The Structural Diversity of Marine Microbial Secondary Metabolites Based on Co-Culture Strategy: 2009-2019

Hexadecanoic acid produced in the co-culture of S. cerevisiae and E.coli promotes oxidative stress tolerance of the S.cerevisiae cells

Co-fermentation performed by Saccharomyces cerevisiae and Escherichia coli or other microbes has been widely used in industrial fermentation. Meanwhile, the co-cultured microbes might regulate each other's metabolisms or cell behaviors including oxidative stress tolerance through secreting molecules. Here, results based on the co-culture system of S. cerevisiae and E. coli suggested the promoting effect of E. coli on the oxidative stress tolerance of S. cerevisiae cells. The co-cultured E. coli could enhance S. cerevisiae cell viability through improving its membrane stability and reducing the oxidized lipid level. Meanwhile, promoting effect of the co-cultured supernatant on the oxidative stress tolerance of S. cerevisiae illustrated by the supernatant substitution strategy suggested that secreted compounds contained in the co-cultured supernatant contributed to the higher oxidative stress tolerance of S. cerevisiae. The potential key regulatory metabolite (i.e., hexadecanoic acid) with high content difference between co-cultured supernatant and the pure-cultured S. cerevisiae supernatant was discovered by GC-MS-based metabolomics strategy. And exogenous addition of hexadecanoic acid did suggest its contribution to higher oxidative stress tolerance of S. cerevisiae. Results presented here would contribute to the understanding of the microbial interactions and provide the foundation for improving the efficiency of co-fermentation performed by S. cerevisiae and E. coli.

Chae-type cytochalasans from coculture of Aspergillus flavipes and Chaetomium globosum

Cocultivation of the high cytochalasan-producing fungi Aspergillus flavipes and Chaetomium globosum resulted in the isolation of 11 undescribed Chae-type cytochalasans. Their structures were determined by spectroscopic data and NMR data calculations. Asperchaetoglobin A (1) was the first Chae-type cytochalasan possessing an unprecedented nitrogen bridge between C-17 and C-20 to generate a surprising 5/6/12/5 multiple ring system; asperchaetoglobins B and C (2 and 3) displayed higher oxidation with an additional epoxide at the thirteen-member ring; asperchaetoglobin D (4) was the second Chae-type cytochalasin featuring a 5/6/12 tricyclic ring system. The cytotoxic activities against five human cancer cell lines and antibacterial activities against Staphylococcus aureus and Colon bacillus of selected compounds were evaluated in vitro.

Bioactive Polyketides from the Natural Complex of the Sea Urchin-Associated Fungi Penicillium sajarovii KMM 4718 and Aspergillus protuberus KMM 4747

The marine-derived fungal strains KMM 4718 and KMM 4747 isolated from sea urchin Scaphechinus mirabilis as a natural fungal complex were identified as Penicillium sajarovii and Aspergillus protuberus based on Internal Transcribed Spacer (ITS), partial β-tubulin (BenA), and calmodulin (CaM) molecular markers as well as an ribosomal polymerase two, subunit two (RPB2) region for KMM 4747. From the ethyl acetate extract of the co-culture, two new polyketides, sajaroketides A (1) and B (2), together with (2'S)-7-hydroxy-2-(2'-hydroxypropyl)-5-methylchromone (3), altechromone A (4), norlichexanthone (5), griseoxanthone C (6), 1,3,5,6-tetrahydroxy-8-methylxanthone (7), griseofulvin (8), 6-O-desmethylgriseofulvin (9), dechlorogriseofulvin (10), and 5,6-dihydro-4-methyl-2H-pyran-2-one (11) were identified. The structures of the compounds were elucidated using spectroscopic analyses. The absolute configurations of the chiral centers of sajaroketides A and B were determined using time-dependent density functional theory (TDDFT)-based calculations of the Electronic Circular Dichroism (ECD) spectra. The inhibitory effects of these compounds on urease activity and the growth of Staphylococcus aureus, Escherichia coli, and Candida albicans were observed. Sajaroketide A, altechromone A, and griseofulvin showed significant cardioprotective effects in an in vitro model of S. aureus-induced infectious myocarditis.

