristics with the nearest species showed significant differences with the closely related species. Halophilic Nocardiopsis isolated from Algerian Sahara soil represents a distinct phyletic line suggesting a potential new species. Furthermore, the isolated strains of halophilic Nocardiopsis were screened for their antagonistic properties against a broad spectrum of microorganisms by the conventional agar method (agar cylinders method) and found to have the capacity to produce bioactive secondary metabolites. Except one isolate (AH37), all isolated Nocardiopsis showed moderate to high biological activities against Pseudomonas syringae and Salmonella enterica, and some isolates showed activities against Agrobacterium tumefaciens, Serratia marcescens, and Klebsiella pneumoniae. However, no isolates were active against Bacillus subtilis, Aspergillus flavus, or Aspergillus niger. The obtained finding implies that the unexplored extreme environments such as the Sahara contain many new bacterial species as a novel drug source for medical and industrial applications.

Combating Antimicrobial Resistance in the Post-Genomic Era: Rapid Antibiotic Discovery

Constantly evolving drug-resistant "superbugs" have caused an urgent demand for novel antimicrobial agents. Natural products and their analogs have been a prolific source of antimicrobial agents, even though a high rediscovery rate and less targeted research has made the field challenging in the pre-genomic era. With recent advancements in technology, natural product research is gaining new life. Genome mining has allowed for more targeted excavation of biosynthetic potential from natural sources that was previously overlooked. Researchers use bioinformatic algorithms to rapidly identify and predict antimicrobial candidates by studying the genome before even entering the lab. In addition, synthetic biology and advanced analytical instruments enable the accelerated identification of novel antibiotics with distinct structures. Here, we reviewed the literature for noteworthy examples of novel antimicrobial agents discovered through various methodologies, highlighting the candidates with potent effectiveness against antimicrobial-resistant pathogens.

Heterologous Synthesis and Characterization of Thiocillin IV

Micrococcin P1 and P2 are thiopeptides with a wide range of biological functions including antibacterial and antimalarial activities. We previously demonstrated optimized enzymatic sequences for the exclusive and scalable biosynthesis of micrococcin P2. Thiocillin IV is predicted to be the congener of O-methylated micrococcin P2, but the exact structure has not been elucidated. In this study, we report the first scalable biosynthesis and full structural characterization of thiocillin IV, a 26-membered thiopeptide. This was achieved by generating a recombinant plasmid by inserting tclO, a gene encoding an O-methyltransferase, and genes responsible for micrococcin P2 production and incorporating them into a Bacillus strain. With the incorporation of precursor peptide genes and optimal culture conditions, production reached 2.4 mg/L of culture. The purified thiocillin IV structure was identified as O-methylated micrococcin P2 at the 8-Thr position, and its promising biological activity toward various Gram-positive pathogens was observed. This study provides tclO-mediated site-selective methylation and opens a biotechnological opportunity to produce selective thiopeptides.

Arthrobacter antioxidans sp. nov., a blue pigment-producing species isolated from Mount Everest

Bacteria in the genus Arthrobacter have been found in extreme environments, e.g. glaciers, brine and mural paintings. Here, we report the discovery of a novel pink-coloured bacterium, strain QL17^T, capable of producing an extracellular water-soluble blue pigment. The bacterium was isolated from the soil of the East Rongbuk Glacier of Mt. Everest, China. 16S rRNA gene sequence analysis showed that strain QL17^T was most closely related to the species Arthrobacter bussei KR32 ^T. However, compared to A.bussei KR32^T and the next closest relatives, the new species demonstrates considerable phylogenetic distance at the whole-genome level, with an average nucleotide identity of <85 % and inferred DNA-DNA hybridization of <30 %. Polyphasic taxonomy results support our conclusion that strain QL17^T represents a novel species of the genus Arthrobacter. Strain QL17^T had the highest tolerance to hydrogen peroxide at 400 mM. Whole-genome sequencing of strain QL17^T revealed the presence of numerous cold-adaptation, antioxidation and UV resistance-associated genes, which are related to adaptation to the extreme environment of Mt. Everest. Results of this study characterized a novel psychrotolerant Arthrobacter species, for which the name Arthrobacter antioxidans sp. nov. is proposed. The type strain is QL17^T (GDMCC 1.2948^T=JCM 35246^T).

Antibacterial potential of inulinase enzyme obtained from Nocardiopsis sp

The enriched nutritional and functional properties of inulinase with wide attention are considered commercial/industrial food enzymes. It can be produced by many microorganisms such as yeasts, fungi, and bacteria. Nocardiopsis is a genus under Actinomycetes, which has biotechnologically important microorganisms. This study aims to isolate and identify marine Actinomycetes Nocardiopsis species and to evaluate the antibacterial potential of the inulinase enzyme obtained from it. Marine actinobacteria (Nocardiopsis sp.) were isolated from sediment samples on YM agar. The isolate was identified by biochemical analysis of cell walls (amino acid and sugar). Enzyme screening assay was performed with temperature and pH influence in the production inulinase enzyme production. Antibacterial activity and minimal inhibitory activity of inulinase enzyme were performed with Staphylococcus, Klebsiella pneumoniae, and Pseudomonas aeruginosa. Antimicrobial testing revealed that with higher concentrations of inulinase enzyme, the zone of inhibition of bacterial growth increased, and the minimum inhibitory concentration of inulinase enzyme that prevented the growth of bacteria was close to the standard tetracycline. Inulinase enzyme obtained from Nocardiopsis species shows good antibacterial activity against Staphylococcus aureus, K. pneumoniae, and P. aeruginosa in comparison to the standard, tetracycline.

Antibacterial Synnepyrroles from Human-Associated Nocardiopsis sp. Show Protonophore Activity and Disrupt the Bacterial Cytoplasmic Membrane

Actinobacteria have traditionally been an important source of bioactive natural products, although many genera remain poorly explored. Here, we report a group of distinctive pyrrole-containing natural products, named synnepyrroles, from Nocardiopsis synnemataformans. Detailed structural characterization by mass spectrometry and nuclear magnetic resonance (NMR) spectroscopy combined with isotope-labeling experiments revealed their molecular structures and biosynthetic precursors acetate, propionate, aspartate, and (for branched analogues) valine. The biosynthetic data points toward an unusual pathway for pyrrole formation via condensation of aspartate with diverse fatty acids that give rise to a unique pyrrole-3,4-dicarboxylate core and variable linear or terminally branched alkyl side chains. In addition, the bioactivity and mode of action of synnepyrrole A were characterized in Bacillus subtilis. Orienting assessment of the phenotype of synnepyrrole A-treated bacteria by high-resolution microscopy suggested the cytoplasmic membrane as the target structure. Further characterization of the membrane effects demonstrated dissipation of the membrane potential and intracellular acidification indicative of protonophore activity. At slightly higher concentrations, synnepyrrole A compromised the barrier function of the cytoplasmic membrane, allowing the passage of otherwise membrane-impermeable dye molecules.

