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

Phylogenomic evaluation of Mangrovimicrobium sediminis gen. nov. sp. nov., the first nitrogen fixing member of the family Halieaceae adapted to mangrove habitat and reclassification of Halioglobus pacificus to Pseudohaliglobus pacificus comb. nov

The taxonomic position and genomic characteristics of a nitrogen fixing and polymer degrading marine bacterium, strain SAOS 164 isolated from a mangrove sediment sample was investigated. Sequence analysis based on 16S rRNA gene identified it as a member of family Halieaceae with closest similarity to Haliea salexigens DSM 19537T (96.3 %), H. alexandrii LZ-16-2T (96.2 %) and Parahaliea maris HSLHS9T (96.0 %) but was distantly related to the genera Haliea, Parahaliea and Halioglobus in phylogenetic trees. In order to ascertain the exact taxonomic position, phylogeny based on RpoBC proteins, whole genome, core and orthologous genes, and comparative analysis of metabolic potential retrieved the strain in an independent lineage clustering along with the genera Halioglobus, Pseudohalioglobus and Seongchinamella. Further, various genome based delimitation parameters represented by mol % GC content, percentage of conserved proteins (POCP), and amino acid identity (AAI) along with chemotaxonomic markers (i.e. fatty acids and polar lipids) supported the inferences of genome based phylogeny and indicated that the strain SAOS 164 belongs to a novel genus. The genome was mapped to 4.8 Mb in size with 65.1 % DNA mol% G + C content. In-silico genomic investigation and phenotyping revealed diverse metabolite genes/pathways related to polymer hydrolysis, nitrogen fixation, light induced growth, carbohydrate, sulfur, phosphorus and amino acid metabolism, virulence factors, defense mechanism, and stress-responsive elements facilitating survival in the mangrove habitat. Based on polyphasic taxonomic approach including genome analyses, a novel genus Mangrovimicrobium sediminis gen. nov. sp. nov. (=SAOS 164T = MTCC 12907T = KCTC 52755T = JCM 32136T) is proposed. Additionally, the reclassification of Halioglobus pacificus (=DSM 27932T = KCTC 23430T = S1-72T) to Pseudhalioglobus pacificus comb. nov. is also proposed.

Diversity and Bioprospection of Gram-positive Bacteria Derived from a Mayan Sinkhole

Water-filled sinkholes known locally as cenotes, found on the Yucatán Peninsula, have remarkable biodiversity. The primary objective of this study was to explore the biotechnological potential of Gram-positive cultivable bacteria obtained from sediment samples collected at the coastal cenote Pol-Ac in Yucatán, Mexico. Specifically, the investigation aimed to assess production of hydrolytic enzymes and antimicrobial compounds. 16 S rRNA gene sequencing led to the identification of 49 Gram-positive bacterial isolates belonging to the phyla Bacillota (n = 29) and Actinomycetota (n = 20) divided into the common genera Bacillus and Streptomyces, as well as the genera Virgibacillus, Halobacillus, Metabacillus, Solibacillus, Neobacillus, Rossellomorea, Nocardiopsis and Corynebacterium. With growth at 55ºC, 21 of the 49 strains were classified as moderately thermotolerant. All strains were classified as halotolerant and 24 were dependent on marine water for growth. Screening for six extracellular hydrolytic enzymes revealed gelatinase, amylase, lipase, cellulase, protease and chitinase activities in 93.9%, 67.3%, 63.3%, 59.2%, 59.2% and 38.8%, of isolated strains, respectively. The genes for polyketide synthases type I, were detected in 24 of the strains. Of 18 strains that achieved > 25% inhibition of growth in the bacterial pathogen Staphylococcus aureus ATCC 6538, 4 also inhibited growth in Escherichia coli ATCC 35,218. Isolates Streptomyces sp. NCA_378 and Bacillus sp. NCA_374 demonstrated 50-75% growth inhibition against at least one of the two pathogens tested, along with significant enzymatic activity across all six extracellular enzymes. This is the first comprehensive report on the biotechnological potential of Gram-positive bacteria isolated from sediments in the cenotes of the Yucatán Peninsula.

Functional Genomics of a Collection of Gammaproteobacteria Isolated from Antarctica

Antarctica, one of the most extreme environments on Earth, hosts diverse microbial communities. These microbes have evolved and adapted to survive in these hostile conditions, but knowledge on the molecular mechanisms underlying this process remains limited. The Italian Collection of Antarctic Bacteria (Collezione Italiana Batteri Antartici (CIBAN)), managed by the University of Messina, represents a valuable repository of cold-adapted bacterial strains isolated from various Antarctic environments. In this study, we sequenced and analyzed the genomes of 58 marine Gammaproteobacteria strains from the CIBAN collection, which were isolated during Italian expeditions from 1990 to 2005. By employing genome-scale metrics, we taxonomically characterized these strains and assigned them to four distinct genera: Pseudomonas, Pseudoalteromonas, Shewanella, and Psychrobacter. Genome annotation revealed a previously untapped functional potential, including secondary metabolite biosynthetic gene clusters and antibiotic resistance genes. Phylogenomic analyses provided evolutionary insights, while assessment of cold-shock protein presence shed light on adaptation mechanisms. Our study emphasizes the significance of CIBAN as a resource for understanding Antarctic microbial life and its biotechnological potential. The genomic data unveil new horizons for insight into bacterial existence in Antarctica.

