A Multi-Omics Characterization of the Natural Product Potential of Tropical Filamentous Marine Cyanobacteria

Microbial natural products are important for the understanding of microbial interactions, chemical defense and communication, and have also served as an inspirational source for numerous pharmaceutical drugs. Tropical marine cyanobacteria have been highlighted as a great source of new natural products, however, few reports have appeared wherein a multi-omics approach has been used to study their natural products potential (i.e., reports are often focused on an individual natural product and its biosynthesis). This study focuses on describing the natural product genetic potential as well as the expressed natural product molecules in benthic tropical cyanobacteria. We collected from several sites around the world and sequenced the genomes of 24 tropical filamentous marine cyanobacteria. The informatics program antiSMASH was used to annotate the major classes of gene clusters. BiG-SCAPE phylum-wide analysis revealed the most promising strains for natural product discovery among these cyanobacteria. LCMS/MS-based metabolomics highlighted the most abundant molecules and molecular classes among 10 of these marine cyanobacterial samples. We observed that despite many genes encoding for peptidic natural products, peptides were not as abundant as lipids and lipopeptides in the chemical extracts. Our results highlight a number of highly interesting biosynthetic gene clusters for genome mining among these cyanobacterial samples.     

茶树种质资源汝城白毛茶的代谢物差异研究

汝城白毛茶是湖南四大茶树地方群体资源之一,也是白毛茶变种（Camellia sinensis var. pubilimba Chang）的典型代表,已有研究表明汝城白毛茶在演化地位上与湖南其他3个地方群体资源差异较大,且在植物学特征、生化成分、制茶品质等方面特色鲜明。但目前对汝城白毛茶种质资源次生代谢物的差异研究较少。本研究采用UPLC-MS/MS分析技术,以汝城白毛茶为研究对象,湖南典型地方茶树资源安化群体（AHQT, C. sinensis var. sinensis）、城步峒茶[CBDC, C. sinensis var. assamica (Masters) Kitamura]、江华苦茶[JHKC, C. sinensis var. assamica (Masters) Kitamura]为对照,筛选汝城白毛茶中的显著差异代谢物,并进行K均值聚类（K-means）分析和差异代谢物富集通路分析。结果表明,与AHQT、CBDC、JHKC相比,分别在汝城白毛茶中筛选到显著差异代谢物189、180、162个,种类最多的为黄酮类（69、51、60个）,其次为酚酸类（31、40、25个）,...     

The Diversity,Metabolomics Profiling,and the Pharmacological Potential of Actinomycetes Isolated from the Estremadura Spur Pockmarks (Portugal)

The Estremadura Spur pockmarks are a unique and unexplored ecosystem located in the North Atlantic, off the coast of Portugal. A total of 85 marine-derived actinomycetes were isolated and cultured from sediments collected from this ecosystem at a depth of 200 to 350 m. Nine genera, Streptomyces, Micromonospora, Saccharopolyspora, Actinomadura, Actinopolymorpha, Nocardiopsis, Saccharomonospora, Stackebrandtia, and Verrucosispora were identified by 16S rRNA gene sequencing analyses, from which the first two were the most predominant. Non-targeted LC-MS/MS, in combination with molecular networking, revealed high metabolite diversity, including several known metabolites, such as surugamide, antimycin, etamycin, physostigmine, desferrioxamine, ikarugamycin, piericidine, and rakicidin derivatives, as well as numerous unidentified metabolites. Taxonomy was the strongest parameter influencing the metabolite production, highlighting the different biosynthetic potentials of phylogenetically related actinomycetes; the majority of the chemical classes can be used as chemotaxonomic markers, as the metabolite distribution was mostly genera-specific. The EtOAc extracts of the actinomycete isolates demonstrated antimicrobial and antioxidant activity. Altogether, this study demonstrates that the Estremadura Spur is a source of actinomycetes with potential applications for biotechnology. It highlights the importance of investigating actinomycetes from unique ecosystems, such as pockmarks, as the metabolite production reflects their adaptation to this habitat.     

