Moving away from traditional antibiotic treatment: can macrocyclic lactones from marine macroalga-associated heterotroph be the alternatives?

Importance of quorum sensing crosstalk in the brown alga Saccharina latissima epimicrobiome

Brown macroalgae are colonized by diverse microorganisms influencing the physiology of their host. However, cell-cell interactions within the surface microbiome (epimicrobiome) are largely unexplored, despite the significance of specific chemical mediators in maintaining host-microbiome homeostasis. In this study, by combining liquid chromatography coupled to mass spectrometry (LC-MS) analysis and bioassays, we demonstrated that the widely diverse fungal epimicrobiota of the brown alga Saccharina latissima can affect quorum sensing (QS), a type of cell-cell interaction, as well as bacterial biofilm formation. We also showed the ability of the bacterial epimicrobiota to form and inhibit biofilm growth, as well as to activate or inhibit QS pathways. Overall, we demonstrate that QS and anti-QS compounds produced by the epimicrobiota are key metabolites in these brown algal epimicrobiota communities and highlight the importance of exploring this epimicrobiome for the discovery of new bioactive compounds, including potentially anti-QS molecules with antifouling properties.

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.

Microbial Genomics: Innovative Targets and Mechanisms

Multidrug resistance (MDR) has become an increasing threat to global health because bacteria can develop resistance to antibiotics over time. Scientists worldwide are searching for new approaches that go beyond traditional antibiotic discovery and development pipelines. Advances in genomics, however, opened up an unexplored therapeutic opportunity for the discovery of new antibacterial agents. Genomic approaches have been used to discover several novel antibiotics that target critical processes for bacterial growth and survival, including histidine kinases (HKs), LpxC, FabI, peptide deformylase (PDF), and aminoacyl-tRNA synthetases (AaRS). In this review, we will discuss the use of microbial genomics in the search for innovative and promising drug targets as well as the mechanisms of action for novel antimicrobial agents. We will also discuss future directions on how the utilization of the microbial genomics approach could improve the odds of antibiotic development having a more successful outcome.

Exploring Oceans for Curative Compounds: Potential New Antimicrobial and Anti-Virulence Molecules against Pseudomonas aeruginosa

Although several antibiotics are already widely used against a large number of pathogens, the discovery of new antimicrobial compounds with new mechanisms of action is critical today in order to overcome the spreading of antimicrobial resistance among pathogen bacteria. In this regard, marine organisms represent a potential source of a wide diversity of unique secondary metabolites produced as an adaptation strategy to survive in competitive and hostile environments. Among the multidrug-resistant Gram-negative bacteria, Pseudomonas aeruginosa is undoubtedly one of the most important species due to its high intrinsic resistance to different classes of antibiotics on the market and its ability to cause serious therapeutic problems. In the present review, we first discuss the general mechanisms involved in the antibiotic resistance of P. aeruginosa. Subsequently, we list the marine molecules identified up until now showing activity against P. aeruginosa, dividing them according to whether they act as antimicrobial or anti-virulence compounds.

Seaweed-associated heterotrophic Bacillus altitudinis MTCC13046: a promising marine bacterium for use against human hepatocellular adenocarcinoma

Since the report of the antibiotic with anticancer properties, scientists have been focusing to isolate and characterize novel anti-microbial natural products possessing anticancer activities. The current study describes the production of seaweed-associated heterotrophic Bacillus altitudinis MTCC13046 with potential anticancer properties. The bacterium was screened for its capacity to diminish the cell proliferation of the human hepatocellular adenocarcinoma (HepG2) cell line, without upsetting the normal cells. The bacterial extract showed anticancer properties in a dose-reactive form against HepG2 (IC₅₀, half maximal inhibitory concentration ~ 29.5 µg/ml) on tetrazolium bromide analysis with less significant cytotoxicity on common fibroblast (HDF) cells (IC₅₀ ~ 77 µg/ml). The potential antioxidant ability of the organic extract of B. altitudinis MTCC13046 (IC₉₀ 133 µg/ml) could corroborate its capacity to attenuate the pathophysiology leading to carcinogenesis. The results of the apoptosis assay showed that the crude extracts of B. altitudinis maintained 68% viability in normal cells compared to 11% in the cancer cells (IC₅₀ 76.9 µg/ml). According to the findings, B. altitudinis MTCC13046 could be used to develop prospective anticancer agents.