New investigation of encoding secondary metabolites gene by genome mining of a marine bacterium, Pseudoalteromonas viridis BBR56

Pseudoalteromonas viridis strain BBR56 was isolated from seawater at Dutungan Island, South Sulawesi, Indonesia. Bacterial DNA was isolated using Promega Genomic DNA TM050. DNA purity and quantity were assessed using NanoDrop spectrophotometers and Qubit fluorometers. The DNA library and sequencing were prepared using Oxford Nanopore Technology GridION MinKNOW 20.06.9 with long read, direct, and comprehensive analysis. High accuracy base calling was assessed with Guppy version 4.0.11. Filtlong and NanoPlot were used for filtering and visualizing the FASTQ data. Flye (2.8.1) was used for de novo assembly analysis. Variant calls and consensus sequences were created using Medaka. The annotation of the genome was elaborated by DFAST. The assembled genome and annotation were tested using Busco and CheckM. Herein, we found that the highest similarity of the BBR56 isolate was 98.37% with the 16 S rRNA gene sequence of P. viridis G-1387. The genome size was 5.5 Mb and included chromosome 1 (4.2 Mbp) and chromosome 2 (1.3 Mbp), which encoded 61 pseudogenes, 4 noncoding RNAs, 113 tRNAs, 31 rRNAs, 4,505 coding DNA sequences, 4 clustered regularly interspaced short palindromic repeats, 4,444 coding genes, and a GC content of 49.5%. The sequence of the whole genome of P. viridis BBR56 was uploaded to GenBank under the accession numbers CP072425-CP072426, biosample number SAMN18435505, and bioproject number PRJNA716373. The sequence read archive (SRR14179986) was successfully obtained from NCBI for BBR56 raw sequencing reads. Digital DNA-DNA hybridization results showed that the genome of BBR56 had the potential to be a new species because no other bacterial genomes were similar to the sample. Biosynthetic gene clusters (BGCs) were assessed using BAGEL4 and the antiSMASH bacterial version. The genome harbored diverse BGCs, including genes that encoded polyketide synthase, nonribosomal peptide synthase, RiPP-like, NRP-metallophore, hydrogen cyanide, betalactone, thioamide-NRP, Lant class I, sactipeptide, and prodigiosin. Thus, BBR56 has considerable potential for further exploration regarding the use of its secondary metabolite products in the human and fisheries sectors.

Isolation of Secondary Metabolites From Marine Actinobacterium of Microbispora sp.T3S11 and Their Antibacterial Activities

Introduction Marine actinobacteria are promising sources of novel bioactive compounds due to their distinct ecological niches and diverse secondary metabolite production capabilities. Among these, Microbispora sp. T3S11 is notable for its unique spore chain structure, which allows for both morphological and genetic identification. Despite its potential, little is understood about the secondary metabolites produced by this strain. In this study, we hope to fill this gap by extracting and analyzing the antibacterial activities of secondary metabolites from Microbispora sp. T3S11, which will be the first time its bioactive compound profile is investigated. Aim To evaluate the antibacterial activity of secondary metabolites isolated from the marine actinobacterium Microbispora sp. T3S11. Materials and methods The antibacterial assays were carried out on agar plates containing the appropriate media for each pathogen. Sterile filter paper disks were impregnated with secondary metabolites extracted from Microbispora sp. T3S11 and placed on the surface of agar plates inoculated with the appropriate pathogens. Similarly, disks containing tetracycline were used as a positive control. The plates were then incubated at the appropriate temperature for each pathogen, and the zones of inhibition around the disks were measured to determine the extracted metabolites' antibacterial activity. Result Secondary metabolites had antimicrobial activity against Streptococcus mutans, Klebsiella pneumonia, and methicillin-resistant Staphylococcus aureus (MRSA). The inhibition of S. mutans was 7.5 mm and 8.5 mm at 75 μg/mL and 100 μg/mL, respectively. Klebsiella pneumonia zones measured 7 mm and 7.5 mm, while MRSA zones measured 7.6 mm and 8.5 mm at the same concentrations. Tetracycline, the standard antibiotic, had larger inhibition zones: 22 mm for S. mutans and Klebsiella pneumonia and 16 mm for MRSA, indicating variable susceptibility. Conclusion We conclude that the secondary metabolites extracted from Microbispora sp. T3S11 exhibits high antibacterial activity. This could be attributed to the presence of various active compounds.

In Silico Screening of Bacteriocin Gene Clusters within a Set of Marine Bacillota Genomes

Due to their potential application as an alternative to antibiotics, bacteriocins, which are ribosomally synthesized antimicrobial peptides produced by bacteria, have received much attention in recent years. To identify bacteriocins within marine bacteria, most of the studies employed a culture-based method, which is more time-consuming than the in silico approach. For that, the aim of this study was to identify potential bacteriocin gene clusters and their potential producers in 51 marine Bacillota (formerly Firmicutes) genomes, using BAGEL4, a bacteriocin genome mining tool. As a result, we found out that a majority of selected Bacillota (60.78%) are potential bacteriocin producers, and we identified 77 bacteriocin gene clusters, most of which belong to class I bacteriocins known as RiPPs (ribosomally synthesized and post-translationally modified peptides). The identified putative bacteriocin gene clusters are an attractive target for further in vitro research, such as the production of bacteriocins using a heterologous expression system.