Exploring Diverse Bioactive Secondary Metabolites from Marine Microorganisms Using Co-Culture Strategy

The isolation and identification of an increasing number of secondary metabolites featuring unique skeletons and possessing diverse bioactivities sourced from marine microorganisms have garnered the interest of numerous natural product chemists. There has been a growing emphasis on how to cultivate microorganisms to enhance the chemical diversity of metabolites and avoid the rediscovery of known ones. Given the significance of secondary metabolites as a means of communication among microorganisms, microbial co-culture has been introduced. By mimicking the growth patterns of microbial communities in their natural habitats, the co-culture strategy is anticipated to stimulate biosynthetic gene clusters that remain dormant under traditional laboratory culture conditions, thereby inducing the production of novel secondary metabolites. Different from previous reviews mainly focusing on fermentation conditions or metabolite diversities from marine-derived co-paired strains, this review covers the marine-derived co-culture microorganisms from 2012 to 2022, and turns to a particular discussion highlighting the selection of co-paired strains for marine-derived microorganisms, especially the fermentation methods for their co-cultural apparatus, and the screening approaches for the convenient and rapid detection of novel metabolites, as these are important in the co-culture. Finally, the structural and bioactivity diversities of molecules are also discussed. The challenges and prospects of co-culture are discussed on behave of the views of the authors.

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.

Secondary Metabolites of Endophytes Associated with the Zingiberaceae Family and Their Pharmacological Activities

Zingiberaceae is commonly known as the ginger family and has been extensively studied in the last decades for its pharmacological purposes. The study of ginger includes microorganisms known as endophytes, which raise interest for the research community because they can produce a wide range of secondary metabolites. This review discusses the secondary metabolites of endophytes from the Zingiberaceae family and their pharmacological activities. We detail the group of secondary metabolites, updated for its absolute structures, source and part origins, and, especially, pharmacological divided properties. Zingiberaceae endophytes have 106 volatile compounds and 52 isolated constituents, including 17 polyketides, five nonribosomal peptides, five aromatic compounds, three alkaloids, and 21 terpene-alkaloids. They have antimicrobial, anticancer, antioxidant, and anti-inflammatory activities. Secondary metabolites from plant endophytes of the Zingiberaceae family have the potential to be therapeutic drugs in the future. Research on endophytic bacteria or fungi has been little performed. Therefore, this study supports a new drug discovery from Zingiberaceae endophytes and compares them for future drug development.

Cytotoxic Drimane-Type Sesquiterpenes from Co-Culture of the Marine-Derived Fungi Aspergillus carneus KMM 4638 and Beauveria felina (=Isaria felina) KMM 4639

Chemical investigation of a coculture of the marine-derived fungi Beauveria felina KMM 4639 and Aspergillus carneus KMM 4638 led to the identification of three new drimane-type sesquiterpenes, asperflavinoids B, D and E (2, 4, 5), and nine previously reported related compounds. The structures of these compounds were established using spectroscopic methods and by comparison with known analogues. We also investigated the cytotoxic activity of the isolated compounds against several cancer and normal cell lines. Asperflavinoid C (3) and ustusolate E (9) exerted a significant effect on human breast cancer MCF-7 cell viability, with IC₅₀ values of 10 µM, and induced in caspase-dependent apoptosis and arrest of the MCF-7 cell cycle in the G2/M phase in these cells.

Harnessing Rare Actinomycete Interactions and Intrinsic Antimicrobial Resistance Enables Discovery of an Unusual Metabolic Inhibitor

Bacterial natural products have historically been a deep source of new medicines, but their slowed discovery in recent decades has put a premium on developing strategies that enhance the likelihood of capturing novel compounds. Here, we used a straightforward approach that capitalizes on the interactive ecology of “rare” actinomycetes. Specifically, we screened for interactions that triggered the production of antimicrobials that inhibited the growth of a bacterial strain with exceptionally diverse natural antimicrobial resistance. This strategy led to the discovery of a family of antimicrobials we term the dynaplanins. Heterologous expression enabled identification of the dynaplanin biosynthetic gene cluster, which was missed by typical algorithms for natural product gene cluster detection. Genome sequencing of partially resistant mutants revealed a 2-oxo acid dehydrogenase E2 subunit as the likely molecular target of the dynaplanins, and this finding was supported by computational modeling of the dynaplanin scaffold within the active site of this enzyme. Thus, this simple strategy, which leverages microbial interactions and natural antibiotic resistance, can enable discovery of molecules with unique antimicrobial activity. In addition, these results indicate that primary metabolism may be a direct target for inhibition via chemical interference in competitive microbial interactions.

