Deep sequencing of non-ribosomal peptide synthetases and polyketide synthases from the microbiomes of Australian marine sponges

Exploring the secrets of marine microorganisms: Unveiling secondary metabolites through metagenomics

Marine microorganisms are increasingly recognized as primary producers of marine secondary metabolites, drawing growing research interest. Many of these organisms are unculturable, posing challenges for study. Metagenomic techniques enable research on these unculturable microorganisms, identifying various biosynthetic gene clusters (BGCs) related to marine microbial secondary metabolites, thereby unveiling their secrets. This review comprehensively analyses metagenomic methods used in discovering marine microbial secondary metabolites, highlighting tools commonly employed in BGC identification, and discussing the potential and challenges in this field. It emphasizes the key role of metagenomics in unveiling secondary metabolites, particularly in marine sponges and tunicates. The review also explores current limitations in studying these metabolites through metagenomics, noting how long-read sequencing technologies and the evolution of computational biology tools offer more possibilities for BGC discovery. Furthermore, the development of synthetic biology allows experimental validation of computationally identified BGCs, showcasing the vast potential of metagenomics in mining marine microbial secondary metabolites.

Secondary Metabolite Production Potential in a Microbiome of the Freshwater Sponge Spongilla lacustris

Marine and freshwater sponges harbor diverse communities of bacteria with vast potential to produce secondary metabolites that may play an important role in protecting the host from predators and infections. In this work, we initially used cultivation and metagenomics to investigate the microbial community of the freshwater sponge Spongilla lacustris collected in an Austrian lake. Representatives of 41 bacterial genera were isolated from the sponge sample and classified according to their 16S rRNA gene sequences. The genomes of 33 representative isolates and the 20 recovered metagenome-assembled genomes (MAGs) contained in total 306 secondary metabolite biosynthesis gene clusters (BGCs). Comparative 16S rRNA gene and genome analyses showed very little taxon overlap between the recovered isolates and the sponge community as revealed by cultivation-independent methods. Both culture-independent and -dependent analyses suggested high biosynthetic potential of the S. lacustris microbiome, which was confirmed experimentally even at the subspecies level for two Streptomyces isolates. To our knowledge, this is the most thorough description of the secondary metabolite production potential of a freshwater sponge microbiome to date. IMPORTANCE A large body of research is dedicated to marine sponges, filter-feeding animals harboring rich bacterial microbiomes believed to play an important role in protecting the host from predators and infections. Freshwater sponges have received so far much less attention with respect to their microbiomes, members of which may produce bioactive secondary metabolites with potential to be developed into drugs to treat a variety of diseases. In this work, we investigated the potential of bacteria associated with the freshwater sponge Spongilla lacustris to biosynthesize diverse secondary metabolites. Using culture-dependent and -independent methods, we discovered over 300 biosynthetic gene clusters in sponge-associated bacteria and proved production of several compounds by selected isolates using genome mining. Our results illustrate the importance of a complex approach when dealing with microbiomes of multicellular organisms that may contain producers of medically important secondary metabolites.

The natural product biosynthesis potential of the microbiomes of Earth – Bioprospecting for novel anti-microbial agents in the meta-omics era

As we stand on the brink of the post-antibiotic era, we are in dire need of novel antimicrobial compounds. Microorganisms produce a wealth of so-called secondary metabolites and have been our most prolific source of antibiotics so far. However, rediscovery of known antibiotics from well-studied cultured microorganisms, and the fact that the majority of microorganisms in the environment are out of reach by means of conventional cultivation techniques, have led to the exploration of the biosynthetic potential in natural microbial communities by novel approaches. In this mini review we discuss how sequence-based analyses have exposed an unprecedented wealth of potential for secondary metabolite production in soil, marine, and host-associated microbiomes, with a focus on the biosynthesis of non-ribosomal peptides and polyketides. Furthermore, we discuss how the complexity of natural microbiomes and the lack of standardized methodology has complicated comparisons across biomes. Yet, as even the most commonly sampled microbiomes hold promise of providing novel classes of natural products, we lastly discuss the development of approaches applied in the translation of the immense biosynthetic diversity of natural microbiomes to the procurement of novel antibiotics.