Computational assessment of marine natural products as LasR inhibitors for attenuating quorum sensing in Pseudomonas aeruginosa

The Quorum Sensing (QS) system in bacteria has become a focal point for researchers aiming to develop novel antimicrobials to combat multidrug-resistant bacteria. Pseudomonas aeruginosa, an opportunistic Gram-negative bacterium, has developed resistance against a variety of antimicrobial agents, making it a formidable pathogen responsible for nosocomial infections. QS system mainly controls the expression of genes responsible for biofilm formation and virulence of bacteria. Within the QS system of P. aeruginosa, the transcription activator LasR plays a pivotal role and is an appealing target for the development of antimicrobial agents. In this study, we employed molecular docking and molecular dynamics simulations to identify potential inhibitors of LasR by screening marine natural products (MNPs) from the CMNPD database. We identified ten MNPs with excellent docking scores (less than -11.7 kcal/mol) against LasR, surpassing the binding energy of the co-crystal 3-oxo-C12-HSL (-8.594 kcal/mol) and the reference compound cladodionen (-6.71 kcal/mol). Furthermore, we selected five of these MNPs with the highest MM/GBSA binding energies for extensive 100 ns molecular simulations to assess their stability. The molecular dynamics simulations indicated three MNPs, namely CMNPD10886, CMNPD20987, and CMNPD20960, maintained high stability throughout the 100 ns simulation period, as evidenced by their root mean square deviation, root mean square fluctuation, radius of gyration, and hydrogen bond interactions within the ligand-protein complex analysis. Furthermore, essential dynamics (PCA and DCCM) were performed to analyse the correlated motion of amino acids. These findings suggest that these compounds hold potential as inhibitors of LasR, offering promising prospects for the development of treatments against infections.Communicated by Ramaswamy H. Sarma.

Development of Biological Coating from Novel Halophilic Exopolysaccharide Exerting Shelf-Life-Prolonging and Biocontrol Actions for Post-Harvest Applications

The literature presents the preserving effect of biological coatings developed from various microbial sources. However, the presented work exhibits its uniqueness in the utilization of halophilic exopolysaccharides as food coating material. Moreover, such extremophilic exopolysaccharides are more stable and economical production is possible. Consequently, the aim of the presented research was to develop a coating material from marine exopolysaccharide (EPS). The significant EPS producers having antagonistic attributes against selected phytopathogens were screened from different marine water and soil samples. TSIS01 isolate revealed the maximum antagonism well and EPS production was selected further and characterized as Bacillus tequilensis MS01 by 16S rRNA analysis. EPS production was optimized and deproteinized EPS was assessed for biophysical properties. High performance thin layer chromatography (HPTLC) analysis revealed that EPS was a heteropolymer of glucose, galactose, mannose, and glucuronic acid. Fourier transform infrared spectroscopy, X-ray diffraction, and UV-visible spectra validated the presence of determined sugars. It showed high stability at a wide range of temperatures, pH and incubation time, ≈1.63 × 106 Da molecular weight, intermediate solubility index (48.2 ± 3.12%), low water holding capacity (12.4 ± 1.93%), and pseudoplastic rheologic shear-thinning comparable to xanthan gum. It revealed antimicrobial potential against human pathogens and antioxidants as well as anti-inflammatory potential. The biocontrol assay of EPS against phytopathogens revealed the highest activity against Alternaria solani. The EPS-coated and control tomato fruits were treated with A. solani suspension to check the % disease incidence, which revealed a significant (p < 0.001) decline compared to uncoated controls. Moreover, it revealed shelf-life prolonging action on tomatoes comparable to xanthan gum and higher than chitosan. Consequently, the presented marine EPS was elucidated as a potent coating material to mitigate post-harvest losses.

Study of marine microorganism metabolites: new resources for bioactive natural products

The marine environment has remained a source of novel biological molecules with diversified applications. The ecological and biological diversity, along with a unique physical environment, have provided the evolutionary advantage to the plant, animals and microbial species thriving in the marine ecosystem. In light of the fact that marine microorganisms frequently interact symbiotically or mutualistically with higher species including corals, fish, sponges, and algae, this paper intends to examine the potential of marine microorganisms as a niche for marine bacteria. This review aims to analyze and summarize modern literature data on the biotechnological potential of marine fungi and bacteria as producers of a wide range of practically valuable products (surfactants, glyco-and lipopeptides, exopolysaccharides, enzymes, and metabolites with different biological activities: antimicrobial, antitumor, and cytotoxic). Hence, the study on bioactive secondary metabolites from marine microorganisms is the need of the hour. The scientific novelty of the study lies in the fact that for the first time, the data on new resources for obtaining biologically active natural products - metabolites of marine bacteria and fungi - were generalized. The review investigates the various kinds of natural products derived from marine microorganisms, specifically focusing on marine bacteria and fungi as a valuable source for new natural products. It provides a summary of the data regarding the antibacterial, antimalarial, anticarcinogenic, antibiofilm, and anti-inflammatory effects demonstrated by marine microorganisms. There is currently a great need for scientific and applied research on bioactive secondary metabolites of marine microorganisms from the standpoint of human and animal health.