Phylogenetic Diversity and Biological Activity of Actinobacteria Isolated from the Chukchi Shelf Marine Sediments in the Arctic Ocean

Marine environments are a rich source of Actinobacteria and have the potential to produce a wide variety of biologically active secondary metabolites. In this study, we used four selective isolation media to culture Actinobacteria from the sediments collected from the Chukchi Shelf in the Arctic Ocean. A total of 73 actinobacterial strains were isolated. Based on repetitive DNA fingerprinting analysis, we selected 30 representatives for partial characterization according to their phylogenetic diversity, antimicrobial activities and secondary-metabolite biosynthesis genes. Results from the 16S rRNA gene sequence analysis indicated that the 30 strains could be sorted into 18 phylotypes belonging to 14 different genera: Agrococcus, Arsenicicoccus, Arthrobacter, Brevibacterium, Citricoccus, Janibacter, Kocuria, Microbacterium, Microlunatus, Nocardioides, Nocardiopsis, Saccharopolyspora, Salinibacterium and Streptomyces. To our knowledge, this paper is the first report on the isolation of Microlunatus genus members from marine habitats. Of the 30 isolates, 11 strains exhibited antibacterial and/or antifungal activity, seven of which have activities against Bacillus subtilis and Candida albicans. All 30 strains have at least two biosynthetic genes, one-third of which possess more than four biosynthetic genes. This study demonstrates the significant diversity of Actinobacteria in the Chukchi Shelf sediment and their potential for producing biologically active compounds and novel material for genetic manipulation or combinatorial biosynthesis.     

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.     

Symbiodinium-invertebrate symbioses and the role of metabolomics

Symbioses play an important role within the marine environment. Among the most well known of these symbioses is that between coral and the photosynthetic dinoflagellate, Symbiodinium spp. Understanding the metabolic relationships between the host and the symbiont is of the utmost importance in order to gain insight into how this symbiosis may be disrupted due to environmental stressors. Here we summarize the metabolites related to nutritional roles, diel cycles and the common metabolites associated with the invertebrate-Symbiodinium relationship. We also review the more obscure metabolites and toxins that have been identified through natural products and biomarker research. Finally, we discuss the key role that metabolomics and functional genomics will play in understanding these important symbioses.     

Investigation of Interspecies Interactions within Marine Micromonosporaceae Using an Improved Co-Culture Approach

With respect to bacterial natural products, a significant outcome of the genomic era was that the biosynthetic potential in many microorganisms surpassed the number of compounds isolated under standard laboratory growth conditions, particularly among certain members in the phylum Actinobacteria. Our group, as well as others, investigated interspecies interactions, via co-culture, as a technique to coax bacteria to produce novel natural products. While co-culture provides new opportunities, challenges exist and questions surrounding these methods remain unanswered. In marine bacteria, for example, how prevalent are interspecies interactions and how commonly do interactions result in novel natural products? In an attempt to begin to answer basic questions surrounding co-culture of marine microorganisms, we have tested both antibiotic activity-based and LC/MS-based methods to evaluate Micromonosporaceae secondary metabolite production in co-culture. Overall, our investigation of 65 Micromonosporaceae led to the identification of 12 Micromonosporaceae across three genera that produced unique metabolites in co-culture. Our results suggest that interspecies interactions were prevalent between marine Micromonosporaceae and marine mycolic acid-containing bacteria. Furthermore, our approach highlights a sensitive and rapid method for investigating interspecies interactions in search of novel antibiotics, secondary metabolites, and genes.     

克隆文库分析红树林土壤中放线菌的多样性

直接提取8个红树林土壤的总DNA,用放线菌门的特异性PCR引物进行扩增,通过构建16S rRNA文库,测序及系统发育分析,获取新颖放线菌菌株.结果发现,有酸微菌亚纲(Acidimicrobidae) (30.2％)、放线菌亚纲(Actinobacteridae) (68.0％)、红蝽菌亚纲(Coriobacteridae)(1.1％)和去腈基菌亚纲(Nitriliruptoridae)( 0.7％)成员,没有红色杆菌亚纲( Rubrobacteridae)成员.仙农指数和Chao1物种多样性指数(Schao1)表明,红树林土壤样品中含有丰富的放线菌多样性.以16S rDNA基因的相似率≥97％作为临界点,45.1％可能代表新候选种(candidate species)(未培养、分离).本研究为进一步获取新颖的红树林放线菌资源提供了基础.     

Novel Alkaloids from Marine Actinobacteria: Discovery and Characterization

The marine environment is an excellent resource for natural products with therapeutic potential. Its microbial inhabitants, often associated with other marine organisms, are specialized in the synthesis of bioactive secondary metabolites. Similar to their terrestrial counterparts, marine Actinobacteria are a prevalent source of these natural products. Here, we discuss 77 newly discovered alkaloids produced by such marine Actinobacteria between 2017 and mid-2021, as well as the strategies employed in their elucidation. While 12 different classes of alkaloids were unraveled, indoles, diketopiperazines, glutarimides, indolizidines, and pyrroles were most dominant. Discoveries were mainly based on experimental approaches where microbial extracts were analyzed in relation to novel compounds. Although such experimental procedures have proven useful in the past, the methodologies need adaptations to limit the chance of compound rediscovery. On the other hand, genome mining provides a different angle for natural product discovery. While the technology is still relatively young compared to experimental screening, significant improvement has been made in recent years. Together with synthetic biology tools, both genome mining and extract screening provide excellent opportunities for continued drug discovery from marine Actinobacteria.     