Inhibition of heterotrophic bacterial biofilm in the soil ferrosphere by Streptomyces spp. and Bacillus velezensis

The soil microbiome is involved in the processes of microbial corrosion, in particular, by the formation of biofilm. It has been proposed that an environmentally friendly solution to this corrosion might be through biological control. Bacillus velezensis NUChC C2b, Streptomyces gardneri ChNPU F3 and S. canus NUChC F2 were investigated as potentially 'green' biocides to prevent attachment to glass as a model surface and the formation of heterotrophic bacterial biofilm which participates in the corrosion process. Results showed high antagonistic and antibiofilm properties of S. gardneri ChNPU F3; which may be related to the formation of secondary antimicrobial metabolites by this strain. B. velezensis NUChC C2b and S. gardneri ChNPU F3 could be incorporated into green biocides - as components of antibiofilm agents that will protect material from bacterial corrosion or as agents that will prevent historical heritage damage.

Taxonomic Characterization, Antiviral Activity and Induction of Three New Kenalactams in Nocardiopsis sp. CG3

Exploration of secondary metabolites secreted by new Actinobacteria taxa isolated from unexplored areas, can increase the possibility to obtain new compounds which can be developed into new drugs for the treatment of serious diseases such as hepatitis C. In this context, one actinobacterial strain, CG3, has been selected based on the results of polyphasic characterization, which indicate that it represents a new putative species within the genus Nocardiopsis. Two fractions (F2 and F3), prepared from the culture of strain CG3 in soybean medium, exhibited a pronounced antiviral activity against the HCV strain Luc-Jc1. LC-HRESIMS analysis showed different bioactive compounds in both active fractions (F2 and F3), including five polyenic macrolactams (kenalactams A-E), three isoflavone metabolites, along with mitomycin C and one p-phenyl derivative. Furthermore, feeding with 1% of methionine, lysine or alanine as a unique nitrogen source, induced the production of three novel kenalactam derivatives.

iChip-Inspired Isolation, Bioactivities and Dereplication of Actinomycetota from Portuguese Beach Sediments

Oceans hold a stunning number of unique microorganisms, which remain unstudied by culture-dependent methods due to failures in establishing the right conditions for these organisms to grow. In this work, an isolation effort inspired by the iChip was performed using marine sediments from Memoria beach, Portugal. The isolates obtained were identified by 16S rRNA gene analysis, fingerprinted using BOX-PCR and ERIC-PCR, searched for the putative presence of secondary metabolism genes associated with polyketide synthase I (PKS-I) and non-ribosomal peptide synthetases (NRPS), screened for antimicrobial activity against Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC 29213, and had bioactive extracts dereplicated by LC/HRMS. Of the 158 isolated strains, 96 were affiliated with the phylum Actinomycetota, PKS-I and NRPS genes were detected in 53 actinomycetotal strains, and 11 proved to be bioactive (10 against E. coli, 1 against S. aureus and 1 against both pathogens). Further bioactivities were explored using an "one strain many compounds" approach, with six strains showing continued bioactivity and one showing a novel one. Extract dereplication showed the presence of several known bioactive molecules and potential novel ones in the bioactive extracts. These results indicate the use of the bacteria isolated here as sources of new bioactive natural products.

Genomic analysis uncovers laccase-coding genes and biosynthetic gene clusters encoding antimicrobial compounds in laccase-producing Acinetobacter baumannii

Laccases are multicopper oxidase family enzymes that can oxidize various substrates. In this study, we isolated laccase-producing Acinetobacter spp. from the environment, and one isolate of laccase-producing Acinetobacter baumannii, designated NI-65, was identified. The NI-65 strain exhibited constitutive production of extracellular laccase in a crude extract using 2,6-dimethoxyphenol as a substrate when supplemented with 2 mM CuSO₄. Whole-genome sequencing of the NI-65 strain revealed a genome size of 3.6 Mb with 3,471 protein-coding sequences. The phylogenetic analysis showed high similarity to the genome of A. baumannii NCIMB8209. Three laccase proteins, PcoA and CopA, that belong to bacterial CopA superfamilies, and LAC-AB, that belongs to the I-bacterial bilirubin oxidase superfamily, were identified. These proteins were encoded by three laccase-coding genes (pcoA, copA, and lac-AB). The lac-AB gene showed a sequence similar to that of polyphenol oxidase (PPO). Gene clusters encoding the catabolized compounds involved in the utilization of plant substances and secondary metabolite biosynthesis gene clusters encoding antimicrobial compounds were identified. This is the first report of whole-genome sequencing of laccase-producing A. baumannii, and the data from this study help to elucidate the genome of A. baumannii to facilitate its application in synthetic biology for enzyme production.

Marine Cyclic Peptides: Antimicrobial Activity and Synthetic Strategies

Oceans are a rich source of structurally unique bioactive compounds from the perspective of potential therapeutic agents. Marine peptides are a particularly interesting group of secondary metabolites because of their chemistry and wide range of biological activities. Among them, cyclic peptides exhibit a broad spectrum of antimicrobial activities, including against bacteria, protozoa, fungi, and viruses. Moreover, there are several examples of marine cyclic peptides revealing interesting antimicrobial activities against numerous drug-resistant bacteria and fungi, making these compounds a very promising resource in the search for novel antimicrobial agents to revert multidrug-resistance. This review summarizes 174 marine cyclic peptides with antibacterial, antifungal, antiparasitic, or antiviral properties. These natural products were categorized according to their sources—sponges, mollusks, crustaceans, crabs, marine bacteria, and fungi—and chemical structure—cyclic peptides and depsipeptides. The antimicrobial activities, including against drug-resistant microorganisms, unusual structural characteristics, and hits more advanced in (pre)clinical studies, are highlighted. Nocathiacins I–III (91–93), unnarmicins A (114) and C (115), sclerotides A (160) and B (161), and plitidepsin (174) can be highlighted considering not only their high antimicrobial potency in vitro, but also for their promising in vivo results. Marine cyclic peptides are also interesting models for molecular modifications and/or total synthesis to obtain more potent compounds, with improved properties and in higher quantity. Solid-phase Fmoc- and Boc-protection chemistry is the major synthetic strategy to obtain marine cyclic peptides with antimicrobial properties, and key examples are presented guiding microbiologist and medicinal chemists to the discovery of new antimicrobial drug candidates from marine sources.