In Silico Virtual Screening of Marine Aldehyde Derivatives from Seaweeds against SARS-CoV-2

Coronavirus disease 2019, caused by the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is an ongoing global pandemic that poses an unprecedented threat to the global economy and human health. Several potent inhibitors targeting SARS-CoV-2 have been published; however, most of them have failed in clinical trials. This study aimed to assess the therapeutic compounds among aldehyde derivatives from seaweeds as potential SARS-CoV-2 inhibitors using a computer simulation protocol. The absorption, distribution, metabolism, excretion, and toxicity (ADME/Tox) properties of the compounds were analyzed using a machine learning algorithm, and the docking simulation of these compounds to the 3C-like protease (Protein Data Bank (PDB) ID: 6LU7) was analyzed using a molecular docking protocol based on the CHARMm algorithm. These compounds exhibited good drug-like properties following the Lipinski and Veber rules. Among the marine aldehyde derivatives, 4-hydroxybenzaldehyde, 3-hydroxybenzaldehyde, 3,4-dihydroxybenzaldehyde, and 5-bromoprotocatechualdehyde were predicted to have good absorption and solubility levels and non-hepatotoxicity in the ADME/Tox prediction. 3-hydroxybenzaldehyde and 3,4-dihydroxybenzaldehyde were predicted to be non-toxic in TOPKAT prediction. In addition, 3,4-dihydroxybenzaldehyde was predicted to exhibit interactions with the 3C-like protease, with binding energies of −71.9725 kcal/mol. The computational analyses indicated that 3,4-dihydroxybenzaldehyde could be regarded as potential a SARS-CoV-2 inhibitor.

Antibacterial diphenyl ether production induced by co-culture of Aspergillus nidulans and Aspergillus fumigatus

Fungi are a rich source of secondary metabolites with potent biological activities. Co-culturing a fungus with another microorganism has drawn much attention as a practical method for stimulating fungal secondary metabolism. However, in most cases, the molecular mechanisms underlying the activation of secondary metabolite production in co-culture are poorly understood. To elucidate such a mechanism, in this study, we established a model fungal-fungal co-culture system, composed of Aspergillus nidulans and Aspergillus fumigatus. In the co-culture of A. nidulans and A. fumigatus, production of antibacterial diphenyl ethers was enhanced. Transcriptome analysis by RNA-sequencing showed that the co-culture activated expression of siderophore biosynthesis genes in A. fumigatus and two polyketide biosynthetic gene clusters (the ors and cic clusters) in A. nidulans. Gene disruption experiments revealed that the ors cluster is responsible for diphenyl ether production in the co-culture. Interestingly, the ors cluster was previously reported to be upregulated by co-culture of A. nidulans with the bacterium Streptomyces rapamycinicus; orsellinic acid was the main product of the cluster in that co-culture. In other words, the main product of the ors cluster was different in fungal-fungal and bacterial-fungal co-culture. The genes responsible for biosynthesis of the bacterial- and fungal-induced polyketides were deduced using a heterologous expression system in Aspergillus oryzae. The molecular genetic mechanisms that trigger biosynthesis of two different types of compounds in A. nidulans in response to the fungus and the bacterium were demonstrated, which provides an insight into complex secondary metabolic response of fungi to microorganisms. KEY POINTS: • Co-culture of two fungal species triggered antibiotic diphenyl ether production. • The co-culture affected expression levels of several genes for secondary metabolism. • Gene cluster essential for induction of the antibiotics production was determined.

Potential Inhibitors of CYP51 Enzyme in Dermatophytes by Red Sea Soft Coral Nephthea sp.: In Silico and Molecular Networking Studies

In this study, the n-hexane fraction of soft coral Nephthea sp. gathered from the Red Sea was evaluated for its antidermatophyte activity. The antidermatophyte activity was performed versus different fungi, including Microsporum canis, Trichophyton gypseum, and Microsporum mentagrophytes, using a broth microdilution method. The n-hexane fraction showed minimum inhibitory concentrations (MICs) against the tested dermatophytes of 104.2 ± 20.8, 125 ± 0.0, and 83.33 ± 20.83 μg/mL respectively. The chemical constitution of the lipoidal matter (n-hexane fraction) was characterized by gas chromatography coupled with a mass spectrometer (GC-MS). The unsaponifiable fraction (USAP) of Nephthea sp. showed relative percentages of hydrocarbons and vitamins of 69.61% and 3.26%, respectively. Moreover, the percentages of saturated and unsaturated fatty acids were 53.67% and 42.05%, respectively. In addition, a molecular networking study (MN) of the GC-MS analysis performed using the Global Natural Products Social Molecular Networking (GNPS) platform was described. The molecular docking study illustrated that the highest binding energy score for spathulenol toward the CYP51 enzyme was -8.3674 kcal/mol, which predicted the mode of action of the antifungal activity, and then the results were confirmed by the inhibitory effect of Nephthea sp. against CYP51 with an IC₅₀ value of 12.23 μg/mL. Our results highlighted the antifungal potential of Nephthea sp. metabolites.