Production of Induced Secondary Metabolites by a Co-Culture of Sponge-Associated Actinomycetes,Actinokineospora sp. EG49 and Nocardiopsis sp. RV163

Two sponge-derived actinomycetes, Actinokineospora sp. EG49 and Nocardiopsis sp. RV163, were grown in co-culture and the presence of induced metabolites monitored by ¹H NMR. Ten known compounds, including angucycline, diketopiperazine and β-carboline derivatives 1–10, were isolated from the EtOAc extracts of Actinokineospora sp. EG49 and Nocardiopsis sp. RV163. Co-cultivation of Actinokineospora sp. EG49 and Nocardiopsis sp. RV163 induced the biosynthesis of three natural products that were not detected in the single culture of either microorganism, namely N-(2-hydroxyphenyl)-acetamide (11), 1,6-dihydroxyphenazine (12) and 5a,6,11a,12-tetrahydro-5a,11a-dimethyl[1,4]benzoxazino[3,2-b][1,4]benzoxazine (13a). When tested for biological activity against a range of bacteria and parasites, only the phenazine 12 was active against Bacillus sp. P25, Trypanosoma brucei and interestingly, against Actinokineospora sp. EG49. These findings highlight the co-cultivation approach as an effective strategy to access the bioactive secondary metabolites hidden in the genomes of marine actinomycetes.     

普洱茶茶褐素对大鼠尿液影响的代谢组学研究

本研究采用核磁共振(NMR)代谢组学法研究普洱茶茶褐素(TB,分子量50 k Da)对大鼠尿液代谢的影响。将实验大鼠分为正常对照组、正常+TB组、高脂组和高脂+TB组,以生物核磁共振技术结合正交偏最小二乘-判别分析(OPLS-DA)研究灌胃高剂量普洱茶茶褐素后大鼠尿液内源性代谢物的变化。结果表明,正常+TB组与正常对照组,高脂+TB组与高脂组的尿液代谢谱有明显差异;筛选出缬氨酸、柠檬酸、牛磺酸、丙酸盐、α-酮戊二酸、β-羟基丁酸等6种普洱茶茶褐素标志性代谢物;普洱茶茶褐素对大鼠尿液的影响可能涉及到氨基酸代谢、能量代谢、三羧酸循环、脂类代谢和氧化应激反应。     

2株高产蛋白微藻细胞代谢物的比较

以2株新近分离出来的链带藻(Desmodesmus sp. QL96和Desmodesmus sp. QJ74)为研究对象,检测胞内主要细胞代谢产物组成及含量变化,找出优势细胞代谢产物。收集相同时间间隔下培养的2株微藻,经过冻干、研磨、复溶,制备成细胞溶解液,再进行逐级萃取,分级检测每个萃取步骤中所得细胞代谢产物的含量。结果表明:在BG11培养基中生长30 d,链带藻Desmodesmus sp. QL96和Desmodesmus sp. QJ74的最高蛋白含量分别达到细胞干重的71.68%和62.14%,其他代谢产物,如碳水化合物、脂质和色素,在2株微藻中的含量都没有超过20%。对比其他微藻的文献报道,链带藻Desmodesmus sp. QL96是目前发现的蛋白含量最高的藻株,其蛋白的表达模式和蛋白相关产品的开发具有研究价值。     

Comparative metabolic profiling of pigmented rice (Oryza sativa L.) cultivars reveals primary metabolites are correlated with secondary metabolites

Gas-chromatography coupled with time-of-flight mass spectrometry (GC-TOFMS) was used to analyze the relationships between primary metabolites and phenolic acids in rice (Oryza sativa L.), including six black cultivars and one white cultivar. A total of 52 metabolites were identified, including 45 primary metabolites and seven phenolic acids from rice seeds. The metabolite profiles were subjected to data mining processes, including principal component analysis (PCA), Pearson's correlation analysis, and hierarchical clustering analysis (HCA). PCA could fully distinguish between these cultivars. HCA of these metabolites resulted in clusters derived from common or closely related biochemical pathways. There was a positive relationship between all phenolic and shikimic acids. Projection to latent structure using partial least squares (PLS) was applied to predict the total phenolic content based on primary metabolite profiles from rice grain. The predictive model showed good fit and predictability. The GC-TOFMS-based metabolic profiling approach could be used as an alternative method to predict food quality and identify metabolic links in complex biological systems.     