OSMAC Method to Assess Impact of Culture Parameters on Metabolomic Diversity and Biological Activity of Marine-Derived Actinobacteria

Actinobacteria are known for their production of bioactive specialized metabolites, but they are still under-exploited. This study uses the "One Strain Many Compounds" (OSMAC) method to explore the potential of three preselected marine-derived actinobacteria: Salinispora arenicola (SH-78) and two Micromonospora sp. strains (SH-82 and SH-57). Various parameters, including the duration of the culture and the nature of the growth medium, were modified to assess their impact on the production of specialized metabolites. This approach involved a characterization based on chemical analysis completed with the construction of molecular networks and biological testing to evaluate cytotoxic and antiplasmodial activities. The results indicated that the influence of culture parameters depended on the studied species and also varied in relation with the microbial metabolites targeted. However, common favorable parameters could be observed for all strains such as an increase in the duration of the culture or the use of the A1 medium. For Micromonospora sp. SH-82, the solid A1 medium culture over 21 days favored a greater chemical diversity. A rise in the antiplasmodial activity was observed with this culture duration, with a IC50 twice as low as for the 14-day culture. Micromonospora sp. SH-57 produced more diverse natural products in liquid culture, with approximately 54% of nodes from the molecular network specifically linked to the type of culture support. Enhanced biological activities were also observed with specific sets of parameters. Finally, for Salinispora arenicola SH-78, liquid culture allowed a greater diversity of metabolites, but intensity variations were specifically observed for some metabolites under other conditions. Notably, compounds related to staurosporine were more abundant in solid culture. Consequently, in the range of the chosen parameters, optimal conditions to enhance metabolic diversity and biological activities in these three marine-derived actinobacteria were identified, paving the way for future isolation works.

Heterologously expressed SacP23, a novel bacteriocin from Paenibacillus polymyxa #23, is active against methicillin resistant Staphylococcus aureus

Antimicrobial peptides have the potential to be used in a range of applications, including as an alternative to conventional antibiotics for the treatment of bacterial infections of humans and animals. Therefore, there is interest in identifying novel bacteriocins which have desirable physico-chemical properties or antimicrobial activities. Paenibacillus polymyxa #23, isolated from a marine sponge, has wide spectrum antimicrobial activity against Gram-negative and Gram-positive bacteria. To explore the basis of this antimicrobial activity, the complete genome sequence of the strain was examined. Multiple genes predicted to encode antimicrobial peptides were identified. One gene was predicted to encode a novel sactipeptide bacteriocin, named SacP23. To confirm that SacP23 does have antimicrobial activity and to explore the antimicrobial spectrum of the peptide it was heterologously expressed in Bacillus subtilis. A cluster of eight genes, encoding a full complement of accessory genes as well as the structural gene expressed from the native promoter, was cloned into B. subtilis BS54A. The recombinant strain displayed antimicrobial activity against several Gram-positive bacteria, including multi-drug resistant Staphylococcus aureus. Heterologous expression of a whole gene cluster offers a powerful way to interrogate and resolve the various antimicrobial activities expressed by native strains that encode multiple compounds of interest.

Biosynthetic gene cluster profiling from North Java Sea Virgibacillus salarius reveals hidden potential metabolites

Virgibacillus salarius 19.PP.SC1.6 is a coral symbiont isolated from Indonesia's North Java Sea; it has the ability to produce secondary metabolites that provide survival advantages and biological functions, such as ectoine, which is synthesized by an ectoine gene cluster. Apart from being an osmoprotectant for bacteria, ectoine is also known as a chemical chaperone with numerous biological activities such as maintaining protein stability, which makes ectoine in high demand in the market industry and makes it beneficial to investigate V. salarius ectoine. However, there has been no research on genome-based secondary metabolite and ectoine gene cluster characterization from Indonesian marine V. salarius. In this study, we performed a genomic analysis and ectoine identification of V. salarius. A high-quality draft genome with total size of 4.45 Mb and 4426 coding sequence (CDS) was characterized and then mapped into the Cluster of Orthologous Groups (COG) category. The genus Virgibacillus has an "open" pangenome type with total of 18 genomic islands inside the V. salarius 19.PP.SC1.6 genome. There were seven clusters of secondary metabolite-producing genes found, with a total of 80 genes classified as NRPS, PKS (type III), terpenes, and ectoine biosynthetic related genes. The ectoine gene cluster forms one operon consists of ectABC gene with 2190 bp gene cluster length, and is successfully characterized. The presence of ectoine in V. salarius was confirmed using UPLC-MS/MS operated in Multiple Reaction Monitoring (MRM) mode, which indicates that V. salarius has an intact ectoine gene clusters and is capable of producing ectoine as compatible solutes.