Bioinoculants-Natural Biological Resources for Sustainable Plant Production

Agricultural sustainability is of foremost importance for maintaining high food production. Irresponsible resource use not only negatively affects agroecology, but also reduces the economic profitability of the production system. Among different resources, soil is one of the most vital resources of agriculture. Soil fertility is the key to achieve high crop productivity. Maintaining soil fertility and soil health requires conscious management effort to avoid excessive nutrient loss, sustain organic carbon content, and minimize soil contamination. Though the use of chemical fertilizers have successfully improved crop production, its integration with organic manures and other bioinoculants helps in improving nutrient use efficiency, improves soil health and to some extent ameliorates some of the constraints associated with excessive fertilizer application. In addition to nutrient supplementation, bioinoculants have other beneficial effects such as plant growth-promoting activity, nutrient mobilization and solubilization, soil decontamination and/or detoxification, etc. During the present time, high energy based chemical inputs also caused havoc to agriculture because of the ill effects of global warming and climate change. Under the consequences of climate change, the use of bioinputs may be considered as a suitable mitigation option. Bioinoculants, as a concept, is not something new to agricultural science, however; it is one of the areas where consistent innovations have been made. Understanding the role of bioinoculants, the scope of their use, and analysing their performance in various environments are key to the successful adaptation of this technology in agriculture.

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.

An Overview of Bioactive 1,3-Oxazole-Containing Alkaloids from Marine Organisms

1,3-Oxazole chemicals are a unique class of five-membered monocyclic heteroarenes, containing a nitrogen atom and an oxygen. These alkaloids have attracted extensive attention from medicinal chemists and pharmacologists owing to their diverse arrays of chemical structures and biological activities, and a series of 1,3-oxazole derivatives has been developed into therapeutic agents (e.g., almoxatone, befloxatone, cabotegravir, delpazolid, fenpipalone, haloxazolam, inavolisib). A growing amount of evidence indicates that marine organisms are one of important sources of 1,3-oxazole-containing alkaloids. To improve our knowledge regarding these marine-derived substances, as many as 285 compounds are summarized in this review, which, for the first time, highlights their sources, structural features and biological properties, as well as their biosynthesis and chemical synthesis. Perspective for the future discovery of new 1,3-oxazole compounds from marine organisms is also provided.

The intriguing chemistry and biology of sulfur-containing natural products from marine microorganisms (1987-2020)

Natural products derived from marine microorganisms have received great attention as a potential resource of new compound entities for drug discovery. The unique marine environment brings us a large group of sulfur-containing natural products with abundant biological functionality including antitumor, antibiotic, anti-inflammatory and antiviral activities. We reviewed all the 484 sulfur-containing natural products (non-sulfated) isolated from marine microorganisms, of which 59.9% are thioethers, 29.8% are thiazole/thiazoline-containing compounds and 10.3% are sulfoxides, sulfones, thioesters and many others. A selection of 133 compounds was further discussed on their structure-activity relationships, mechanisms of action, biosynthesis, and druggability. This is the first systematic review on sulfur-containing natural products from marine microorganisms conducted from January 1987, when the first one was reported, to December 2020.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-021-00101-2.

Host-dependent heterologous expression of berninamycin gene cluster leads to linear thiopeptide antibiotics

Berninamycins are a class of thiopeptide antibiotics with potent activity against Gram-positive bacteria. Heterologous expression of the berninamycin (ber) biosynthetic gene cluster from marine-derived Streptomyces sp. SCSIO 11878 in different terrestrial model Streptomyces hosts led to the production of berninamycins A (1) and B (2) in Streptomyces lividans SBT18 and Streptomyces coelicolor M1154, while two new linearized berninamycins J (3) and K (4) were obtained in Streptomyces albus J1074. Their structures were elucidated by detailed interpretation of NMR data and Marfey's method. Bioactivity assays showed that the linear thiopeptides 3 and 4 were less potent than 1 and 2 in antibacterial activity. This work indicates that undefined host-dependent enzymes might be responsible for generating the linear thiopeptides 3 and 4 in S. albus J1074.

Marine Bacterial Secondary Metabolites: A Treasure House for Structurally Unique and Effective Antimicrobial Compounds

The prevalence of antimicrobial resistance reduces the effectiveness of antimicrobial drugs in preventing and treating infectious diseases caused by pathogenic organisms, such as bacteria, fungi, and viruses. Because of the burgeoning growth of microbes with antimicrobial-resistant traits, there is a dire need to identify and develop novel and effective antimicrobial agents to treat infections from antimicrobial-resistant strains. The marine environment is rich in ecological biodiversity and can be regarded as an untapped resource for prospecting novel bioactive compounds. Therefore, exploring the marine environment for antimicrobial agents plays a significant role in drug development and biomedical research. Several earlier scientific investigations have proven that bacterial diversity in the marine environment represents an emerging source of structurally unique and novel antimicrobial agents. There are several reports on marine bacterial secondary metabolites, and many are pharmacologically significant and have enormous promise for developing effective antimicrobial drugs to combat microbial infections in drug-resistant pathogens. In this review, we attempt to summarize published articles from the last twenty-five years (1996–2020) on antimicrobial secondary metabolites from marine bacteria evolved in marine environments, such as marine sediment, water, fauna, and flora.

Combining OSMAC Approach and Untargeted Metabolomics for the Identification of New Glycolipids with Potent Antiviral Activity Produced by a Marine Rhodococcus

Natural products of microbial origin have inspired most of the commercial pharmaceuticals, especially those from Actinobacteria. However, the redundancy of molecules in the discovery process represents a serious issue. The untargeted approach, One Strain Many Compounds (OSMAC), is one of the most promising strategies to induce the expression of silent genes, especially when combined with genome mining and advanced metabolomics analysis. In this work, the whole genome of the marine isolate Rhodococcus sp. I2R was sequenced and analyzed by antiSMASH for the identification of biosynthetic gene clusters. The strain was cultivated in 22 different growth media and the generated extracts were subjected to metabolomic analysis and functional screening. Notably, only a single growth condition induced the production of unique compounds, which were partially purified and structurally characterized by liquid chromatography high-resolution tandem mass spectrometry (LC-HRMS/MS). This strategy led to identifying a bioactive fraction containing >30 new glycolipids holding unusual functional groups. The active fraction showed a potent antiviral effect against enveloped viruses, such as herpes simplex virus and human coronaviruses, and high antiproliferative activity in PC3 prostate cancer cell line. The identified compounds belong to the biosurfactants class, amphiphilic molecules, which play a crucial role in the biotech and biomedical industry.