Pharmacological potential of seaweed-associated heterotrophic bacterium Bacillus atrophaeus

Extremities in marine environmental conditions led the marine macroalga-associated bacteria to adapt and biosynthesize potential bioactive agents. The myriad of marine macroalgae and the bacterial flora they are associated with constitute a potential source of bioactive components with significant biotechnological and pharmacological applications. Heterotrophic bacteria associated with the intertidal macroalgae were isolated and assessed for their pharmacological properties. Subsequently, Firmicutes dominated more than half of the 152 cultivable isolates from macroalgae-associated bacteria collected from the Gulf of Mannar (9°17'0'' N, 79°7'0'' E), on Peninsular India's southern coast. A total of 43 of those demonstrated steady antibacterial activities against a wide range of nosocomial pathogens. Among the bacteria isolated from marine macroalgae, Bacillus atrophaeus SHB2097 (MW821482) exhibited significant antimicrobial activities against clinically important pathogens. Organic extract of B. atrophaeus SHB2097 showed potential antimicrobial activities against test pathogens (minimum inhibitory concentration 6.25 µg/mL). Organic extract of B. atrophaeus SHB2097 revealed promising inhibition potential against cyclooxygenase-2 (IC₉₀ 53.26 µg/mL) and 5-lipoxygenase (IC₉₀ 9.74 µg/mL). The carbolytic enzyme α-glucosidase inhibition potential of the organic extract of the studied heterotrophic bacterium was significantly greater than (IC₉₀ 118 µg/mL) than that displayed by acarbose (IC₉₀ 645 µg/mL, p < 0.05). The significance of nuclear magnetic resonance-centered analyses of distinguishing signals in the organic extract and correlating those with bioactive potential was accentuated. The utilities of nuclear magnetic resonance-based fingerprinting emphasized the assessment of the distinctive signals in the solvent extracts and their correlation with the pharmacological properties. Thus, the heterotrophic B. atrophaeus SHB2097 could be used to develop potential therapeutic and biomedical agents.

Discovery of Marine Natural Products as Promising Antibiotics against Pseudomonas aeruginosa

Pseudomonas aeruginosa, one of the most intractable Gram-negative bacteria, has become a public health threat due to its outer polysaccharide layer, efflux transporter system, and high level of biofilm formation, all of which contribute to multi-drug resistance. Even though it is a pathogen of the highest concern, the status of the antibiotic development pipeline is unsatisfactory. In this review, we summarize marine natural products (MNPs) isolated from marine plants, animals, and microorganisms which possess unique structures and promising antibiotic activities against P. aeruginosa. In the last decade, nearly 80 such MNPs, ranging from polyketides to alkaloids, peptides, and terpenoids, have been discovered. Representative compounds exhibited impressive in vitro anti-P. aeruginosa activities with MIC values in the single-digit nanomolar range and in vivo efficacy in infectious mouse models. For some of the compounds, the preliminary structure-activity-relationship (SAR) and anti-bacterial mechanisms of selected compounds were introduced. Compounds that can disrupt biofilm formation or membrane integrity displayed potent inhibition of multi-resistant clinical P. aeruginosa isolates and could be considered as lead compounds for future development. Challenges on how to translate hits into useful candidates for clinical development are also proposed and discussed.

Marine natural products

Covering: 2020This review covers the literature published in 2020 for marine natural products (MNPs), with 757 citations (747 for the period January to December 2020) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1407 in 420 papers for 2020), together with the relevant biological activities, source organisms and country of origin. Pertinent reviews, biosynthetic studies, first syntheses, and syntheses that led to the revision of structures or stereochemistries, have been included. A meta analysis of bioactivity data relating to new MNPs reported over the last five years is also presented.