海洋青霉HN89菌株次生代谢产物抗菌活性的研究

海洋青霉HN89菌株次生代谢产物的抗菌活性与发酵条件对抗生素产量影响的研究结果表明:海洋青霉HN89菌株的次生代谢产物对细菌、酵母、霉菌均有抑制作用;摇瓶发酵产生抗生素(HN89A)的最佳培养基成分为:玉米淀粉20g/L,黄豆粉2g/L,K2HPO41g/L,NaCl0.5g/L,MgSO4 0.5g/L,FeSO4·7H2O0.01g/L,蛋白胨1g/L,用海水配制的海带汁(W/V,2%)1L,最佳发酵条件为28℃下振荡培养(200r/min)96~108h。合适的温度刺激能促进HN89A的合成。      

Targeted Large-Scale Genome Mining and Candidate Prioritization for Natural Product Discovery

Large-scale genome-mining analyses have identified an enormous number of cryptic biosynthetic gene clusters (BGCs) as a great source of novel bioactive natural products. Given the sheer number of natural product (NP) candidates, effective strategies and computational methods are keys to choosing appropriate BGCs for further NP characterization and production. This review discusses genomics-based approaches for prioritizing candidate BGCs extracted from large-scale genomic data, by highlighting studies that have successfully produced compounds with high chemical novelty, novel biosynthesis pathway, and potent bioactivities. We group these studies based on their BGC-prioritization logics: detecting presence of resistance genes, use of phylogenomics analysis as a guide, and targeting for specific chemical structures. We also briefly comment on the different bioinformatics tools used in the field and examine practical considerations when employing a large-scale genome mining study.     

Advances in the Study of the Structures and Bioactivities of Metabolites Isolated from Mangrove-Derived Fungi in the South China Sea

Many metabolites with novel structures and biological activities have been isolated from the mangrove fungi in the South China Sea, such as anthracenediones, xyloketals, sesquiterpenoids, chromones, lactones, coumarins and isocoumarin derivatives, xanthones, and peroxides. Some compounds have anticancer, antibacterial, antifungal and antiviral properties, but the biosynthesis of these compounds is still limited. This review summarizes the advances in the study of secondary metabolites from the mangrove-derived fungi in the South China Sea, and their biological activities reported between 2008 and mid-2013.     

Structures and Biological Activities of Secondary Metabolites from Trichoderma harzianum

The biocontrol fungus Trichoderma harzianum, from both marine and terrestrial environments, has attracted considerable attention. T. harzianum has a tremendous potential to produce a variety of bioactive secondary metabolites (SMs), which are an important source of new herbicides and antibiotics. This review prioritizes the SMs of T. harzianum from 1988 to June 2022, and their relevant biological activities. Marine-derived SMs, especially terpenoids, polyketides, and macrolides compounds, occupy a significant proportion of natural products from T. harzianum, deserving more of our attention.     

Insights into the Variation in Bioactivities of Closely Related Streptomyces Strains from Marine Sediments of the Visayan Sea against ESKAPE and Ovarian Cancer

Marine sediments host diverse actinomycetes that serve as a source of new natural products to combat infectious diseases and cancer. Here, we report the biodiversity, bioactivities against ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) and ovarian cancer, and metabolites variation among culturable actinomycetes isolated from the marine sediments of Visayan Sea, Philippines. We identified 15 Streptomyces species based on a 16S rRNA gene sequence analysis. The crude extracts of 10 Streptomyces species have inhibited the growth of ESKAPE pathogens with minimum inhibitory concentration (MIC) values ranging from 0.312 mg/mL to 20 mg/mL depending on the strain and pathogens targeted. Additionally, ten crude extracts have antiproliferative activity against A2780 human ovarian carcinoma at 2 mg/mL. To highlight, we observed that four phylogenetically identical Streptomyces albogriseolus strains demonstrated variation in antibiotic and anticancer activities. These strains harbored type I and II polyketide synthase (PKS) and non-ribosomal synthetase (NRPS) genes in their genomes, implying that their bioactivity is independent of the polymerase chain reaction (PCR)-detected bio-synthetic gene clusters (BGCs) in this study. Metabolite profiling revealed that the taxonomically identical strains produced core and strain-specific metabolites. Thus, the chemical diversity among these strains influences the variation observed in their biological activities. This study expanded our knowledge on the potential of marine-derived Streptomyces residing from the unexplored regions of the Visayan Sea as a source of small molecules against ESKAPE pathogens and cancer. It also highlights that Streptomyces species strains produce unique strain-specific secondary metabolites; thus, offering new chemical space for natural product discovery.