Streptomonospora litoralis sp. nov., a halophilic thiopeptides producer isolated from sand collected at Cuxhaven beach

Strain M2^T was isolated from the beach of Cuxhaven, Wadden Sea, Germany, in course of a program to attain new producers of bioactive natural products. Strain M2^T produces litoralimycin and sulfomycin-type thiopeptides. Bioinformatic analysis revealed a potential biosynthetic gene cluster encoding for the M2^T thiopeptides. The strain is Gram-stain-positive, rod shaped, non-motile, spore forming, showing a yellow colony color and forms extensively branched substrate mycelium and aerial hyphae. Inferred from the 16S rRNA gene phylogeny strain M2^T affiliates with the genus Streptomonospora. It shows 96.6% 16S rRNA gene sequence similarity to the type species Streptomonospora salina DSM 44593 ^T and forms a distinct branch with Streptomonospora sediminis DSM 45723 ^T with 97.0% 16S rRNA gene sequence similarity. Genome-based phylogenetic analysis revealed that M2^T is closely related to Streptomonospora alba YIM 90003 ^T with a digital DNA-DNA hybridisation (dDDH) value of 26.6%. The predominant menaquinones of M2^T are MK-10(H₆), MK-10(H₈), and MK-11(H₆) (> 10%). Major cellular fatty acids are iso-C_16:0, anteiso C_17:0 and C_18:0 10-methyl. The polar lipid profile consisted of diphosphatidylglycerol phosphatidyl glycerol, phosphatidylinositol, phosphatidylcholine, phosphatidylethanolamine, three glycolipids, two unknown phospholipids, and two unknown lipids. The genome size of type strain M2^T is 5,878,427 bp with 72.1 mol % G + C content. Based on the results obtained from phylogenetic and chemotaxonomic studies, strain M2^T (= DSM 106425 ^T = NCCB 100650 ^T) is considered to represent a novel species within the genus Streptomonospora for which the name Streptomonospora litoralis sp. nov. is proposed.

Naturally Occurring Oxazole Structural Units as Ligands of Vanadium Catalysts for Ethylene-Norbornene (Co)polymerization

1,3-Oxazole and 4,5-dihydro-1,3-oxazole are common structural motifs in naturally occurring peptides. A series of vanadium complexes were synthesized using VCl3(THF)3 and methyl substituted (4,5-dihydro-1,3-oxazol-2-yl)-1,3-oxazoles as ligands and analyzed using NMR and MS methods. The complexes were found to be active catalysts both in ethylene polymerization and ethylene-norbornene copolymerization. The position of methyl substituent in the ligand has considerable impact on the performance of (co)polymerization reaction, as well as on the microstructure, and thus physical properties of the obtained copolymers.

A Strong Synergy Between the Thiopeptide Bacteriocin Micrococcin P1 and Rifampicin Against MRSA in a Murine Skin Infection Model

Antibiotic-resistant bacterial pathogens have become a serious threat worldwide. One of these pathogens is methicillin-resistant Staphylococcus aureus (MRSA), a major cause of skin and soft tissue infections. In this study we identified a strain of Staphylococcus equorum producing a substance with high antimicrobial activity against many Gram-positive bacteria, including MRSA. By mass spectrometry and whole genome sequencing the antimicrobial substance was identified as the thiopeptide bacteriocin micrococcin P1 (MP1). Based on its properties we developed a one-step purification protocol resulting in high yield (15 mg/L) and high purity (98%) of MP1. For shorter incubation times (5-7 h) MP1 was very potent against MRSA but the inhibitory effect was overshadowed by resistance development during longer incubation time (24h or more). To overcome this problem a synergy study was performed with a number of commercially available antibiotics. Among the antibiotics tested, the combination of MP1 and rifampicin gave the best synergistic effect, with MIC values 25 and 60 times lower than for the individual drugs, respectively. To assess the therapeutic potential of the MP1-rifampicin combination, we used a murine skin infection model based on the use of the multidrug-resistant luciferase-tagged MRSA strain Xen31. As expected, neither of the single antimicrobials (MP1 or rifampicin) could eradicate Xen31 from the wounds. By contrary, the MP1-rifampicin combination was efficient not only to eradicate but also to prevent the recurrence of Xen31 infection. Furthermore, compared to fucidin cream, which is commonly used in skin infection treatments, MP1-rifampicin combination was superior in terms of preventing resistance development. Our results show that combining MP1, and probably other thiopeptides, with antibiotics can be a promising strategy to treat SSTIs caused by MRSA and likely many other Gram-positive bacteria.

Thiazole-amino acids: influence of thiazole ring on conformational properties of amino acid residues

Post-translational modified thiazole-amino acid (Xaa-Tzl) residues have been found in macrocyclic peptides (e.g., thiopeptides and cyanobactins), which mostly inhibit protein synthesis in Gram + bacteria. Conformational study of the series of model compounds containing this structural motif with alanine, dehydroalanine, dehydrobutyrine and dehydrophenylalanine were performed using DFT method in various environments. The solid-state crystal structure conformations of thiazole-amino acid residues retrieved from the Cambridge Structural Database were also analysed. The studied structural units tend to adopt the unique semi-extended β2 conformation; which is stabilised mainly by N-H⋯NTzl hydrogen bond, and for dehydroamino acids also by π-electron conjugation. The conformational preferences of amino acids with a thiazole ring were compared with oxazole analogues and the role of the sulfur atom in stabilising the conformations of studied peptides was discussed.

Harnessing the natural pool of polyketide and non-ribosomal peptide family: A route map towards novel drug development

Emergence of communicable and non-communicable diseases possess health challenge to millions of people worldwide and is a major threat to the economic and social development in the coming century. The occurrence of recent pandemic, SARS-CoV-2 caused by lethal severe acute respiratory syndrome coronavirus 2 is one such example. Rapid research and development of drugs for the treatment and management of these diseases has been an incredibly challenging task for the pharmaceutical industry. Although, substantial focus has been made in the discovery of therapeutic compounds from natural sources having significant medicinal potential, their synthesis has shown a slow progress. Hence, the discovery of new targets by the application of the latest biotechnological and synthetic biology approaches is very much the need of the hour. Polyketides (PKs) and non-ribosomal peptides (NRPs) found in bacteria, fungi and plants are a large diverse family of natural products synthesized by two classes of enzymes: polyketide synthases (PKS) and non-ribosomal peptide synthetases (NRPS). These enzymes possess immense biomedical potential due to their simple architecture, catalytic capacity, as well as diversity. With the advent of latest in-silico and in-vitro strategies, these enzymes and their related metabolic pathways, if targeted, can contribute highly towards the biosynthesis of an array of potentially natural drug leads that have antagonist effects on biopolymers associated with various human diseases. In the face of the rising threat from the multidrug-resistant pathogens, this will further open new avenues for the discovery of novel and improved drugs by combining the natural and the synthetic approaches. This review discusses the relevance of polyketides and non-ribosomal peptides and the improvement strategies for the development of their derivatives and scaffolds, and how they will be beneficial to the future bioprospecting and drug discovery.