Natural Products and Pharmacological Properties of Symbiotic Bacillota (Firmicutes) of Marine Macroalgae

The shift from the terrestrial to the marine environment to discover natural products has given rise to novel bioactive compounds, some of which have been approved for human medicine. However, the ocean, which makes up nearly three-quarters of the Earth's surface, contains macro- and microorganisms whose natural products are yet to be explored. Among these underexplored marine organisms are macroalgae and their symbiotic microbes, such as Bacillota, a phylum of mostly Gram-positive bacteria previously known as Firmicutes. Macroalgae-associated Bacillota often produce chemical compounds that protect them and their hosts from competitive and harmful rivals. Here, we summarised the natural products made by macroalgae-associated Bacillota and their pharmacological properties. We discovered that these Bacillota are efficient producers of novel biologically active molecules. However, only a few macroalgae had been investigated for chemical constituents of their Bacillota: nine brown, five red and one green algae. Thus, Bacillota, especially from the marine habitat, should be investigated for potential pharmaceutical leads. Moreover, additional diverse biological assays for the isolated molecules of macroalgae Bacillota should be implemented to expand their bioactivity profiles, as only antibacterial properties were tested for most compounds.

Shotgun metagenomics and computational profiling of the plastisphere microbiome: unveiling the potential of enzymatic production and plastic degradation

Plastic pollution is one of the most resilient types of pollution and is considered a global environmental threat, particularly in the marine environment. This study aimed to identify plastic-degrading bacteria from the plastisphere and their pharmaceutical and therapeutic potential. We collected samples from soil and aquatic plastisphere to identify the bacterial communities using shotgun metagenomic sequencing and bioinformatic tools. Results showed that the microbiome comprised 93% bacteria, 0.29% archaea, and 3.87% unidentified microbes. Of these 93% of bacteria, 54% were Proteobacteria, 23.9% were Firmicutes, 13% were Actinobacteria, and 2.1% were other phyla. We found that the plastisphere microbiome was involved in degrading synthetic and polyhydroxy alkanoate (PHA) plastic, biosurfactant production, and can thrive under high temperatures. However, no association existed between thermophiles, synthetic plastic or PHA degraders, and biosurfactant-producing bacterial species except for Pseudomonas. Other plastisphere inhabiting plastic degrading microbes include Streptomyces, Bacillus, Achromobacter, Azospirillum, Bacillus, Brevundimonas, Clostridium, Paenibacillus, Rhodococcus, Serratia, Staphylococcus, Thermobifida, and Thermomonospora. However, the plastisphere microbiome showed potential for producing secondary metabolites that were found to act as anticancer, antitumor, anti-inflammatory, antimicrobial, and enzyme stabilizers. These results revealed that the plastisphere microbiome upholds clinical and environmental significance as it can open future portals in a multi-directional way.

Evaluation of Antimicrobial Activity by Marine Nocardiopsis dassonvillei against Foodborne Listeria monocytogenes and Shiga Toxin-Producing Escherichia coli

The emergence of multidrug-resistant pathogens creates public health challenges, prompting a continuous search for effective novel antimicrobials. This study aimed to isolate marine actinomycetes from South Africa, evaluate their in vitro antimicrobial activity against Listeria monocytogenes and Shiga toxin-producing Escherichia coli, and characterize their mechanisms of action. Marine actinomycetes were isolated and identified by 16S rRNA sequencing. Gas chromatography-mass spectrometry (GC-MS) was used to identify the chemical constituents of bioactive actinomycetes' secondary metabolites. Antibacterial activity of the secondary metabolites was assessed by the broth microdilution method, and their mode of actions were predicted using computational docking. While five strains showed antibacterial activity during primary screening, only Nocardiopsis dassonvillei strain SOD(B)ST2SA2 exhibited activity during secondary screening for antibacterial activity. GC-MS identified five major bioactive compounds: 1-octadecene, diethyl phthalate, pentadecanoic acid, 6-octadecenoic acid, and trifluoroacetoxy hexadecane. SOD(B)ST2SA2's extract demonstrated minimum inhibitory concentration and minimum bactericidal concentration, ranging from 0.78-25 mg/mL and 3.13 to > 25 mg/mL, respectively. Diethyl phthalate displayed the lowest bacterial protein-binding energies (kcal/mol): -7.2, dihydrofolate reductase; -6.0, DNA gyrase B; and -5.8, D-alanine:D-alanine ligase. Thus, marine N. dassonvillei SOD(B)ST2SA2 is a potentially good source of antibacterial compounds that can be used to control STEC and Listeria monocytogenes.

MariClus: Your One-Stop Platform for Information on Marine Natural Products, Their Gene Clusters and Producing Organisms

BACKGROUND

The marine environment hosts the vast majority of living species and marine microbes that produce natural products with great potential in providing lead compounds for drug development. With over 70% of Earth's surface covered in water and the high interaction rate associated with liquid environments, this has resulted in many marine natural product discoveries. Our improved understanding of the biosynthesis of these molecules, encoded by gene clusters, along with increased genomic information will aid us in uncovering even more novel compounds.

RESULTS

We introduce MariClus (https://www.mariclus.com), an online user-friendly platform for mining and visualizing marine gene clusters. The first version contains information on clusters and the predicted molecules for over 500 marine-related prokaryotes. The user-friendly interface allows scientists to easily search by species, cluster type or molecule and visualize the information in table format or graphical representation.

CONCLUSIONS

This new online portal simplifies the exploration and comparison of gene clusters in marine species for scientists and assists in characterizing the bioactive molecules they produce. MariClus integrates data from public sources, like GenBank, MIBiG and PubChem, with genome mining results from antiSMASH. This allows users to access and analyze various aspects of marine natural product biosynthesis and diversity.

