Marine microbiome as source of natural products

A guide to the use of bioassays in exploration of natural resources

Bioassays are the main tool to decipher bioactivities from natural resources thus their selection and quality are critical for optimal bioprospecting. They are used both in the early stages of compounds isolation/purification/identification, and in later stages to evaluate their safety and efficacy. In this review, we provide a comprehensive overview of the most common bioassays used in the discovery and development of new bioactive compounds with a focus on marine bioresources. We present a comprehensive list of practical considerations for selecting appropriate bioassays and discuss in detail the bioassays typically used to explore antimicrobial, antibiofilm, cytotoxic, antiviral, antioxidant, and anti-ageing potential. The concept of quality control and bioassay validation are introduced, followed by safety considerations, which are critical to advancing bioactive compounds to a higher stage of development. We conclude by providing an application-oriented view focused on the development of pharmaceuticals, food supplements, and cosmetics, the industrial pipelines where currently known marine natural products hold most potential. We highlight the importance of gaining reliable bioassay results, as these serve as a starting point for application-based development and further testing, as well as for consideration by regulatory authorities.

Prophages: an integral but understudied component of the human microbiome

Phages integrated into a bacterial genome - called prophages - continuously monitor the vigour of the host bacteria to determine when to escape the genome and to protect their host from other phage infections, and they may provide genes that promote bacterial growth. Prophages are essential to almost all microbiomes, including the human microbiome. However, most human microbiome studies have focused on bacteria, ignoring free and integrated phages, so we know little about how these prophages affect the human microbiome. To address this gap in our knowledge, we compared the prophages identified in 14 987 bacterial genomes isolated from human body sites to characterize prophage DNA in the human microbiome. Here, we show that prophage DNA is ubiquitous, comprising on average 1-5 % of each bacterial genome. The prophage content per genome varies with the isolation site on the human body, the health of the human and whether the disease was symptomatic. The presence of prophages promotes bacterial growth and sculpts the microbiome. However, the disparities caused by prophages vary throughout the body.

Identification of the Biosynthetic Gene Cluster of New Piperazic Acid-Containing Lipopeptides with Cytotoxic Activity in the Genome of Marine Streptomyces PHM034

Three novel lipopeptides, PM130391 (1), PM130392 (2), and PM140293 (3) were obtained from cultures of Streptomyces tuirus PHM034 isolated from a marine sediment. Structural elucidation of the three compounds showed they belong to the nonribosomal peptides family, and they all contain an acylated alanine, three piperazic acids, a methylated glycine, and an N-hydroxylated alanine. The difference between the three compounds resides in the acyl chain bound to the alanine residue. All three compounds showed cytotoxic activity against human cancer cell lines. Genome sequence and bioinformatics analysis allowed the identification of the gene cluster responsible for the biosynthesis. Inactivation of a nonribosomal peptide synthase of this cluster abolished the biosynthesis of the three compounds, thus demonstrating the involvement of this cluster in the biosynthesis of these lipopeptides.

Prophage rates in the human microbiome vary by body site and host health

Phages integrated into a bacterial genome-called prophages-continuously monitor the health of the host bacteria to determine when to escape the genome, protect their host from other phage infections, and may provide genes that promote bacterial growth. Prophages are essential to almost all microbiomes, including the human microbiome. However, most human microbiome studies focus on bacteria, ignoring free and integrated phages, so we know little about how these prophages affect the human microbiome. We compared the prophages identified in 11,513 bacterial genomes isolated from human body sites to characterise prophage DNA in the human microbiome. Here, we show that prophage DNA comprised an average of 1-5% of each bacterial genome. The prophage content per genome varies with the isolation site on the human body, the health of the human, and whether the disease was symptomatic. The presence of prophages promotes bacterial growth and sculpts the microbiome. However, the disparities caused by prophages vary throughout the body.