Bacteria as a treasure house of secondary metabolites with anticancer potential

Cancer stands in the frontline among leading killers worldwide and the annual mortality rate is expected to reach 16.4 million by 2040. Humans suffer from about 200 different types of cancers and many of them have a small number of approved therapeutic agents. Moreover, several types of major cancers are diagnosed at advanced stages as a result of which the existing therapies have limited efficacy against them and contribute to a dismal prognosis. Therefore, it is essential to develop novel potent anticancer agents to counteract cancer-driven lethality. Natural sources such as bacteria, plants, fungi, and marine microorganisms have been serving as an inexhaustible source of anticancer agents. Notably, over 13,000 natural compounds endowed with different pharmacological properties have been isolated from different bacterial sources. In the present article, we have discussed about the importance of natural products, with special emphasis on bacterial metabolites for cancer therapy. Subsequently, we have comprehensively discussed the various sources, mechanisms of action, toxicity issues, and off-target effects of clinically used anticancer drugs (such as actinomycin D, bleomycin, carfilzomib, doxorubicin, ixabepilone, mitomycin C, pentostatin, rapalogs, and romidepsin) that have been derived from different bacteria. Furthermore, we have also discussed some of the major secondary metabolites (antimycins, chartreusin, elsamicins, geldanamycin, monensin, plicamycin, prodigiosin, rebeccamycin, salinomycin, and salinosporamide) that are currently in the clinical trials or which have demonstrated potent anticancer activity in preclinical models. Besides, we have elaborated on the application of metagenomics in drug discovery and briefly described about anticancer agents (bryostatin 1 and ET-743) identified through the metagenomics approach.

Next Generation High Throughput Sequencing to Assess Microbial Communities: An Application Based on Water Quality

Traditional techniques to identify different contaminants (biological or chemical) in the waters are slow, laborious, and can require specialized expertise. Hence, the rapid determination of water quality using more sensitive and reliable metagenomic based approaches attains special importance. Metagenomics deals with the study of genetic material that is recovered from microbial communities present in environmental samples. In traditional techniques cultivation-based methodologies were used to describe the diversity of microorganisms in environmental samples. It has failed to function as a robust marker because of limited taxonomic and phylogenetic implications. In this backdrop, high-throughput DNA sequencing approaches have proven very powerful in microbial source tracking because of investigating the full variety of genome-based analysis such as microbial genetic diversity and population structure played by them. Next generation sequencing technologies can reveal a greater proportion of microbial communities that have not been reported earlier by traditional techniques. The present review highlights the shift from traditional techniques for the basic study of community composition to next-generation sequencing (NGS) platforms and their potential applications to the biomonitoring of water quality in relation to human health.

Microorganisms Associated with the Marine Sponge Scopalina hapalia: A Reservoir of Bioactive Molecules to Slow Down the Aging Process

Aging research aims at developing therapies that delay normal aging processes and some related pathologies. Recently, many compounds and extracts from natural products have been shown to slow aging and/or extend lifespan. Marine sponges and their associated microorganisms have been found to produce a wide variety of bioactive secondary metabolites; however, those from the Southwest of the Indian Ocean are much less studied, especially regarding anti-aging activities. In this study, the microbial diversity of the marine sponge Scopalina hapalia was investigated by metagenomic analysis. Twenty-six bacterial and two archaeal phyla were recovered from the sponge, of which the Proteobacteria phylum was the most abundant. In addition, 30 isolates from S. hapalia were selected and cultivated for identification and secondary metabolites production. The selected isolates were affiliated to the genera Bacillus, Micromonospora, Rhodoccocus, Salinispora, Aspergillus, Chaetomium, Nigrospora and unidentified genera related to the family Thermoactinomycetaceae. Crude extracts from selected microbial cultures were found to be active against seven clinically relevant targets (elastase, tyrosinase, catalase, sirtuin 1, Cyclin-dependent kinase 7 (CDK7), Fyn kinase and proteasome). These results highlight the potential of microorganisms associated with a marine sponge from Mayotte to produce anti-aging compounds. Future work will focus on the isolation and the characterization of bioactive compounds.

Assessing the Efficiency of Cultivation Techniques To Recover Natural Product Biosynthetic Gene Populations from Sediment

Despite decades of cultivating microorganisms for use in drug discovery, few attempts have been made to measure the extent to which common cultivation techniques have accessed existing chemical space. Metagenomic studies have shown that cultivable bacteria represent a fraction of those that exist in the environment, and that uncultivated populations in sediment have genes that encode for a high diversity of novel natural product (NP) biosynthetic enzymes. Quantifying these genes in both sediment and cultivatable bacterial populations allows us to assess how much diversity is present on nutrient agar and is critical to guiding the trajectory of future NP discovery platforms. Herein, we employed next-generation amplicon sequencing to assess the NP biosynthetic gene populations present in two Lake Huron sediment samples, and compared these with populations from their corresponding cultivatable bacteria. We highlight three findings from our study: (1) after cultivation, we recovered between 7.7% and 23% of three common types of NP biosynthetic genes from the original sediment population; (2) between 76.3% and 91.5% of measured NP biosynthetic genes from nutrient agar have yet to be characterized in known biosynthetic gene cluster databases, indicating that readily cultivatable bacteria harbor the potential to produce new NPs; and (3) even though the predominant taxa present on nutrient media represented some of the major producers of bacterial NPs, the sediment harbored a significantly greater pool of NP biosynthetic genes that could be mined for structural novelty, and these likely belong to taxa that typically have not been represented in microbial drug discovery libraries.