New Imidazolium Alkaloids with Broad Spectrum of Action from the Marine Bacterium Shewanella aquimarina

The continuous outbreak of drug-resistant bacterial and viral infections imposes the need to search for new drug candidates. Natural products from marine bacteria still inspire the design of pharmaceuticals. Indeed, marine bacteria have unique metabolic flexibility to inhabit each ecological niche, thus expanding their biosynthetic ability to assemble unprecedented molecules. The One-Strain-Many-Compounds approach and tandem mass spectrometry allowed the discovery of a Shewanella aquimarina strain as a source of novel imidazolium alkaloids via molecular networking. The alkaloid mixture was shown to exert bioactivities such as: (a) antibacterial activity against antibiotic-resistant Staphylococcus aureus clinical isolates at 100 µg/mL, (b) synergistic effects with tigecycline and linezolid, (c) restoration of MRSA sensitivity to fosfomycin, and (d) interference with the biofilm formation of S. aureus 6538 and MRSA. Moreover, the mixture showed antiviral activity against viruses with and without envelopes. Indeed, it inhibited the entry of coronavirus HcoV-229E and herpes simplex viruses into human cells and inactivated poliovirus PV-1 in post-infection assay at 200 µg/mL. Finally, at the same concentration, the fraction showed anthelminthic activity against Caenorhabditis elegans, causing 99% mortality after 48 h. The broad-spectrum activities of these compounds are partially due to their biosurfactant behavior and make them promising candidates for breaking down drug-resistant infectious diseases.

Marine Resources Offer New Compounds and Strategies for the Treatment of Skin and Soft Tissue Infections

Bioprospecting of the marine environment for drug development has gained much attention in recent years owing to its massive chemical and biological diversity. Drugs for the treatment of skin and soft tissue infections have become part of the search, mainly with respect to enlarging the number of available antibiotics, with a special focus on multidrug-resistant Gram-positive bacteria, being the major causative agents in this field. Marine resources offer novel natural products with distinct biological activities of pharmaceutical importance, having the chance to provide new chemical scaffolds and new modes of action. New studies advance the field by proposing new strategies derived from an ecosystemic understanding for preventive activities against biofilms and new compounds suitable as disinfectants, which sustain the natural flora of the skin. Still, the development of new compounds is often stuck at the discovery level, as marine biotechnology also needs to overcome technological bottlenecks in drug development. This review summarizes its potential and shows these bottlenecks and new approaches.

Global analysis of the biosynthetic chemical space of marine prokaryotes

BACKGROUND

Marine prokaryotes are a rich source of novel bioactive secondary metabolites for drug discovery. Recent genome mining studies have revealed their great potential to bio-synthesize novel secondary metabolites. However, the exact biosynthetic chemical space encoded by the marine prokaryotes has yet to be systematically evaluated.

RESULTS

We first investigated the secondary metabolic potential of marine prokaryotes by analyzing the diversity and novelty of the biosynthetic gene clusters (BGCs) in 7541 prokaryotic genomes from cultivated and single cells, along with 26,363 newly assembled medium-to-high-quality genomes from marine environmental samples. To quantitatively evaluate the unexplored biosynthetic chemical space of marine prokaryotes, the clustering thresholds for constructing the biosynthetic gene cluster and molecular networks were optimized to reach a similar level of the chemical similarity between the gene cluster family (GCF)-encoded metabolites and molecular family (MF) scaffolds using the MIBiG database. The global genome mining analysis demonstrated that the predicted 70,011 BGCs were organized into 24,536 mostly new (99.5%) GCFs, while the reported marine prokaryotic natural products were only classified into 778 MFs at the optimized clustering thresholds. The number of MF scaffolds is only 3.2% of the number of GCF-encoded scaffolds, suggesting that at least 96.8% of the secondary metabolic potential in marine prokaryotes is untapped. The unexplored biosynthetic chemical space of marine prokaryotes was illustrated by the 88 potential novel antimicrobial peptides encoded by ribosomally synthesized and post-translationally modified peptide BGCs. Furthermore, a sea-water-derived Aquimarina strain was selected to illustrate the diverse biosynthetic chemical space through untargeted metabolomics and genomics approaches, which identified the potential biosynthetic pathways of a group of novel polyketides and two known compounds (didemnilactone B and macrolactin A 15-ketone).

CONCLUSIONS

The present bioinformatics and cheminformatics analyses highlight the promising potential to explore the biosynthetic chemical diversity of marine prokaryotes and provide valuable knowledge for the targeted discovery and biosynthesis of novel marine prokaryotic natural products. Video Abstract.

Genomic insights into secondary metabolites of pharmaceutical utility for Hyphococcus flavus MCCC 1K03223T, isolated from bathypelagic seawater

During an attempt to screen secondary metabolites of pharmaceutical utility, we sequenced the complete genome of type strain of a novel marine bacterial genus, named genus Hyphococcus. The type strain, Hyphococcus flavus MCCC 1K03223^T, was isolated from bathypelagic seawater of South China Sea at a depth of 2500 m. The complete genome of strain MCCC 1K03223^T is composed of a circular chromosome of 3,472,649 bp with a mean G + C content of 54.8%. Functional genomic analysis showed that this genome encodes five biosynthetic gene clusters, which were annotated to synthesize medicinally important secondary metabolites. Secondary metabolites annotated include ectoine which acts cytoprotection, ravidomycin which is an antitumor antibiotic and three other different metabolites of terpene type. The secondary metabolic potentials of H. flavus revealed in this study provide more evidences on mining bioactive substances from marine bathypelagic microorganisms.