Microbiome network in the pelagic and benthic offshore systems of the northern Adriatic Sea (Mediterranean Sea)

Because of their recognized global importance, there is now the urgent need to map diversity and distribution patterns of marine microbial communities. Even if available studies provided some advances in the understanding the biogeographical patterns of marine microbiomes at the global scale, their degree of plasticity at the local scale it is still underexplored, and functional implications still need to be dissected. In this scenario here we provide a synoptical study on the microbiomes of the water column and surface sediments from 19 sites in a 130 km2 area located 13.5 km afar from the coast in the North-Western Adriatic Sea (Italy), providing the finest-scale mapping of marine microbiomes in the Mediterranean Sea. Pelagic and benthic microbiomes in the study area showed sector specific-patterns and distinct assemblage structures, corresponding to specific variations in the microbiome network structure. While maintaining a balanced structure in terms of potential ecosystem services (e.g., hydrocarbon degradation and nutrient cycling), sector-specific patterns of over-abundant modules—and taxa—were defined, with the South sector (the closest to the coast) characterized by microbial groups of terrestrial origins, both in the pelagic and the benthic realms. By the granular assessment of the marine microbiome changes at the local scale, we have been able to describe, to our knowledge at the first time, the integration of terrestrial microorganisms in the marine microbiome networks, as a possible natural process characterizing eutrophic coastal area. This raises the question about the biological threshold for terrestrial microorganisms to be admitted in the marine microbiome networks, without altering the ecological balance.

How Metagenomics Has Transformed Our Understanding of Bacteriophages in Microbiome Research

The microbiome is an essential part of most ecosystems. It was originally studied mostly through culturing but relatively few microbes can be cultured, so much of the microbiome was left unexplored. The emergence of metagenomic sequencing techniques changed that and allowed the study of microbiomes from all sorts of habitats. Metagenomic sequencing also allowed for a more thorough exploration of prophages, viruses that integrate into bacterial genomes, and how they benefit their hosts. One issue with using open-access metagenomic data is that sequences added to databases often have little to no metadata to work with, so finding enough sequences can be difficult. Many metagenomes have been manually curated but this is a time-consuming process and relies heavily on the uploader to be accurate and thorough when filling in metadata fields and the curators to be working with the same ontologies. Using algorithms to automatically sort metagenomes based on either the taxonomic profile or the functional profile may be a viable solution to the issues with manually curated metagenomes, but it requires that the algorithm is trained on carefully curated datasets and using the most informative profile possible in order to minimize errors.

Bioactivity and Biotechnological Overview of Naturally Occurring Compounds from the Dinoflagellate Family Symbiodiniaceae: A Systematic Review

Marine invertebrates are a significant source of biologically active compounds. Recent studies have highlighted the role of microbiota associated with marine invertebrates in the production of bioactive compounds. Corals and sponges are the main marine invertebrates producing bioactive substances, and Symbiodiniaceae dinoflagellates are well-recognized endosymbionts with corals and sponges playing vital functions. The biological properties of Symbiodiniaceae-derived compounds have garnered attention in the past decades owing to their ecological implications and potentiality for bioprospecting initiatives. This study aims to systematically review studies on bioactivities and potential biotechnological applications of Symbiodiniaceae-derived compounds. The PRISMA guidelines were followed. Our study showed that anti-inflammatory and vasoconstrictive activities of Symbiodiniaceae-derived compounds have been the most investigated. However, very few studies have been published, with in vitro culturing of Symbiodiniaceae being the most significant challenge. Therefore, we surveyed for the metabolites reported so far, analyzed their chemodiversity, and discussed approaches to overcome culturing-related limitations.

Biotechnological applications of marine bacteria in bioremediation of environments polluted with hydrocarbons and plastics

Marine ecosystems are some of the most adverse environments on Earth and contain a considerable portion of the global bacterial population, and some of these bacterial species play pivotal roles in several biogeochemical cycles. Marine bacteria have developed different molecular mechanisms to address fluctuating environmental conditions, such as changes in nutrient availability, salinity, temperature, pH, and pressure, making them attractive for use in diverse biotechnology applications. Although more than 99% of marine bacteria cannot be cultivated with traditional microbiological techniques, several species have been successfully isolated and grown in the laboratory, facilitating investigations of their biotechnological potential. Some of these applications may contribute to addressing some current global problems, such as environmental contamination by hydrocarbons and synthetic plastics. In this review, we first summarize and analyze recently published information about marine bacterial diversity. Then, we discuss new literature regarding the isolation and characterization of marine bacterial strains able to degrade hydrocarbons and petroleum-based plastics, and species able to produce biosurfactants. We also describe some current limitations for the implementation of these biotechnological tools, but also we suggest some strategies that may contribute to overcoming them. KEY POINTS: • Marine bacteria have a great metabolic capacity to degrade hydrocarbons in harsh conditions. • Marine environments are an important source of new bacterial plastic-degrading enzymes. • Secondary metabolites from marine bacteria have diverse potential applications in biotechnology.