Concepts and Methods to Access Novel Antibiotics from Actinomycetes

Actinomycetes have been proven to be an excellent source of secondary metabolites for more than half a century. Exhibiting various bioactivities, they provide valuable approved drugs in clinical use. Most microorganisms are still untapped in terms of their capacity to produce secondary metabolites, since only a small fraction can be cultured in the laboratory. Thus, improving cultivation techniques to extend the range of secondary metabolite producers accessible under laboratory conditions is an important first step in prospecting underexplored sources for the isolation of novel antibiotics. Currently uncultured actinobacteria can be made available by bioprospecting extreme or simply habitats other than soil. Furthermore, bioinformatic analysis of genomes reveals most producers to harbour many more biosynthetic gene clusters than compounds identified from any single strain, which translates into a silent biosynthetic potential of the microbial world for the production of yet unknown natural products. This review covers discovery strategies and innovative methods recently employed to access the untapped reservoir of natural products. The focus is the order of actinomycetes although most approaches are similarly applicable to other microbes. Advanced cultivation methods, genomics- and metagenomics-based approaches, as well as modern metabolomics-inspired methods are highlighted to emphasise the interplay of different disciplines to improve access to novel natural products.

Secondary metabolism in the lichen symbiosis

Lichens, which are defined by a core symbiosis between a mycobiont (fungal partner) and a photobiont (photoautotrophic partner), are in fact complex assemblages of microorganisms that constitute a largely untapped source of bioactive secondary metabolites. Historically, compounds isolated from lichens have predominantly been those produced by the dominant fungal partner, and these continue to be of great interest for their unique chemistry and biotechnological potential. In recent years it has become apparent that many photobionts and lichen-associated bacteria also produce a range of potentially valuable molecules. There is evidence to suggest that the unique nature of the symbiosis has played a substantial role in shaping many aspects of lichen chemistry, for example driving bacteria to produce metabolites that do not bring them direct benefit but are useful to the lichen as a whole. This is most evident in studies of cyanobacterial photobionts, which produce compounds that differ from free living cyanobacteria and are unique to symbiotic organisms. The roles that these and other lichen-derived molecules may play in communication and maintaining the symbiosis are poorly understood at present. Nonetheless, advances in genomics, mass spectrometry and other analytical technologies are continuing to illuminate the wealth of biological and chemical diversity present within the lichen holobiome. Implementation of novel biodiscovery strategies such as metagenomic screening, coupled with synthetic biology approaches to reconstitute, re-engineer and heterologously express lichen-derived biosynthetic gene clusters in a cultivable host, offer a promising means for tapping into this hitherto inaccessible wealth of natural products.

Diversity of Gene Clusters for Polyketide and Nonribosomal Peptide Biosynthesis Revealed by Metagenomic Analysis of the Yellow Sea Sediment

Polyketides (PKs) and nonribosomal peptides (NRPs) are widely applied as drugs in use today, and one potential source for novel PKs and NRPs is the marine sediment microbes. However, the diversities of microbes and their PKs and NRPs biosynthetic genes in the marine sediment are rarely reported. In this study, 16S rRNA gene fragments of the Yellow Sea sediment were analyzed, demonstrating that Proteobacteria and Bacteroidetes accounted for 62% of all the bacterial species and Actinobacteria bacteria which were seen as the typical PKs and NRPs producers only accounted for 0.82% of all the bacterial species. At the same time, PKs and NRPs diversities were evaluated based on the diversity of gene fragments of type I polyketide synthase (PKS) ketosynthase domain (KS), nonribosomal peptide synthetase (NRPS) adenylation domain (AD), and dTDP-glucose-4,6-dehydratase (dTGD). The results showed that AD genes and dTGD genes were abundant and some of them had less than 50% identities with known ones; By contrast, only few KS genes were identified and most of them had more than 60% identities with known KS genes. Moreover, one 70,000-fosmid clone library was further constructed to screen for fosmid clones harboring PKS or NRPS gene clusters of the Yellow Sea sediment. Nine selected fosmid clones harboring KS or AD were sequenced, and three of the clones were assigned to Proteobacteria. Though only few Actinobacteria 16S rRNA gene sequences were detected in the microbial community, five of the screened fosmid clones were assigned to Actinobacteria. Further assembly of the 9 fosmid clones resulted in 11 contigs harboring PKS, NRPS or hybrid NPRS-PKS gene clusters. These gene clusters showed less than 60% identities with the known ones and might synthesize novel natural products. Taken together, we revealed the diversity of microbes in the Yellow Sea sediments and found that most of the microbes were uncultured. Besides, evaluation of PKS and NRPS biosynthetic gene clusters suggested that the marine sediment might have the ability to synthesize novel natural products and more NRPS gene clusters than PKS gene clusters distributed in this environment.