Modern Trends in Natural Antibiotic Discovery

Natural scaffolds remain an important basis for drug development. Therefore, approaches to natural bioactive compound discovery attract significant attention. In this account, we summarize modern and emerging trends in the screening and identification of natural antibiotics. The methods are divided into three large groups: approaches based on microbiology, chemistry, and molecular biology. The scientific potential of the methods is illustrated with the most prominent and recent results.

Exploring Possible Ways to Enhance the Potential and Use of Natural Products through Nanotechnology in the Battle against Biofilms of Foodborne Bacterial Pathogens

Biofilms enable pathogenic bacteria to survive in unfavorable environments. As biofilm-forming pathogens can cause rapid food spoilage and recurrent infections in humans, especially their presence in the food industry is problematic. Using chemical disinfectants in the food industry to prevent biofilm formation raises serious health concerns. Further, the ability of biofilm-forming bacterial pathogens to tolerate disinfection procedures questions the traditional treatment methods. Thus, there is a dire need for alternative treatment options targeting bacterial pathogens, especially biofilms. As clean-label products without carcinogenic and hazardous potential, natural compounds with growth and biofilm-inhibiting and biofilm-eradicating potentials have gained popularity as natural preservatives in the food industry. However, the use of these natural preservatives in the food industry is restricted by their poor availability, stability during food processing and storage. Also there is a lack of standardization, and unattractive organoleptic qualities. Nanotechnology is one way to get around these limitations and as well as the use of underutilized bioactives. The use of nanotechnology has several advantages including traversing the biofilm matrix, targeted drug delivery, controlled release, and enhanced bioavailability, bioactivity, and stability. The nanoparticles used in fabricating or encapsulating natural products are considered as an appealing antibiofilm strategy since the nanoparticles enhance the activity of the natural products against biofilms of foodborne bacterial pathogens. Hence, this literature review is intended to provide a comprehensive analysis of the current methods in nanotechnology used for natural products delivery (biofabrication, encapsulation, and nanoemulsion) and also discuss the different promising strategies employed in the recent and past to enhance the inhibition and eradication of foodborne bacterial biofilms.

β-Lactams from the Ocean

The title of this essay is as much a question as it is a statement. The discovery of the β-lactam antibiotics-including penicillins, cephalosporins, and carbapenems-as largely (if not exclusively) secondary metabolites of terrestrial fungi and bacteria, transformed modern medicine. The antibiotic β-lactams inactivate essential enzymes of bacterial cell-wall biosynthesis. Moreover, the ability of the β-lactams to function as enzyme inhibitors is of such great medical value, that inhibitors of the enzymes which degrade hydrolytically the β-lactams, the β-lactamases, have equal value. Given this privileged status for the β-lactam ring, it is therefore a disappointment that the exemplification of this ring in marine secondary metabolites is sparse. It may be that biologically active marine β-lactams are there, and simply have yet to be encountered. In this report, we posit a second explanation: that the value of the β-lactam to secure an ecological advantage in the marine environment might be compromised by its close structural similarity to the β-lactones of quorum sensing. The steric and reactivity similarities between the β-lactams and the β-lactones represent an outside-of-the-box opportunity for correlating new structures and new enzyme targets for the discovery of compelling biological activities.

N-(2-hydroxyphenyl)-2-phenazinamine from Nocardiopsis exhalans induces p53-mediated intrinsic apoptosis signaling in lung cancer cell lines

The present study aims to investigate the effect and the molecular mechanism of N-(2-hydroxyphenyl)-2-phenazinamine (NHP) isolated from Nocardiopsis exhalans against the proliferation of human lung cancer cells. The cytotoxic activity of NHP against A549 and H520 cells was determined using MTT assay. The cytotoxic activity of NHP against A549 and H520 lung cancer cells showed excellent activity at 75 μg/mL and damage the mitochondrial membrane and nucleus by generating oxidative stress. NHP causes nuclear condensation and induces apoptosis which was confirmed using AO/EB and PI/DAPI dual staining assay. Moreover, the NHP downregulates the oncogenic genes such as IL-8, TNFα, MMPs and BcL2 and also upregulates the expression of apoptosis marker genes such as Cyto C, p53, p21, caspase 9/3 in A549 and H520 human lung cancer cells. Considering the strong anticancer activity of NHP against lung cancer, NHP may be further evaluated as a potential anticancer drug for the treatment of lung cancer.