Diversity of Actinobacteria Isolated from Date Palms Rhizosphere and Saline Environments: Isolation, Identification and Biological Activity Evaluation

The diversity of cultural Actinobacteria in two types of Algerian Sahara environments, including saline environments and date palms rhizosphere, was investigated. In this study, a total of 40 strains of actinomycetes was isolated from different soil samples, using a rehydration and centrifugation method. Molecular identification, based on 16S rRNA gene sequence analysis, revealed that these isolates were affiliated to six clusters corresponding to eight genera, including Streptomyces, Nocardiopsis, Saccharopolyspora, Actinomadura, Actinocorallia, Micromonospora, Couchioplanes, and Planomonospora. A taxonomic analysis, based on the morphological, physiological, biochemical, and molecular investigation, of selected strains, which belong to the rare Actinobacteria, was undertaken. Four strains (CG3, A111, A93, and A79) were found to form distinct phyletic lines and represent new actinobacterial taxa. An assessment of antimicrobial proprieties of the 40 obtained actinomycetes strains, showed moderate to strong antimicrobial activities against fungi and bacteria. This study demonstrated the richness of Algerian Sahara with rare Actinobacteria, which can provide novel bioactive metabolites, to solving some of the most challenging problems of the day, such as multi-drug resistance.

Antimicrobial compounds from marine actinomycetes

Marine actinomycetes were the main origin of marine natural products in the past 40 years. This review was to present the sources, structures and antimicrobial activities of 313 new natural products from marine actinomycetes reported from 1976 to 2019.

Natural Bioactive Thiazole-Based Peptides from Marine Resources: Structural and Pharmacological Aspects

Peptides are distinctive biomacromolecules that demonstrate potential cytotoxicity and diversified bioactivities against a variety of microorganisms including bacteria, mycobacteria, and fungi via their unique mechanisms of action. Among broad-ranging pharmacologically active peptides, natural marine-originated thiazole-based oligopeptides possess peculiar structural features along with a wide spectrum of exceptional and potent bioproperties. Because of their complex nature and size divergence, thiazole-based peptides (TBPs) bestow a pivotal chemical platform in drug discovery processes to generate competent scaffolds for regulating allosteric binding sites and peptide–peptide interactions. The present study dissertates on the natural reservoirs and exclusive structural components of marine-originated TBPs, with a special focus on their most pertinent pharmacological profiles, which may impart vital resources for the development of novel peptide-based therapeutic agents.

Fouda M, Sayed AM, A. Hamed A, F. AbouZid S, Rateb ME, Alhadrami HA, Abdelmohsen UR. Induction of Antibacterial Metabolites by Co-Cultivation of Two Red-Sea-Sponge-Associated Actinomycetes Micromonospora sp. UR56 and Actinokinespora sp. EG49

Liquid chromatography coupled with high resolution mass spectrometry (LC-HRESMS)-assisted metabolomic profiling of two sponge-associated actinomycetes, Micromonospora sp. UR56 and Actinokineospora sp. EG49, revealed that the co-culture of these two actinomycetes induced the accumulation of metabolites that were not traced in their axenic cultures. Dereplication suggested that phenazine-derived compounds were the main induced metabolites. Hence, following large-scale co-fermentation, the major induced metabolites were isolated and structurally characterized as the already known dimethyl phenazine-1,6-dicarboxylate (1), phenazine-1,6-dicarboxylic acid mono methyl ester (phencomycin; 2), phenazine-1-carboxylic acid (tubermycin; 3), N-(2-hydroxyphenyl)-acetamide (9), and p-anisamide (10). Subsequently, the antibacterial, antibiofilm, and cytotoxic properties of these metabolites (1–3, 9, and 10) were determined in vitro. All the tested compounds except 9 showed high to moderate antibacterial and antibiofilm activities, whereas their cytotoxic effects were modest. Testing against Staphylococcus DNA gyrase-B and pyruvate kinase as possible molecular targets together with binding mode studies showed that compounds 1–3 could exert their bacterial inhibitory activities through the inhibition of both enzymes. Moreover, their structural differences, particularly the substitution at C-1 and C-6, played a crucial role in the determination of their inhibitory spectra and potency. In conclusion, the present study highlighted that microbial co-cultivation is an efficient tool for the discovery of new antimicrobial candidates and indicated phenazines as potential lead compounds for further development as antibiotic scaffold.

Targeting antimicrobial drug resistance with marine natural products

The rise and spread of antimicrobial resistance represents one of the most pressing health issues of today. Antimicrobial resistance in micro-organisms can arise due to a multiplicity of factors, including permeability changes in the cell membrane, increase of drug efflux pumps, enzymatic modification or inactivation of the antibiotic, target site modification, alternative metabolic pathways and biofilm formation. The marine environment is a valuable source of diverse natural products with a huge variety of biological activities. Among them, antimicrobial compounds show promising biological activities against numerous drug-resistant bacteria and fungi, making marine natural products a very promising resource in the search for novel antimicrobial agents. This review summarises the state-of-art of marine natural products with antibacterial and antifungal properties against drug-resistant micro-organisms. These natural products were categorised based on their chemical structure, and their respective sources and activities are highlighted. The chemical diversity associated with these marine-derived molecules is enormous, including peptides, polyketides, alkaloids, sterols, terpenoids, lactones, halogenated compounds, nucleosides, etc., some of which have rare substructures. Some of the marine compounds mentioned do not have intrinsic antimicrobial activity but potentiate the antimicrobial effect of other antimicrobials via inhibition of efflux pumps. Although these agents are still in preclinical studies, evidence of their in vivo efficacy suggest research of new drugs from the ocean to overcome antimicrobial resistance in order to fulfil an unmet medical need.