Recovering Genomics Clusters of Secondary Metabolites from Lakes Using Genome-Resolved Metagenomics

Metagenomic approaches became increasingly popular in the past decades due to decreasing costs of DNA sequencing and bioinformatics development. So far, however, the recovery of long genes coding for secondary metabolites still represents a big challenge. Often, the quality of metagenome assemblies is poor, especially in environments with a high microbial diversity where sequence coverage is low and complexity of natural communities high. Recently, new and improved algorithms for binning environmental reads and contigs have been developed to overcome such limitations. Some of these algorithms use a similarity detection approach to classify the obtained reads into taxonomical units and to assemble draft genomes. This approach, however, is quite limited since it can classify exclusively sequences similar to those available (and well classified) in the databases. In this work, we used draft genomes from Lake Stechlin, north-eastern Germany, recovered by MetaBat, an efficient binning tool that integrates empirical probabilistic distances of genome abundance, and tetranucleotide frequency for accurate metagenome binning. These genomes were screened for secondary metabolism genes, such as polyketide synthases (PKS) and non-ribosomal peptide synthases (NRPS), using the Anti-SMASH and NAPDOS workflows. With this approach we were able to identify 243 secondary metabolite clusters from 121 genomes recovered from our lake samples. A total of 18 NRPS, 19 PKS, and 3 hybrid PKS/NRPS clusters were found. In addition, it was possible to predict the partial structure of several secondary metabolite clusters allowing for taxonomical classifications and phylogenetic inferences. Our approach revealed a high potential to recover and study secondary metabolites genes from any aquatic ecosystem.

Bacterial natural product biosynthetic domain composition in soil correlates with changes in latitude on a continent-wide scale

Although bacterial bioactive metabolites have been one of the most prolific sources of lead structures for the development of small-molecule therapeutics, very little is known about the environmental factors associated with changes in secondary metabolism across natural environments. Large-scale sequencing of environmental microbiomes has the potential to shed light on the richness of bacterial biosynthetic diversity hidden in the environment, how it varies from one environment to the next, and what environmental factors correlate with changes in biosynthetic diversity. In this study, the sequencing of PCR amplicons generated using primers targeting either ketosynthase domains from polyketide biosynthesis or adenylation domains from nonribosomal peptide biosynthesis was used to assess biosynthetic domain composition and richness in soils collected across the Australian continent. Using environmental variables collected at each soil site, we looked for environmental factors that correlated with either high overall domain richness or changes in the domain composition. Among the environmental variables we measured, changes in biosynthetic domain composition correlate most closely with changes in latitude and to a lesser extent changes in pH. Although it is unclear at this time the exact mix of factors that may drive the relationship between biosynthetic domain composition and latitude, from a practical perspective the identification of a latitudinal basis for differences in soil metagenome biosynthetic domain compositions should help guide future natural product discovery efforts.

Thermoactinoamide A, an Antibiotic Lipophilic Cyclopeptide from the Icelandic Thermophilic Bacterium Thermoactinomyces vulgaris

The thermophilic bacterium Thermoactinomyces vulgaris strain ISCAR 2354, isolated from a coastal hydrothermal vent in Iceland, was shown to contain thermoactinoamide A (1), a new cyclic hexapeptide composed of mixed d and l amino acids, along with five minor analogues (2-6). The structure of 1 was determined by one- and two-dimensional NMR spectroscopy, high-resolution tandem mass spectrometry, and advanced Marfey's analysis of 1 and of the products of its partial hydrolysis. Thermoactinoamide A inhibited the growth of Staphylococcus aureus ATCC 6538 with an MIC value of 35 μM. On the basis of literature data and this work, cyclic hexapeptides with mixed d/l configurations, one aromatic amino acid residue, and a prevalence of lipophilic residues can be seen as a starting point to define a new, easily accessible scaffold in the search for new antibiotic agents.