Amycolachromones A–F, Isolated from a Streptomycin-Resistant Strain of the Deep-Sea Marine Actinomycete Amycolatopsis sp. WP1

In this study, a detailed chemical investigation of a streptomycin-resistant strain of the deep-sea marine, actinomycete Amycolatopsis sp. WP1, yielded six novel amycolachromones A–F (1–6), together with five known analogues (7–11). Amycolachromones A–B (1–2) possessed unique dimer skeletons. The structures and relative configurations of compounds 1–11 were elucidated by extensive spectroscopic data analyses combined with X-ray crystal diffraction analysis. Plausible biogenetic pathways of amycolachromones A–F were also proposed.

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.

Ligiamycins A and B, Decalin-Amino-Maleimides from the Co-Culture of Streptomyces sp. and Achromobacter sp. Isolated from the Marine Wharf Roach, Ligia exotica

Streptomyces sp. GET02.ST and Achromobacter sp. GET02.AC were isolated together from the gut of the wharf roach, Ligia exotica, inhabiting the intertidal zone of the west coast of Korea. The co-cultivation of these two strains significantly induced the production of two new metabolites, ligiamycins A (1) and B (2), which were barely detected in the single culture of Streptomyces sp. GET02.ST. The planar structures of ligiamycins A (1) and B (2) were elucidated as new decalins coupled with amino-maleimides by the analysis of various spectroscopic data, including nuclear magnetic resonance (NMR), ultraviolet (UV), and mass (MS) data. The assignment of two nitrogen atoms in amino-maleimide in 1 was accomplished based on 1H-15N heteroatom single quantum coherence spectroscopy (HSQC) NMR experiments. The relative configurations of the ligiamycins were determined using rotating frame Overhauser effect spectroscopy (ROESY) NMR data, and their absolute configurations were deduced by comparing their experimental and calculated optical rotations. Ligiamycin A (1) displayed antibacterial effects against Staphylococcus aureus and Salmonella enterica, while ligiamycin B (2) exhibited mild cell cytotoxicity against human colorectal cancer cells.

Acremopeptaibols A-F, 16-Residue Peptaibols from the Sponge-Derived Acremonium sp. IMB18-086 Cultivated with Heat-Killed Pseudomonas aeruginosa

Six new 16-residue peptaibols, acremopeptaibols A-F (1-6), along with five known compounds, were isolated from the cultures of the sponge-associated fungus Acremonium sp. IMB18-086 grown in the presence of the autoclaved bacterium Pseudomonas aeruginosa on solid rice medium. The peptaibol sequences were established based on comprehensive analysis of 1D and 2D NMR spectroscopic data in conjunction with HRESIMS/MS experiments. The configurations of the amino acid residues were determined by advanced Marfey's analysis. Compounds 1-6 feature the lack of the highly conserved Thr⁶ and Hyp¹⁰ residues in comparison with other members of the SF3 subfamily peptaibols. A plausible biosynthetic pathway of compounds 1-6 was proposed on the basis of genomic analysis. Compounds 1, 5, 7, and 10 exhibited significant antimicrobial activity against Staphylococcus aureus, methicillin-resistant S. aureus, Bacillus subtilis, and Candida albicans. Compounds 7-10 showed potent cytotoxicities against the A549 and/or HepG2 cancer cell lines.

A bioprocess perspective on the production of secondary metabolites by Streptomyces in submerged co-cultures

Filamentous microorganisms are potent sources of bioactive secondary metabolites, the molecules formed in response to complex environmental signals. The chemical diversity encoded in microbial genomes is only partially revealed by following the standard microbiological approaches. Mimicking the natural stimuli through laboratory co-cultivation is one of the most effective methods of awakening the formation of high-value metabolic products. Whereas the biosynthetic outcomes of co-cultures are reviewed extensively, the bioprocess aspects of such efforts are often overlooked. The aim of the present review is to discuss the submerged co-cultivation strategies used for triggering and enhancing secondary metabolites production in Streptomyces, a heavily investigated bacterial genus exhibiting an impressive repertoire of secondary metabolites, including a vast array of antibiotics. The previously published studies on influencing the biosynthetic capabilities of Streptomyces through co-cultivation are comparatively analyzed in the bioprocess perspective, mainly with the focus on the approaches of co-culture initiation, the experimental setup, the design of experimental controls and the ways of influencing the outcomes of co-cultivation processes. These topics are discussed in the general context of secondary metabolites production in submerged microbial co-cultures by referring to the Streptomyces-related studies as illustrative examples.