Antimicrobial lead compounds from marine plants

Marine environment is a home to a very wide diversity of flora and fauna, which includes an array of genetically diverse coastline and under seawater plant species, animal species, microbial species, their habitats, ecosystems, and supporting ecological processes. The Earth is home to an estimated 10 million species, of which a large chunk belongs to marine environment. Marine plants are a store house of a variety of antimicrobial compounds like classes of marine flavonoids—flavones and flavonols, terpenoids, alkaloids, peptides, carbohydrates, fatty acids, polyketides, polysaccharides, phenolic compounds, and steroids. Lot of research today is directed toward marine species, which have proved to be a potent source of structurally widely diverse and yet highly bioactive secondary metabolites. Varied species of phylum Porifera, algae including diatoms, Chlorophyta, Euglenophyta, Dinoflagellata, Chrysophyta, cyanobacteria, Rhodophyta, and Phaeophyta, bacteria, fungi, and weeds have been exploited by mankind for their inherent indigenous biological antimicrobial compounds, produced under the extreme stressful underwater conditions of temperature, atmospheric pressure, light, and nutrition. The present study aims at presenting a brief review of bioactive marine compounds possessing antimicrobial potency.

Isolation and characterization of bioactive compounds with antibacterial, antioxidant and enzyme inhibitory activities from marine-derived rare actinobacteria, Nocardiopsis sp. SCA21

A rare actinobacteria strain designated SCA21, producing bioactive metabolites was isolated from marine sediment of Havelock Island, Andaman and Nicobar Islands, India. Analysis of 16S rRNA sequences suggested that the strain SCA21 belonged to the genus Nocardiopsis. Chemical investigation of the fermentation broth led to the isolation of two pure bioactive compounds (1-2). Compound 1: 4-bromophenol, a bromophenol derivative; Compound 2: Bis (2-ethylhexyl) phthalate, a phthalate ester. The structure of compound 1 and 2 were elucidated by the detailed analysis of FT-IR, HR-ESI-MS, 1D and 2D NMR, along with literature data analysis. The isolated metabolites were evaluated for enzyme inhibition activity against α-glucosidase and α-amylase, free radical scavenging activity against DPPH and ABTS radicals, metal chelating and antibacterial activity against clinical pathogens. 1 and 2 exhibited remarkable enzyme inhibitory activities against α-glucosidase. However, Compound 2 was found less active against α-amylase. They showed significant free radical scavenging activity against DPPH and ABTS radicals. In addition, except the strain Salmonella typhi ATCC 25241 and Listeria cytogens ATCC 13932, 1 and 2 showed broad spectrum inhibitory activity against MRSA ATCC NR-46171, MRSA ATCC-46071, Klebsiella pneumonia ATCC 13883, Bacillus subtilis ATCC 6633, Staphylococcus aureus ATCC 12600. In conclusion, to best of our knowledge these findings are the first report of isolation of 4-bromophenol and Bis (2-ethylhexyl) phthalate from genus Nocardiopsis, thus suggesting that rare actinomycetes are promising source of therapeutically important bioactive metabolites.

The Biotechnological Potential of Secondary Metabolites from Marine Bacteria

Marine habitats are a rich source of molecules of biological interest. In particular, marine bacteria attract attention with their ability to synthesize structurally diverse classes of bioactive secondary metabolites with high biotechnological potential. The last decades were marked by numerous discoveries of biomolecules of bacterial symbionts, which have long been considered metabolites of marine animals. Many compounds isolated from marine bacteria are unique in their structure and biological activity. Their study has made a significant contribution to the discovery and production of new natural antimicrobial agents. Identifying the mechanisms and potential of this type of metabolite production in marine bacteria has become one of the noteworthy trends in modern biotechnology. This path has become not only one of the most promising approaches to the development of new antibiotics, but also a potential target for controlling the viability of pathogenic bacteria.

Heteroaryl Rings in Peptide Macrocycles

This Review is devoted to the chemistry of macrocyclic peptides having heterocyclic fragments in their structure. These motifs are present in many natural products and synthetic macrocycles designed against a particular biochemical target. Thiazole and oxazole are particularly common constituents of naturally occurring macrocyclic peptide molecules. This frequency of occurrence is because the thiazole and oxazole rings originate from cysteine, serine, and threonine residues. Whereas other heteroaryl groups are found less frequently, they offer many insightful lessons that range from conformational control to receptor/ligand interactions. Many options to develop new and improved technologies to prepare natural products have appeared in recent years, and the synthetic community has been pursuing synthetic macrocycles that have no precedent in nature. This Review attempts to summarize progress in this area.

Function and Distribution of a Lantipeptide in Strawberry Fusarium Wilt Disease-Suppressive Soils

Streptomyces griseus S4-7 is representative of strains responsible for the specific soil suppressiveness of Fusarium wilt of strawberry caused by Fusarium oxysporum f. sp. fragariae. Members of the genus Streptomyces secrete diverse secondary metabolites including lantipeptides, heat-stable lanthionine-containing compounds that can exhibit antibiotic activity. In this study, a class II lantipeptide provisionally named grisin, of previously unknown biological function, was shown to inhibit F. oxysporum. The inhibitory activity of grisin distinguishes it from other class II lantipeptides from Streptomyces spp. Results of quantitative reverse transcription-polymerase chain reaction with lanM-specific primers showed that the density of grisin-producing Streptomyces spp. in the rhizosphere of strawberry was positively correlated with the number of years of monoculture and a minimum of seven years was required for development of specific soil suppressiveness to Fusarium wilt disease. We suggest that lanM can be used as a diagnostic marker of whether a soil is conducive or suppressive to the disease.

Antimicrobial potential of haloalkaliphilic Nocardiopsis sp. AJ1 isolated from solar salterns in India

Antagonistic haloalkaliphilic Nocardiopsis sp. AJ1 (GenBank JX575136.1), isolated and identified from the saline soil of Kovalam solar salterns was able to produce antimicrobial secondary metabolites and effectively suppressed several bacterial and fungal pathogens. The metabolite extracted from ethyl acetate precipitation suppressed the bacterial and fungal pathogens to the range between 2.14 and 20.14 mm and also controlled the shrimp killer virus WSSV by 83% than the control and significantly (p < 0.05) differed. GC-MS analysis revealed that, the ethyl acetate precipitation contains pyrrolo (1,2-A(pyrazine-1,4-dione, hexahydro-3-(2-methylpropyl)-) and actinomycin C2. Non ribosomal peptide synthetase (NRPS) was amplified by PCR with the amplicon size of 750-800 bp length and further predicted the secondary structure by Iterative Threading Assembly Refinement (I-TASSER) bioinformatics approach. I-TASSER prediction helped to find out the secondary, 3-D structure, and ligand binding sites. The top ten modelling concluded that, the NRPS gene is closely similar to surfactin synthesizing gene, surfactin A synthetase C (SRFA-C). The findings revealed that, the active compounds from the secondary metabolites effectively suppressed the pathogenic bacteria, fungi, and virus and useful to develop antimicrobials.