Antibacterial Activities of Bacteria Isolated from the Marine Sponges Isodictya compressa and Higginsia bidentifera Collected from Algoa Bay, South Africa

Due to the rise in multi-drug resistant pathogens and other diseases, there is renewed interest in marine sponge endosymbionts as a rich source of natural products (NPs). The South African marine environment is rich in marine biota that remains largely unexplored and may represent an important source for the discovery of novel NPs. We first investigated the bacterial diversity associated with five South African marine sponges, whose microbial populations had not previously been investigated, and select the two sponges (Isodictya compressa and Higginsia bidentifera) with highest species richness to culture bacteria. By employing 33 different growth conditions 415 sponge-associated bacterial isolates were cultured and screened for antibacterial activity. Thirty-five isolates showed antibacterial activity, twelve of which exhibited activity against the multi-drug resistant Escherichia coli 1699, implying that some of the bioactive compounds could be novel. Genome sequencing of two of these isolates confirmed that they harbour uncharacterized biosynthetic pathways that may encode novel chemical structures.

A computationally simplistic poly-phasic approach to explore microbial communities from the Yucatan aquifer as a potential sources of novel natural products

The need for new antibiotics has sparked a search for the microbes that might potentially produce them. Current sequencing technologies allow us to explore the biotechnological potential of microbial communities in diverse environments without the need for cultivation, benefitting natural product discovery in diverse ways. A relatively recent method to search for the possible production of novel compounds includes studying the diverse genes belonging to polyketide synthase pathways (PKS), as these complex enzymes are an important source of novel therapeutics. In order to explore the biotechnological potential of the microbial community from the largest underground aquifer in the world located in the Yucatan, we used a polyphasic approach in which a simple, non-computationally intensive method was coupled with direct amplification of environmental DNA to assess the diversity and novelty of PKS type I ketosynthase (KS) domains. Our results suggest that the bioinformatic method proposed can indeed be used to assess the novelty of KS enzymes; nevertheless, this in silico study did not identify some of the KS diversity due to primer bias and stringency criteria outlined by the metagenomics pipeline. Therefore, additionally implementing a method involving the direct cloning of KS domains enhanced our results. Compared to other freshwater environments, the aquifer was characterized by considerably less diversity in relation to known ketosynthase domains; however, the metagenome included a family of KS type I domains phylogenetically related, but not identical, to those found in the curamycin pathway, as well as an outstanding number of thiolases. Over all, this first look into the microbial community found in this large Yucatan aquifer and other fresh water free living microbial communities highlights the potential of these previously overlooked environments as a source of novel natural products.

Diversity of Natural Product Biosynthetic Genes in the Microbiome of the Deep Sea Sponges Inflatella pellicula, Poecillastra compressa, and Stelletta normani

Three different deep sea sponge species, Inflatella pellicula, Poecillastra compressa, and Stelletta normani comprising seven individual samples, retrieved from depths of 760–2900 m below sea level, were investigated using 454 pyrosequencing for their secondary metabolomic potential targeting adenylation domain and ketosynthase domain sequences. The data obtained suggest a diverse microbial origin of nonribosomal peptide synthetases and polyketide synthase fragments that in part correlates with their respective microbial community structures that were previously described and reveals an untapped source of potential novelty. The sequences, especially the ketosynthase fragments, display extensive clade formations which are clearly distinct from sequences hosted in public databases, therefore highlighting the potential of the microbiome of these deep sea sponges to produce potentially novel small-molecule chemistry. Furthermore, sequence similarities to gene clusters known to be involved in the production of many classes of antibiotics and toxins including lipopeptides, glycopeptides, macrolides, and hepatotoxins were also identified.

The evolution of genome mining in microbes - a review

Covering: 2006 to 2016The computational mining of genomes has become an important part in the discovery of novel natural products as drug leads. Thousands of bacterial genome sequences are publically available these days containing an even larger number and diversity of secondary metabolite gene clusters that await linkage to their encoded natural products. With the development of high-throughput sequencing methods and the wealth of DNA data available, a variety of genome mining methods and tools have been developed to guide discovery and characterisation of these compounds. This article reviews the development of these computational approaches during the last decade and shows how the revolution of next generation sequencing methods has led to an evolution of various genome mining approaches, techniques and tools. After a short introduction and brief overview of important milestones, this article will focus on the different approaches of mining genomes for secondary metabolites, from detecting biosynthetic genes to resistance based methods and "evo-mining" strategies including a short evaluation of the impact of the development of genome mining methods and tools on the field of natural products and microbial ecology.