Polyketide-derived macrobrevins from marine macroalga-associated Bacillus amyloliquefaciens as promising antibacterial agents against pathogens causing nosocomial infections

Marine heterotrophs are treasured bio-resources of antimicrobial metabolites, and herein we report the biosynthetic potential of Bacillus amyloliquefaciens (ex. Fukumoto) Priest et al. (Bacillaceae) strain MTCC 12713 isolated from an intertidal macroalga Kappaphycus alvarezii (Doty) L.M.Liao (Rhodophyta: Solieriaceae). The bacterium showed promising biological activities against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecalis. Genome mining of B. amyloliquefaciens MTCC 12713 predicted the gene clusters coding for biosynthesis of antibacterial metabolites. Bioactivity-guided purification was directed to isolate four homologous members of trans-acyltransferase polyketide synthase-derived antibiotics, which were classified as macrobrevin analogues. The compounds exhibited antibacterial activities against nosocomial pathogens, for example, methicillin-resistant S. aureus, vancomycin-resistant E. faecalis, Klebsiella pneumoniae and Pseudomonas aeruginosa with a range of MIC values from 1.56 to 6.25 μg/mL, although standard antibiotic chloramphenicol was active at 6.25-12.5 μg/mL. Conspicuously, the macrobrevin compound encompassing hexahydro-41-hydroxy-macrobrevin-31-acetate functionality, displayed considerably greater antagonistic activities against methicillin-resistant S. aureus, vancomycin-resistant E. faecalis, Vibrio parahaemolyticus, P. aeruginosa, K. pneumoniae, and Streptococcus pyogenes (MIC 1.56 μg/mL) compared to the positive controls and other macrobrevin analogues. Trans-AT polyketide synthase-stimulated biosynthetic pathway of macrobrevin compounds, through repetitive decarboxylative Claisen condensation between acetyl-S-KS domain and malonate-S-ACP units could corroborate the structural elucidation. In the genome mining study, among the 34 biosynthetic gene clusters, a hybrid trans-acyltransferase (trans-AT) pks/nrps gene cluster, which extends up to ∼81 Kb, was recognized in the genome of B. amyloliquefaciens MTCC 12713. The pks/nrps cluster revealed 46% similarity to trans-AT PKS-derived macrobrevin isolated from a mesophilic bacterium Brevibacillus sp. Leaf182 associated with the phyllosphere of the wild-type genotype of Arabidopsis thaliana. The binding positions for macrobrevins with S. aureus peptide deformylase showed docking score of larger than 14 kcal/mol, which was considerably greater than macrolactin N and actinonin (<10 kcal/mol). These present findings documented that the marine heterotrophic B. amyloliquefaciens MTCC 12713 could be used to develop prospective antibacterial agents belonging to macrobrevin analogues for biotechnological and pharmaceutical applications.

Bacillibactin class of siderophore antibiotics from a marine symbiotic Bacillus as promising antibacterial agents

Preliminary antibacterial metabolite production screening unveiled that B. amyloliquefaciens MTCC 12,713 associated with the intertidal red alga Kappaphycus alverezii exhibited potential inhibitory effects against drug-resistant pathogens methicillin-resistant Staphylococcus aureus, vancomycin-resistant Enterococcus faecalis, Pseudomonas aeruginosa, and Klebsiella pneumoniae. Four homologous siderophore types of bacillibactins were isolated from a heterotrophic marine bacterium through bioactivity-guided purification. All detectable natural product gene clusters in B. amyloliquefaciens MTCC 12,713 were analyzed by sequencing the complete genome of the bacterium. The studied compounds displayed broad spectrum bactericidal activity against multidrug-resistant strains with a range of minimum inhibitory concentration values from 1.56 to 6.25 µg/mL, whereas standard antibiotic chloramphenicol was active at 6.25 to 12.5 µg/mL. Structure-bioactivity relationship assessment showed that higher electronic values were responsible for antibacterial properties against the nosocomial pathogens. The 2, 3-dihydroxybenzoate (dhb)-assisted biosynthetic pathway of catecholate-enclosed bacillibactins was proposed through the bacillibactin synthase multienzyme complex catalysis followed by dimerization of dhbACEBF operons with 16 genes (~ 12 kb bacterial genome). The present findings recognized an undescribed 4-methoxy-11'-pentanoyloxy-bacillibactin C as a source of potential antibacterial agent for use against drug-resistant pathogens for pharmaceutical applications. KEY POINTS: • Bacillus amyloliquefaciens in association with Kappaphycus alverezii was isolated • Four antibacterial bacillibactin analogs were identified from symbiotic bacterium • 4-Methoxy-11'-pentanoyloxy-bacillibactin C showed potential antibacterial activity.