Genome Mining of Streptomyces sp. YIM 130001 Isolated From Lichen Affords New Thiopeptide Antibiotic

Streptomyces bacteria are recognized as an important source for antibiotics with broad applications in human medicine and animal health. Here, we report the isolation of a new lichen-associating Streptomyces sp. YIM 130001 from the tropical rainforest in Xishuangbanna (Yunnan, China), which displayed antibacterial activity against Bacillus subtilis. The draft genome sequence of this isolate strain revealed 18 putative biosynthetic gene clusters (BGCs) for secondary metabolites, which is an unusually low number compared to a typical streptomycete. Inactivation of a lantibiotic dehydrogenase-encoding gene from the BGC presumed to govern biosynthesis of a thiopeptide resulted in the loss of bioactivity. Using comparative HPLC analysis, two peaks in the chromatogram were identified in the extract from the wild-type strain, which were missing in the extract from the mutant. The compounds corresponding to the identified peaks were purified, and structure of one compound was elucidated using NMR. The compound, designated geninthiocin B, showed high similarity to several 35-membered macrocyclic thiopeptides geninthiocin, Val-geninthiocin and berninamycin A. Bioinformatics analysis of the geninthiocin B BGC revealed its close homology to that of berninamycins.

Geninthiocins C and D from Streptomyces as 35-membered macrocyclic thiopeptides with modified tail moiety

Geninthiocin is a thiopeptide with 35-membered macrocyclic core moiety. It has potent anti-Gram-positive (G⁺) bacteria activity. Herein, we reported two new congeners (2-3) of geninthiocin (geninthiocin A, 1) from Streptomyces sp. CPCC 200267, and designated them as geninthiocins C and D, whose structures were determined by NMR. Geninthiocins A, C and D had the same 35-membered macrocyclic core moiety, but possessed a -Dha-Dha-NH₂, -Dha-Ala-NH₂, and -NH₂ tail, respectively. Besides, the Ala residue in geninthiocin C was determined as L- configuration by C₃ Marfey's method. In vitro assays indicated that geninthiocins C-D showed no antibacterial activity, in contrast to the potent anti-G⁺ bacteria activity displayed by geninthiocin A. Therefore, the -Dha-Dha-NH₂ tail of geninthiocin A played an important role in its potent activity against G⁺ bacteria.

Molecular identification and structural characterization of marine endophytic actinomycetes Nocardiopsis sp. GRG 2 (KT 235641) and its antibacterial efficacy against isolated ESBL producing bacteria

The present study was designed to identify the potential bioactive compound from endophytic actinomycetes (EA) Nocardiopsis sp. GRG 2 (KT 235641) against selected extended spectrum beta lactamase (ESBL) producing Pseudomonas aeruginosa (P. aeruginosa) and Klebsiella pneumoniae (K. pneumoniae). Initially, the multi drug resistance (MDR) effect of selected uropathogens was confirmed by respective UTI panel of Hexa antibiotics disc methods. The zone of inhibition ≤22 mm for ceftazidime, ≤ 27 mm for cefotaxime and ≤8 mm zone of MIC stripe against both the uropathogens of phenotypic methods confirmed, the selected strains were ESBL producer. Among the various EA extracts, GRG 2 extract showed excellent antibacterial activity against both ESBL producing P. aeruginosa and K. pneumonia by agar well diffution method. The molecular identification of selected GRG 2 strain was named as Nocardiopsis sp. GRG 2 (KT235641). The antibacterial metabolites present in the TLC elution was exhibited at 274 nm by UV visible spectrometer. The partial purification of preparative HPLC fraction 3 showed 14, 16 mm against P. aeruginosa and K. pneumoniae, respectively. Based on the antibacterial effect, the FT-IR, GC-MS and LC-MS analysis of fraction 3 was confirmed as 1, 4-diaza-2, 5-dioxo-3-isobutyl bicyclo[4.3.0]nonane (DDIBN). Further, the dose dependent inhibition of DDIBN against both ESBL producing pathogens was observed at 75 μg/mL by minimum inhibition concentration (MIC) and minimum bactericidal concentration (MBC). The increased cell death and disrupted cell membrane integrity were observed at MIC of DDIBN by confocal laser scanning electron microscope (CLSM) and scanning electron microscope (SEM). The results were proved that the DDIBN has potential antibacterial metabolites against ESBL producing pathogens and it can be applied for various other biomedical fields.

Molecular Characterization of Plasmids Harbored by Actinomycetes Isolated From the Great Salt Plains of Oklahoma Using PFGE and Next Generation Whole Genome Sequencing

One of the unique features of actinomycetes, especially the genus Streptomyces, is the presence of linear plasmids. These range in size from 12 to 600 kb, and are often termed mega-plasmids. While many of the genes involved in secondary metabolite production reside in clusters on the chromosome, several studies have identified biosynthetic clusters on large linear plasmids that produce important secondary metabolites, including antibiotics. In this study, Pulse Field Gel Electrophoresis (PFGE) was used to screen 176 actinomycete isolates for the presence of plasmids; these bacterial strains were previously isolated from the Great Salt Plains of Oklahoma. Seventy-eight of the 176 actinomycete isolates (44%) contained plasmids. Several strains contained more than one plasmid, accounting for a total of 109 plasmids. Ten isolates showed extrachromosomal DNA larger than 200 kb, thus falling into the category of mega-plasmids. A subset of plasmids from 55 isolates was treated with S1 nuclease to determine topology; all plasmids examined appeared to be linear and ranged from ~55 to 400 kb. Eleven isolates were chosen for Whole Genome Next Generation Sequencing. From the 11 sequenced isolates, seven plasmids were partially assembled. While the majority of the genes identified on the plasmids coded for hypothetical proteins, others coded for general functions, stress response, and antibiotic and heavy metal resistance. Draft genome sequences of two mega-plasmid-bearing Streptomyces sp. strains, BF-3 and 4F, revealed the presence of genes involved in antibiotic production, antibiotic, and heavy metal resistance, osmoregulation, and stress response, which likely facilitate their survival in this extreme halophilic environment. To our knowledge, this is the first study to explore plasmids harbored by actinomycetes isolated from the Great Salt Plains of Oklahoma.