Ubiquitousness of Haloferax and Carotenoid Producing Genes in Arabian Sea Coastal Biosystems of India

This study presents a comparative analysis of halophiles from the global open sea and coastal biosystems through shotgun metagenomes (n = 209) retrieved from public repositories. The open sea was significantly enriched with Prochlorococcus and Candidatus pelagibacter. Meanwhile, coastal biosystems were dominated by Marinobacter and Alcanivorax. Halophilic archaea Haloarcula and Haloquandratum, predominant in the coastal biosystem, were significantly (p < 0.05) enriched in coastal biosystems compared to the open sea. Analysis of whole genomes (n = 23,540), retrieved from EzBioCloud, detected crtI in 64.66% of genomes, while cruF was observed in 1.69% Bacteria and 40.75% Archaea. We further confirmed the viability and carotenoid pigment production by pure culture isolation (n = 1351) of extreme halophiles from sediments (n = 410 × 3) sampling at the Arabian coastline of India. All red-pigmented isolates were represented exclusively by Haloferax, resistant to saturated NaCl (6 M), and had >60% G + C content. Multidrug resistance to tetracycline, gentamicin, ampicillin, and chloramphenicol were also observed. Our study showed that coastal biosystems could be more suited for bioprospection of halophiles rather than the open sea.

Genome Mining for Antimicrobial Compounds in Wild Marine Animals-Associated Enterococci

New ecosystems are being actively mined for new bioactive compounds. Because of the large amount of unexplored biodiversity, bacteria from marine environments are especially promising. Further, host-associated microbes are of special interest because of their low toxicity and compatibility with host health. Here, we identified and characterized biosynthetic gene clusters encoding antimicrobial compounds in host-associated enterococci recovered from fecal samples of wild marine animals remote from human-affected ecosystems. Putative biosynthetic gene clusters in the genomes of 22 Enterococcus strains of marine origin were predicted using antiSMASH5 and Bagel4 bioinformatic software. At least one gene cluster encoding a putative bioactive compound precursor was identified in each genome. Collectively, 73 putative antimicrobial compounds were identified, including 61 bacteriocins (83.56%), 10 terpenes (13.70%), and 2 (2.74%) related to putative nonribosomal peptides (NRPs). Two of the species studied, Enterococcus avium and Enterococcus mundtti, are rare causes of human disease and were found to lack any known pathogenic determinants but yet possessed bacteriocin biosynthetic genes, suggesting possible additional utility as probiotics. Wild marine animal-associated enterococci from human-remote ecosystems provide a potentially rich source for new antimicrobial compounds of therapeutic and industrial value and potential probiotic application.

CRISPR/Cas9 mutagenesis reveals a role for ABCB1 in gut immune responses to Vibrio diazotrophicus in sea urchin larvae

The ABC transporter ABCB1 plays an important role in the disposition of xenobiotics. Embryos of most species express high levels of this transporter in early development as a protective mechanism, but its native substrates are not known. Here, we used larvae of the sea urchin Strongylocentrotus purpuratus to characterize the early life expression and role of Sp-ABCB1a, a homolog of ABCB1. The results indicate that while Sp-ABCB1a is initially expressed ubiquitously, it becomes enriched in the developing gut. Using optimized CRISPR/Cas9 gene editing methods to achieve high editing efficiency in the F0 generation, we generated ABCB1a crispant embryos with significantly reduced transporter efflux activity. When infected with the opportunistic pathogen Vibrio diazotrophicus, Sp-ABCB1a crispant larvae demonstrated significantly stronger gut inflammation, immunocyte migration and cytokine Sp-IL-17 induction, as compared with infected control larvae. The results suggest an ancestral function of ABCB1 in host-microbial interactions, with implications for the survival of invertebrate larvae in the marine microbial environment.