Discovery Strategies of Bioactive Compounds Synthesized by Nonribosomal Peptide Synthetases and Type-I Polyketide Synthases Derived from Marine Microbiomes

Considering that 70% of our planet's surface is covered by oceans, it is likely that undiscovered biodiversity is still enormous. A large portion of marine biodiversity consists of microbiomes. They are very attractive targets of bioprospecting because they are able to produce a vast repertoire of secondary metabolites in order to adapt in diverse environments. In many cases secondary metabolites of pharmaceutical and biotechnological interest such as nonribosomal peptides (NRPs) and polyketides (PKs) are synthesized by multimodular enzymes named nonribosomal peptide synthetases (NRPSes) and type-I polyketide synthases (PKSes-I), respectively. Novel findings regarding the mechanisms underlying NRPS and PKS evolution demonstrate how microorganisms could leverage their metabolic potential. Moreover, these findings could facilitate synthetic biology approaches leading to novel bioactive compounds. Ongoing advances in bioinformatics and next-generation sequencing (NGS) technologies are driving the discovery of NRPs and PKs derived from marine microbiomes mainly through two strategies: genome-mining and metagenomics. Microbial genomes are now sequenced at an unprecedented rate and this vast quantity of biological information can be analyzed through genome mining in order to identify gene clusters encoding NRPSes and PKSes of interest. On the other hand, metagenomics is a fast-growing research field which directly studies microbial genomes and their products present in marine environments using culture-independent approaches. The aim of this review is to examine recent developments regarding discovery strategies of bioactive compounds synthesized by NRPS and type-I PKS derived from marine microbiomes and to highlight the vast diversity of NRPSes and PKSes present in marine environments by giving examples of recently discovered bioactive compounds.

Sample Processing Impacts the Viability and Cultivability of the Sponge Microbiome

Sponges host complex microbial communities of recognized ecological and biotechnological importance. Extensive cultivation efforts have been made to isolate sponge bacteria, but most still elude cultivation. To identify the bottlenecks of sponge bacterial cultivation, we combined high-throughput 16S rRNA gene sequencing with a variety of cultivation media and incubation conditions. We aimed to determine the extent to which sample processing and cultivation conditions can impact bacterial viability and recovery in culture. We isolated 325 sponge bacteria from six specimens of Cymbastela concentrica and three specimens of Scopalina sp. These isolates were distributed over 37 different genera and 47 operational taxonomic units (defined at 97% 16S rRNA gene sequence identity). The cultivable bacterial community was highly specific to its sponge host and different media compositions yielded distinct microbial isolates. Around 97% of the isolates could be detected in the original sponge and represented a large but highly variable proportion (0.5–92% total abundance, depending on sponge species) of viable bacteria obtained after sample processing, as determined by propidium monoazide selective DNA modification of compromised cells. Our results show that the most abundant viable bacteria are also the most predominant groups found in cultivation, reflecting, to some extent, the relative abundances of the viable bacterial community, rather than the overall community estimated by direct molecular approaches. Cultivation is therefore shaped not only by the growth conditions provided, but also by the different cell viabilities of the bacteria that constitute the cultivation inoculum. These observations highlight the need to perform experiments to assess each method of sample processing for its accurate representation of the actual in situ bacterial community and its yield of viable cells.

Genome-Guided Discovery of Natural Products and Biosynthetic Pathways from Australia’s Untapped Microbial Megadiversity

Historically microbial natural product biosynthesis pathways were elucidated mainly by isotope labelled precursor directed feeding studies. Now the genetics underpinning the assembly of microbial natural products biosynthesis is so well understood that some pathways and their products can be predicted from DNA sequences alone. The association between microbial natural products and their biosynthesis gene clusters is now driving the field of ‘genetics guided natural product discovery’. This account overviews our research into cyanotoxin biosynthesis before the genome sequencing era through to some recent discoveries resulting from the mining of Australian biota for natural product biosynthesis pathways.

Genomic insights into the distribution, genetic diversity and evolution of polyketide synthases and nonribosomal peptide synthetases

Polyketides and nonribosomal peptides are important secondary metabolites that exhibit enormous structural diversity, have many pharmaceutical applications, and include a number of clinically important drugs. These complex metabolites are most commonly synthesized on enzymatic assembly lines of polyketide synthases and nonribosomal peptide synthetases. Genome-mining studies making use of the recent explosion in the number of genome sequences have demonstrated unexpected enzymatic diversity and greatly expanded the known distribution of these enzyme systems across the three domains of life. The wealth of data now available suggests that genome-mining efforts will uncover new natural products, novel biosynthetic mechanisms, and shed light on the origin and evolution of these important enzymes.