Bioprospecting for Novel Bacterial Sources of Hydrolytic Enzymes and Antimicrobials in the Romanian Littoral Zone of the Black Sea

Marine microorganisms have evolved a large variety of metabolites and biochemical processes, providing great opportunities for biotechnologies. In the search for new hydrolytic enzymes and antimicrobial compounds with enhanced characteristics, the current study explored the diversity of cultured and uncultured marine bacteria in Black Sea water from two locations along the Romanian coastline. Microbial cell density in the investigated samples varied between 65 and 12.7 × 10³ CFU·mL^-1. The total bacterial community identified by Illumina sequencing of 16S rRNA gene comprised 185 genera belonging to 46 classes, mainly Gammaproteobacteria, Alphaproteobacteria, Flavobacteriia, and 24 phyla. The 66 bacterial strains isolated on seawater-based culture media belonged to 33 genera and showed variable growth temperatures, growth rates, and salt tolerance. A great fraction of these strains, including Pseudoalteromonas and Flavobacterium species, produced extracellular proteases, lipases, and carbohydrases, while two strains belonging to the genera Aquimarina and Streptomyces exhibited antimicrobial activity against human pathogenic bacteria. This study led to a broader view on the diversity of microbial communities in the Black Sea, and provided new marine strains with hydrolytic and antimicrobial capabilities that may be exploited in industrial and pharmaceutical applications.

ZnO@Polyvinyl Alcohol/Poly(lactic acid) Nanocomposite Films for the Extended Shelf Life of Pork by Efficient Antibacterial Adhesion

The proliferation of microorganisms is an important reason for meat spoilage and deterioration. Freezing and packaging by polymer films and preservatives are commonly used to preserve meat. While the energy consumption of freezing is very big, the polymer films made by petroleum bring up heavy environmental pressure. In the present study, biodegradable antibacterial ZnO@PLA (ZP) and ZnO@PVA/PLA (ZPP) nanocomposite films used as food packaging have been synthesized by the solvent evaporation method and coating method, respectively. Compared with films without ZnO NPs, ZP and ZPP both had long-term bacteriostasis for 24 and 120 h at temperatures of 25 and 4 °C, respectively. Moreover, the antibacterial effect showed positive relevance with the increase of the ZnO NP concentration. In addition, the antibacterial effect of ZPP was better than that of ZP in the same condition. Scanning electron microscopy showed that the numbers of methicillin-resistant staphylococcus aureus (MRSA) on ZP and ZPP were significantly reduced compared to that in the blank film, and ZPP caused the morphology of MRSA to change, which means that the antibacterial mechanism of ZP and ZPP composite films might be related to antibacterial adhesion. In conclusion, ZPP films have great potential to be regarded as the candidate of food packing to extend the shelf life of pork.

Marine Actinomycetes Associated with Stony Corals: A Potential Hotspot for Specialized Metabolites

Microbial secondary metabolites are an important source of antibiotics currently available for combating drug-resistant pathogens. These important secondary metabolites are produced by various microorganisms, including Actinobacteria. Actinobacteria have a colossal genome with a wide array of genes that code for several bioactive metabolites and enzymes. Numerous studies have reported the isolation and screening of millions of strains of actinomycetes from various habitats for specialized metabolites worldwide. Looking at the extent of the importance of actinomycetes in various fields, corals are highlighted as a potential hotspot for untapped secondary metabolites and new bioactive metabolites. Unfortunately, knowledge about the diversity, distribution and biochemistry of marine actinomycetes compared to hard corals is limited. In this review, we aim to summarize the recent knowledge on the isolation, diversity, distribution and discovery of natural compounds from marine actinomycetes associated with hard corals. A total of 11 new species of actinomycetes, representing nine different families of actinomycetes, were recovered from hard corals during the period from 2007 to 2022. In addition, this study examined a total of 13 new compounds produced by five genera of actinomycetes reported from 2017 to 2022 with antibacterial, antifungal and cytotoxic activities. Coral-derived actinomycetes have different mechanisms of action against their competitors.

Bacillus subtilis BR4 derived stigmatellin Y interferes Pqs-PqsR mediated quorum sensing system of Pseudomonas aeruginosa

Cell-to-cell communication is essentially required in bacteria for the production of multiple virulence factors and successful colonization in the host. Targeting the virulence factors production without hampering the growth of the pathogens is a potential strategy to control pathogenesis. To accomplish this, a total of 43 mangrove isolates were screened for quorum quenching (QQ) activity against Pseudomonas aeruginosa (PA), in which eight bacteria have shown antibiofilm activity without hampering the growth of the PA. Prominent QQ activity was observed in Bacillus subtilis BR4. Previously, we found that BR4 produces stigmatellin Y, a structural analogue of PQS signal of PA, which could competitively bind with PqsR receptor and inhibits the quorum sensing (QS) system of PA. Further, stigmatellin Y containing ethyl acetate extract (S-EAE) (100 µg ml^-1 ) of BR4 significantly inhibits (p < 0.001) the biofilm formation of PA. Confocal laser scanning microscope (CLSM) and scanning electron microscope (SEM) analysis also fortified the QQ activity of BR4. Furthermore, S-EAE of BR4 (500 µg ml^-1 ) has significantly reduced the production of virulence factors, including protease, elastase, pyocyanin and extracellular polysaccharides substances. Furthermore, liquid chromatography-mass spectrometry (LC-MS)/MS analysis affirms that BR4 intercepts the PQS-mediated QS system by reducing the synthesis of as many PQS signals, including precursor molecule (243.162313 Da) of PQS signal. Thus, S-EAE of B. subtilis BR4 could be used as a promising therapeutic agent to combat QS system-mediated pathogenesis of PA. Further therapeutic potentials of stigmatellin Y to be evaluated in clinical studies for the treatment of multidrug resistant PA.