Differential anti-microbial secondary metabolites in different ESKAPE pathogens explain their adaptation in the hospital setup

Nosocomial infections are caused by ESKAPE (E. faecium, S. aureus, K. pneumoniae, A. baumannii, P. aeruginosa, and E. cloacae) pathogens, and their co-existence is associated with their ability to survive in the hospital setup. They may produce molecules, which helps in the better survival of one ESKAPE pathogens over other. We have identified all secondary metabolite gene clusters in six ESKAPE pathogens and predicted antimicrobial and anti-biofilm properties of their product secondary metabolites. To validate our model, we have taken the secondary metabolites of ESKAPE pathogens and studied their interaction with diguanylate cyclase (involved in quorum sensing) and biofilm-associated protein (involved in biofilm formation) of Acinetobacter baumannii. Results suggest the presence of differential secondary metabolites in all ESKAPE pathogens with only three common non-antimicrobial secondary metabolites. Out of twenty-three antimicrobial secondary metabolites, TP-1161, nosiheptide and meilingmycin, showed the best antimicrobial activity and nineteen showed high anti-biofilm activity. Interaction study showed that secondary metabolites produced by other ESKAPE pathogens (non-Acinetobacter) have very good interaction with diguanylate cyclase and biofilm-associated protein of A. baumannii. This concludes that better survival of these ESKAPE pathogens in hospital setup can be correlated with differential production of antimicrobial secondary metabolites. The present study also investigates the molecular mechanism of the competition of different pathogens living in similar hospital setup (similar habitat). Therefore, the present study will initiate research that might lead to the discovery of antibiotics from one ESKAPE pathogen that controls the infection of other ESKAPE pathogens or other pathogens.

New Cytotoxic Cyclic Peptide from the Marine Sponge-Associated Nocardiopsis sp. UR67

A new cyclic hexapeptide, nocardiotide A (1), together with three known compounds—tryptophan (2), kynurenic acid (3), and 4-amino-3-methoxy benzoic acid (4)—were isolated and identified from the broth culture of Nocardiopsis sp. UR67 strain associated with the marine sponge Callyspongia sp. from the Red Sea. The structure elucidation of the isolated compounds were determined based on detailed spectroscopic data including ¹D and ²D nuclear magnetic resonance (NMR) experimental analyses in combination with high resolution electrospray ionization mass spectrometry (HR-ESI-MS), while the absolute stereochemistry of all amino acids components of nocardiotide A (1) was deduced using Marfey’s method. Additionally, ten known metabolites were dereplicated using HR-ESI-MS analysis. Nocardiotide A (1) displayed significant cytotoxic effects towards the murine CT26 colon carcinoma, human HeLa cervix carcinoma, and human MM.1S multiple myeloma cell lines. The results obtained revealed sponge-associated Nocardiopsis as a substantial source of lead natural products with pronounced pharmacological activities.

A Marine Isolate of Bacillus pumilus Secretes a Pumilacidin Active against Staphylococcus aureus

Producing antimicrobials is a common adaptive behavior shared by many microorganisms, including marine bacteria. We report that SF214, a marine-isolated strain of Bacillus pumilus, produces at least two different molecules with antibacterial activity: a molecule smaller than 3 kDa active against Staphylococcus aureus and a molecule larger than 10 kDa active against Listeria monocytogenes. We focused our attention on the anti-Staphylococcus molecule and found that it was active at a wide range of pH conditions and that its secretion was dependent on the growth phase, medium, and temperature. A mass spectrometry analysis of the size-fractionated supernatant of SF214 identified the small anti-Staphylococcus molecule as a pumilacidin, a nonribosomally synthesized biosurfactant composed of a mixture of cyclic heptapeptides linked to fatty acids of variable length. The analysis of the SF214 genome revealed the presence of a gene cluster similar to the srfA-sfp locus encoding the multimodular, nonribosomal peptide synthases found in other surfactant-producing bacilli. However, the srfA-sfp cluster of SF214 differed from that present in other surfactant-producing strains of B. pumilus by the presence of an insertion element previously found only in strains of B. safensis.

Concepts and Methods to Access Novel Antibiotics from Actinomycetes

Actinomycetes have been proven to be an excellent source of secondary metabolites for more than half a century. Exhibiting various bioactivities, they provide valuable approved drugs in clinical use. Most microorganisms are still untapped in terms of their capacity to produce secondary metabolites, since only a small fraction can be cultured in the laboratory. Thus, improving cultivation techniques to extend the range of secondary metabolite producers accessible under laboratory conditions is an important first step in prospecting underexplored sources for the isolation of novel antibiotics. Currently uncultured actinobacteria can be made available by bioprospecting extreme or simply habitats other than soil. Furthermore, bioinformatic analysis of genomes reveals most producers to harbour many more biosynthetic gene clusters than compounds identified from any single strain, which translates into a silent biosynthetic potential of the microbial world for the production of yet unknown natural products. This review covers discovery strategies and innovative methods recently employed to access the untapped reservoir of natural products. The focus is the order of actinomycetes although most approaches are similarly applicable to other microbes. Advanced cultivation methods, genomics- and metagenomics-based approaches, as well as modern metabolomics-inspired methods are highlighted to emphasise the interplay of different disciplines to improve access to novel natural products.

Actinobacteria-Derived peptide antibiotics since 2000

Members of the Actinobacteria, including Streptomyces spp., Kutzneria sp. Actinoplanes spp., Actinomycete sp., Nocardia sp., Brevibacteriumsp.,Actinomadura spp., Micromonospora sp., Amycolatopsis spp., Nonomuraea spp., Nocardiopsis spp., Marinactinospora sp., Rhodococcus sp., Lentzea sp., Actinokineospora sp., Planomonospora sp., Streptomonospora sp., and Microbacterium sp., are an important source of structurally diverse classes of short peptides of ∼30 residues or fewer that will likely play an important role in new antibiotic development and discovery. Additionally, many have unique structures that make them recalcitrant to traditional modes of drug resistance via novel mechanisms, and these are ideal therapeutic tools and potential alternatives to current antibiotics. The need for novel antibiotic is urgent, and this review summarizes 199 Actinobacteria compounds published since 2000, including 35 cyclic lipopeptides containing piperazic or pipecolic acids, eight aromatic peptides, five glycopeptides, 21 bicyclic peptides, 44 other cyclic lipopeptides, five linear lipopeptides, six 2,5-diketopiperazines, one dimeric peptide, four nucleosidyl peptides, two thioamide-containing peptides, 25 thiopeptides, nine lasso peptides, and 34 typical cyclic peptides. The current and potential therapeutic applications of these peptides, including their structure, antituberculotic, antibacterial, antifungal, antiviral, anti-brugia, anti-plasmodial, and anti-trypanosomal activities, are discussed.

Natural Product Potential of the Genus Nocardiopsis

Actinomycetes are a relevant source of novel bioactive compounds. One of the pharmaceutically and biotechnologically important genera that attract natural products research is the genus Nocardiopsis, mainly for its ability to produce a wide variety of secondary metabolites accounting for its wide range of biological activities. This review covers the literature from January 2015 until February 2018 making a complete survey of all the compounds that were isolated from the genus Nocardiopsis, their biological activities, and natural sources, whenever applicable.