Culture-independent discovery of natural products from soil metagenomes

Bacterial natural products have proven to be invaluable starting points in the development of many currently used therapeutic agents. Unfortunately, traditional culture-based methods for natural product discovery have been deemphasized by pharmaceutical companies due in large part to high rediscovery rates. Culture-independent, or "metagenomic," methods, which rely on the heterologous expression of DNA extracted directly from environmental samples (eDNA), have the potential to provide access to metabolites encoded by a large fraction of the earth's microbial biosynthetic diversity. As soil is both ubiquitous and rich in bacterial diversity, it is an appealing starting point for culture-independent natural product discovery efforts. This review provides an overview of the history of soil metagenome-driven natural product discovery studies and elaborates on the recent development of new tools for sequence-based, high-throughput profiling of environmental samples used in discovering novel natural product biosynthetic gene clusters. We conclude with several examples of these new tools being employed to facilitate the recovery of novel secondary metabolite encoding gene clusters from soil metagenomes and the subsequent heterologous expression of these clusters to produce bioactive small molecules.

Designing and Implementing an Assay for the Detection of Rare and Divergent NRPS and PKS Clones in European, Antarctic and Cuban Soils

The ever increasing microbial resistome means there is an urgent need for new antibiotics. Metagenomics is an underexploited tool in the field of drug discovery. In this study we aimed to produce a new updated assay for the discovery of biosynthetic gene clusters encoding bioactive secondary metabolites. PCR assays targeting the polyketide synthases (PKS) and non-ribosomal peptide synthetases (NRPS) were developed. A range of European soils were tested for their biosynthetic potential using clone libraries developed from metagenomic DNA. Results revealed a surprising number of NRPS and PKS clones with similarity to rare Actinomycetes. Many of the clones tested were phylogenetically divergent suggesting they were fragments from novel NRPS and PKS gene clusters. Soils did not appear to cluster by location but did represent NRPS and PKS clones of diverse taxonomic origin. Fosmid libraries were constructed from Cuban and Antarctic soil samples; 17 fosmids were positive for NRPS domains suggesting a hit rate of less than 1 in 10 genomes. NRPS hits had low similarities to both rare Actinobacteria and Proteobacteria; they also clustered with known antibiotic producers suggesting they may encode for pathways producing novel bioactive compounds. In conclusion we designed an assay capable of detecting divergent NRPS and PKS gene clusters from the rare biosphere; when tested on soil samples results suggest the majority of NRPS and PKS pathways and hence bioactive metabolites are yet to be discovered.

Filamentous fungi from extreme environments as a promising source of novel bioactive secondary metabolites

Natural product search is undergoing resurgence upon the discovery of a huge previously unknown potential for secondary metabolite (SM) production hidden in microbial genomes. This is also the case for filamentous fungi, since their genomes contain a high number of "orphan" SM gene clusters. Recent estimates indicate that only 5% of existing fungal species have been described, thus the potential for the discovery of novel metabolites in fungi is huge. In this context, fungi thriving in harsh environments are of particular interest since they are outstanding producers of unusual chemical structures. At present, there are around 16 genomes from extreme environment-isolated fungi in databases. In a preliminary analysis of three of these genomes we found that several of the predicted SM gene clusters are probably involved in the biosynthesis of compounds not yet described. Genome mining strategies allow the exploitation of the information in genome sequences for the discovery of new natural compounds. The synergy between genome mining strategies and the expected abundance of SMs in fungi from extreme environments is a promising path to discover new natural compounds as a source of medically useful drugs.

Targeted metagenomics as a tool to tap into marine natural product diversity for the discovery and production of drug candidates

Microbial natural products exhibit immense structural diversity and complexity and have captured the attention of researchers for several decades. They have been explored for a wide spectrum of applications, most noteworthy being their prominent role in medicine, and their versatility expands to application as drugs for many diseases. Accessing unexplored environments harboring unique microorganisms is expected to yield novel bioactive metabolites with distinguishing functionalities, which can be supplied to the starved pharmaceutical market. For this purpose the oceans have turned out to be an attractive and productive field. Owing to the enormous biodiversity of marine microorganisms, as well as the growing evidence that many metabolites previously isolated from marine invertebrates and algae are actually produced by their associated bacteria, the interest in marine microorganisms has intensified. Since the majority of the microorganisms are uncultured, metagenomic tools are required to exploit the untapped biochemistry. However, after years of employing metagenomics for marine drug discovery, new drugs are vastly under-represented. While a plethora of natural product biosynthetic genes and clusters are reported, only a minor number of potential therapeutic compounds have resulted through functional metagenomic screening. This review explores specific obstacles that have led to the low success rate. In addition to the typical problems encountered with traditional functional metagenomic-based screens for novel biocatalysts, there are enormous limitations which are particular to drug-like metabolites. We also present how targeted and function-guided strategies, employing modern, and multi-disciplinary approaches have yielded some of the most exciting discoveries attributed to uncultured marine bacteria. These discoveries set the stage for progressing the production of drug candidates from uncultured bacteria for pre-clinical and clinical development.