Marine macroalga-associated heterotrophic Bacillus velezensis: a novel antimicrobial agent with siderophore mode of action against drug-resistant nosocomial pathogens

Increased prevalence of microbial resistance and development of drug-resistant pathogens have triggered an urge among researchers to discover potential antimicrobial compounds, particularly from the marine habitat. The present study highlights the cultivable diversity and bioactivities of heterotrophic bacteria associated with marine macroalgae of southeast Indian coastal region. Culture-dependent isolation method resulted in 40 isolates, in which greater part of the isolates represented Gammaproteobacteria (62%) followed by that comprised of the phylum Firmicutes. One of the most active strains isolated from a macroalga, Laurencia papillosa, was characterized based on the integrated phenotypic and genotypic analysis as Bacillus velezensis MBTDLP1 MTCC 13048, with an inhibition zone of about 35 mm against methicillin-resistant Staphylococcus aureus (MRSA), was selected for bioprospecting studies. Type-I pks gene (MT394492) of 700 bp could be amplified from the heterotrophic B. velezensis. The bacterium exhibited siderophore production and possessed genes implicated in the biosynthesis of siderophore type of metabolites exhibiting 99% similarity with other GenBank sequences in BLAST search. B. velezensis exhibited promising anti-infective properties against methicillin-resistant Staphylococcus aureus (minimum inhibitory concentration 15 µg/mL), and the activities were positively correlated (r² > 0.9) with iron-chelating activities. Chemical investigation of the organic extract of B. velezensis MBTDLP1 characterized a macrocyclic polyketide exhibiting prospective antibacterial potential against methicillin-resistant S. aureus (MIC 0.38 µg/mL), than that exhibited by positive control chloramphenicol (6.25 µg/mL). Significant antibacterial activity against drug-resistant bacteria combined with the presence of genes coding for bioactive secondary metabolites revealed that this marine symbiotic bacterium could be used against emerging antibiotic resistance.

Novel amylomacins from seaweed-associated Bacillus amyloliquefaciens as prospective antimicrobial leads attenuating resistant bacteria

The rise in antibiotic-resistant bacterial strains prompting nosocomial infections drives the search for new bioactive substances of promising antibacterial properties. The surfaces of seaweeds are rich in heterotrophic bacteria with prospective antimicrobial substances. This study aimed to isolate antibacterial leads from a seaweed-associated bacterium. Heterotrophic Bacillus amyloliquefaciens MTCC 12716 associated with the seaweed Hypnea valentiae, was isolated and screened for antimicrobial properties against drug-resistant pathogens. The bacterial crude extract was purified and three novel amicoumacin-class of isocoumarin analogues, 11'-butyl acetate amicoumacin C (amylomacin A), 4'-hydroxy-11'-methoxyethyl carboxylate amicoumacin C (amylomacin B) and 11'-butyl amicoumacin C (amylomacin C) were isolated to homogeneity. The studied amylomacins possessed potential activities against Pseudomonas aeruginosa, vancomycin-resistant Enterococcus faecalis, Klebsiella pneumoniae, methicillin-resistant Staphylococcus aureus, and Shigella flexneri with a range of minimum inhibitory concentration values from 0.78 to 3.12 µg/mL, although standard antibiotics ampicillin and chloramphenicol were active at 6.25-25 µg/mL. Noticeably, the amylomacin compound encompassing 4'-hydroxy-11'-methoxyethyl carboxylate amicoumacin C functionality (amylomacin B), displayed considerably greater antagonistic activities against methicillin-resistant S. aureus, vancomycin-resistant E. faecalis, Vibrio parahaemolyticus, Escherichia coli, and K. pneumoniae (minimum inhibitory concentration 0.78 μg/mL) compared to the positive controls and other amylomacin analogues. Antimicrobial properties of the amylomacins, coupled with the presence of polyketide synthase-I/non-ribosomal peptide synthetase hybrid gene attributed the bacterium as a promising source of antimicrobial compounds with pharmaceutical and biotechnological applications.