A Cyclic Dipeptide from Marine Fungus Penicillium chrysogenum DXY-1 Exhibits Anti-quorum Sensing Activity

Bacterial quorum sensing (QS) is anticipated as a new potential target for the development of antimicrobial drugs. An anti-QS substance against Chromobacterium violaceum CV026 and Pseudomonas aeruginosa PA01 has been isolated and purified from the crude extracts of the marine fungus Penicillium chrysogenum DXY-1, and the accurate structure was identified as cyclo(l-Tyr-l-Pro). This cyclic dipeptide at sub-minimum inhibitory concentration can decrease the QS-regulated violacein production of C. violaceum CV026 by 79% and QS-mediated pyocyanin production, proteases, and elastase activity of P. aeruginosa PA01 by 41%, 20%, and 32%, respectively. In addition, it can also destroy the biofilm formation and decrease QS gene expression of P. aeruginosa PA01. Molecular docking was further performed, and the obtained data indicated that this dipeptide blocks the effect of QS autoinducers through competitive binding to the same pocket of the receptor proteins. We expect this anti-QS cyclic dipeptide to be a potential pro-drug treating drug-resistant P. aeruginosa infections, and these findings could relieve the alarming problem of microbial resistance to antimicrobial drugs.

Genome mining as a biotechnological tool for the discovery of novel marine natural products

Compared to terrestrial environments, the oceans harbor a variety of environments, creating higher biodiversity, which gives marine natural products a high occurrence of significant biology and novel chemistry. However, traditional bioassay-guided isolation and purification strategies are severely limiting the discovery of additional novel natural products from the ocean. With an increasing number of marine microorganisms being sequenced, genome mining is gradually becoming a powerful tool to retrieve novel marine natural products. In this review, we have summarized genome mining approaches used to analyze key enzymes of biosynthetic pathways and predict the chemical structure of new gene clusters by introducing successful stories that used genome mining strategy to identify new marine-derived compounds. Furthermore, we also put forward challenges for genome mining techniques and their proposed solutions. The detailed analysis of the genome mining strategy will help researchers to understand this novel technique and its application. With the development of a genome sequence, genome mining strategies will be applied more widely, which will drive rapid development in the field of marine natural product development.

Penicilazaphilone C, a New Azaphilone, Induces Apoptosis in Gastric Cancer by Blocking the Notch Signaling Pathway

Penicilazaphilone C (PAC) is a novel azaphilonidal derivative isolated by our group that demonstrates good anticancer activities. Considering that its molecular mechanisms remain largely unknown, here we explore the molecular mechanisms of the anticancer activities of PAC against gastric cancer. The in vitro effects of PAC on cell growth, proliferation, and apoptosis were evaluated by MTT, BrdU, MTS, colony formation assays, Hoechst 33258 staining, and flow cytometry. Related proteins were examined by western blotting. Notch receptor expression was analyzed by RT-PCR. In vivo antitumor activities of PAC were observed in a nude mouse model. We found that compared to the controls, PAC treatment suppressed cell proliferation and promoted apoptosis in MGC-803 and SGC-7901 cells, and the Notch/PTEN/AKT axis was involved in the activating PAC-induced apoptosis. PAC treatment led to decreased levels of Notch (NTM), NICD, pPTEN, and pAKT compared to controls. PAC-induced inhibition of Notch-related protein expression levels and the resulting apoptosis were reversed by overexpression of Notch1 (NTM) or/and Notch2 (NTM). Moreover, PAC treatment clearly inhibited tumor growth in mice both bearing tumors derived from both MGC-803 and SGC-7901 cells. This work reveals that PAC induces the apoptosis by suppressing activation of Notch receptor proteolytic cleavage and subsequently blocking the PTEN/AKT signaling axis in gastric cancer cells. Thus, PAC is a potential alternative agent for the treatment of gastric cancer.