The Biogeography of Putative Microbial Antibiotic Production

Understanding patterns in the distribution and abundance of functional traits across a landscape is of fundamental importance to ecology. Mapping these distributions is particularly challenging for species-rich groups with sparse trait measurement coverage, such as flowering plants, insects, and microorganisms. Here, we use likelihood-based character reconstruction to infer and analyze the spatial distribution of unmeasured traits. We apply this framework to a microbial dataset comprised of 11,732 ketosynthase alpha gene sequences extracted from 144 soil samples from three continents to document the spatial distribution of putative microbial polyketide antibiotic production. Antibiotic production is a key competitive strategy for soil microbial survival and performance. Additionally, novel antibiotic discovery is highly relevant to human health, making natural antibiotic production by soil microorganisms a major target for bioprospecting. Our comparison of trait-based biogeographical patterns to patterns based on taxonomy and phylogeny is relevant to our basic understanding of microbial biogeography as well as the pressing need for new antibiotics.

Analysis of bacterial xylose isomerase gene diversity using gene-targeted metagenomics

Bacterial xylose isomerases (XI) are promising resources for efficient biofuel production from xylose in lignocellulosic biomass. Here, we investigated xylose isomerase gene (xylA) diversity in three soil metagenomes differing in plant vegetation and geographical location, using an amplicon pyrosequencing approach and two newly-designed primer sets. A total of 158,555 reads from three metagenomic DNA replicates for each soil sample were classified into 1127 phylotypes, detected in triplicate and defined by 90% amino acid identity. The phylotype coverage was estimated to be within the range of 84.0-92.7%. The xylA gene phylotypes obtained were phylogenetically distributed across the two known xylA groups. They shared 49-100% identities with their closest-related XI sequences in GenBank. Phylotypes demonstrating <90% identity with known XIs in the database accounted for 89% of the total xylA phylotypes. The differences among xylA members and compositions within each soil sample were significantly smaller than they were between different soils based on a UniFrac distance analysis, suggesting soil-specific xylA genotypes and taxonomic compositions. The differences among xylA members and their compositions in the soil were strongly correlated with 16S rRNA variation between soil samples, also assessed by amplicon pyrosequencing. This is the first report of xylA diversity in environmental samples assessed by amplicon pyrosequencing. Our data provide information regarding xylA diversity in nature, and can be a basis for the screening of novel xylA genotypes for practical applications.

Mining the metabiome: identifying novel natural products from microbial communities

Microbial-derived natural products provide the foundation for most of the chemotherapeutic arsenal available to contemporary medicine. In the face of a dwindling pipeline of new lead structures identified by traditional culturing techniques and an increasing need for new therapeutics, surveys of microbial biosynthetic diversity across environmental metabiomes have revealed enormous reservoirs of as yet untapped natural products chemistry. In this review, we touch on the historical context of microbial natural product discovery and discuss innovations and technological advances that are facilitating culture-dependent and culture-independent access to new chemistry from environmental microbiomes with the goal of reinvigorating the small molecule therapeutics discovery pipeline. We highlight the successful strategies that have emerged and some of the challenges that must be overcome to enable the development of high-throughput methods for natural product discovery from complex microbial communities.

Metagenomic small molecule discovery methods

Metagenomic approaches to natural product discovery provide the means to harvest bioactive small molecules synthesized by environmental bacteria without the requirement of first culturing these organisms. Advances in sequencing technologies and general metagenomic methods are beginning to provide the tools necessary to unlock the unexplored biosynthetic potential encoded by the genomes of uncultured environmental bacteria. Here, we highlight recent advances in sequence-based and functional-based metagenomic approaches that promise to facilitate antibiotic discovery from diverse environmental microbiomes.

Chemical-biogeographic survey of secondary metabolism in soil

In this study, we compare biosynthetic gene richness and diversity of 96 soil microbiomes from diverse environments found throughout the southwestern and northeastern regions of the United States. The 454-pyroseqencing of nonribosomal peptide adenylation (AD) and polyketide ketosynthase (KS) domain fragments amplified from these microbiomes provide a means to evaluate the variation of secondary metabolite biosynthetic diversity in different soil environments. Through soil composition and AD- and KS-amplicon richness analysis, we identify soil types with elevated biosynthetic potential. In general, arid soils show the richest observed biosynthetic diversity, whereas brackish sediments and pine forest soils show the least. By mapping individual environmental amplicon sequences to sequences derived from functionally characterized biosynthetic gene clusters, we identified conserved soil type-specific secondary metabolome enrichment patterns despite significant sample-to-sample sequence variation. These data are used to create chemical biogeographic distribution maps for biomedically valuable families of natural products in the environment that should prove useful for directing the discovery of bioactive natural products in the future.