A Leap Forward Towards Unraveling Newer Anti-infective Agents from an Unconventional Source: a Draft Genome Sequence Illuminating the Future Promise of Marine Heterotrophic Bacillus sp. Against Drug-Resistant Pathogens

During the previous decade, genome-built researches on marine heterotrophic microorganisms displayed the chemical heterogeneity of natural product resources coupled with the efficacies of harnessing the genetic divergence in various strains. Herein, we describe the whole genome data of heterotrophic Bacillus amyloliquefaciens MB6 (MTCC 12,716), isolated from a marine macroalga Hypnea valentiae, a 4,107,511-bp circular chromosome comprising 186 contigs, with 4154 protein-coding DNA sequences and a coding ratio of 86%. Simultaneously, bioactivity-guided purification of the bacterial extract resulted in six polyketide classes of compounds with promising antibacterial activity. Draft genome sequence of B. amyloliquefaciens MB6 unveiled biosynthetic gene clusters (BGCs) engaged in the biosynthesis of polyketide-originated macrolactones with prospective antagonistic activity (MIC ≤ 5 µg/mL) against nosocomial pathogens. Genome analysis manifested 34 putative BGCs necessitated to synthesize biologically active polyketide-originated frameworks or their derivatives. These results provide insights into the genetic basis of heterotrophic B. amyloliquefaciens MTCC 12,716 as a prospective lead for biotechnological and pharmaceutical applications.

Difficidin class of polyketide antibiotics from marine macroalga-associated Bacillus as promising antibacterial agents

A heterotrophoic Bacillus amyloliquefaciens MTCC12713 isolated from an intertidal macroalga Kappaphycus alverezii displayed promising antibacterial activities against multidrug-resistant bacteria. Genome mining of the bacterium predicted biosynthetic gene clusters coding for antibacterial secondary metabolites. Twenty-one membered macrocyclic lactones, identified as difficidin analogues bearing 6-hydroxy-8-propyl carboxylate, 9-methyl-19-propyl dicarboxylate, 6-methyl-9-propyl dicarboxylate-19-propanone, and (20-acetyl)-6-methyl-9-isopentyl dicarboxylate (compounds 1 through 4) functionalities were purified through bioassay-guided fractionation. The difficidin analogues exhibited bactericidal activities against vancomycin-resistant Enterococcus faecalis, methicillin-resistant Staphylococcus aureus, and other drug-resistant strains, such of Klebsiella pneumonia and Pseudomonas aeruginosa with the minimum inhibitory concentration of about 2-9 × 10^-3 μM. A plausible enzyme-catalyzed biosynthetic pathway that is generated through addition of acrylyl initiator unit by repetitive decarboxylative Claisen condensation modules with malonate units was recognized, and their structures were corroborated with gene organization of the dif operon, which could comprehend dif A-O (~ 70 kb). Drug-likeness score for 5-ethoxy-28-methyl-(9-methyl-19-propyl dicarboxylate) difficidin (compound 2, 0.35) was greater than those of other difficidin analogues, which corroborated the potential in vitro antibacterial properties of the former. The present study demonstrated the potential of difficidin analogues for pharmaceutical and biotechnological uses against the bottleneck of emergent drug-resistant pathogens. KEY POINTS: • Difficidins were isolated from marine alga associated Bacillus amyloliquefaciens. • Whole-genome mining of bacterial genome predicted biosynthetic gene clusters. • Greater drug-likeness for difficidin 2 confirmed its potent antibacterial activity.