Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery.

Non-Ribosomal Peptides (NRPs) represent a biomedically important class of natural products that include a multitude of antibiotics and other clinically used drugs. NRPs are not directly encoded in the genome but are instead produced by metabolic pathways encoded by biosynthetic gene clusters (BGCs). Since the existing genome mining tools predict many putative NRPs synthesized by a given BGC, it remains unclear which of these putative NRPs are correct and how to identify post-assembly modifications of amino acids in these NRPs in a blind mode, without knowing which modifications exist in the sample. To address this challenge, here we report NRPminer, a modification-tolerant tool for NRP discovery from large (meta)genomic and mass spectrometry datasets. We show that NRPminer is able to identify many NRPs from different environments, including four previously unreported NRP families from soil-associated microbes and NRPs from human microbiota. Furthermore, in this work we demonstrate the anti-parasitic activities and the structure of two of these NRP families using direct bioactivity screening and nuclear magnetic resonance spectrometry, illustrating the power of NRPminer for discovering bioactive NRPs

Open Access Repository-Scale Propagated Nearest Neighbor Suspect Spectral Library for Untargeted Metabolomics

Abstract Despite the increasing availability of tandem mass spectrometry (MS/MS) community spectral libraries for untargeted metabolomics over the past decade, the majority of acquired MS/MS spectra remain uninterpreted. To further aid in interpreting unannotated spectra, we created a nearest neighbor suspect spectral library, consisting of 87,916 annotated MS/MS spectra derived from hundreds of millions of public MS/MS spectra. Annotations were propagated based on structural relationships to reference molecules using MS/MS-based spectrum alignment. We demonstrate the broad relevance of the nearest neighbor suspect spectral library through representative examples of propagation-based annotation of acylcarnitines, bacterial and plant natural products, and drug metabolism. Our results also highlight how the library can help to better understand an Alzheimer’s brain phenotype. The nearest neighbor suspect spectral library is openly available through the GNPS platform to help investigators hypothesize candidate structures for unknown MS/MS spectra in untargeted metabolomics data

Eliciação da biossíntese de produtos naturais a partir da interação de microorganismos endofíticos

In order to continue with the study of natural products from previously isolated endophytes of the Brazilian medicinal plant Lychnophora ericoides, the main goal of this work focused on the metabolic exchange of endophytic microorganisms from this plant. As it has been demonstrated during the last years, elicitation of different molecules is consequence of microbial interactions, mainly due to the need to compete, survive and establish microbial communities in shared environments. Recent mass spectrometry related approaches, such as imaging and molecular networking, in combination with purification and structural elucidation were applied to the current study of the microbial interactions of endophytes. During this study, several chemical families were identified, such as polyene macrocycles, pyrroloindole alkaloids, leupeptins, angucyclines, siderophores, amongst others. Amongst the polyene macrocycles, the well-known antifungal amphotericin B was identified as a biosynthetic product of the endophytic actinobacteria Streptomyces albospinus RLe7. When S. albospinus RLe7 interacted with an endophytic fungus, Coniochaeta sp. FLe4, a red pigmentation was observed. A new fungal compound was detected from microbial interactions. Isolation and structure elucidation of this new compound enabled to demonstrate the elicitation of fungal secondary metabolites by amphotericin B, an actinobacterial metabolite. It was also demonstrated the elicitation of griseofulvin and its analogue dechlorogriseofulvin from another endophytic fungus, FLe9, as a consequence of exposition to amphotericin B. In addition, investigation of the chemical profile of another endophytic actinobacteria, S. mobaraensis RLe3, led to reveal this strain as angucycline-derivatives producer. Besides that, coculturing of this actinobacteria against Coniochaeta sp. FLe4 also demonstrated elicitation of angucycline analogues. In conclusion, this study demonstrated elicitation of natural products from microbial interactions as well as new compounds from endophytes from L. ericoides and contributed to the identification of microbial metabolitesCom o propósito de continuar com os estudos de produtos naturais de microorganismos endofíticos da planta medicinal Brasileira Lychnophora ericoides, o principal objetivo desse trabalho focou-se no estudo da troca metabólica de microorganismos endofíticos dessa planta. Como tem sido demonstrado durante os últimos anos, a elicitação de diferentes compostos é consequência das interações microbianas, principalmente devido à necessidade de competir, sobreviver e estabelecer comunidades microbianas em diversos ambientes naturais. Abordagens recentes de espectrometria de massas, tais como imageamento e molecular networking, junto com purificação e elucidação estrutural foram aplicadas durante o estudo de interações microbianas de endofíticos. Durante este estudo, várias classes químicas foram identificadas, tais como polienos macrocíclicos, alcaloides pirroloindólicos, leupeptinas, anguciclinas, sideróforos, entre outras. Da classe química de polienos macrocíclicos, foi identificada a anfotericina B como produto da biossíntese da actinobactéria endofítica Streptomyces albospinus RLe7. Durante a interação da S. albospinus RLe7 com o fungo endofítico Coniochaeta sp. FLe4, uma pigmentação vermelha foi observada. Um novo composto de origem fúngica foi detectado a partir de interações microbianas. O isolamento e posterior elucidação estrutural do novo composto permitiu demonstrar a eliciação de metabólitos secundários fúngicos pela anfotericina B, metabólito da actinobactéria S. albospinus RLe7. Foi também demonstrada a eliciação de griseofulvina e desclorogriseofulvina a partir de outro fungo endofítico, FLe9, como consequência da exposição à anfotericina B. Adicionalmente, a investigação do perfil químico de outra actinobactéria endofítica, S. mobaraensis RLe3, evidenciou essa linhagem como produtora de compostos da classe das anguciclinas. Além disso, o cocultivo dessa actinobacteria com o fungo endofítico Coniochaeta sp. FLe4 também eliciou análogos de anguciclinas. Em conclusão, neste estudo demonstrou-se a elicitação de produtos naturais a partir das interações microbianas assim como de novos compostos de endofíticos de L. ericoides e contribuiu-se com a identificação de metabólitos microbiano

Natural products as mediators of disease

Covering: up to 2016Humans are walking microbial ecosystems, each harboring a complex microbiome with the genetic potential to produce a vast array of natural products. Recent sequencing data suggest that our microbial inhabitants are critical for maintaining overall health. Shifts in microbial communities have been correlated to a number of diseases including infections, inflammation, cancer, and neurological disorders. Some of these clinically and diagnostically relevant phenotypes are a result of the presence of small molecules, yet we know remarkably little about their contributions to the health of individuals. Here, we review microbe-derived natural products as mediators of human disease

Propagating annotations of molecular networks using in silico fragmentation

The annotation of small molecules is one of the most challenging and important steps in untargeted mass spectrometry analysis, as most of our biological interpretations rely on structural annotations. Molecular networking has emerged as a structured way to organize and mine data from untargeted tandem mass spectrometry (MS/MS) experiments and has been widely applied to propagate annotations. However, propagation is done through manual inspection of MS/MS spectra connected in the spectral networks and is only possible when a reference library spectrum is available. One of the alternative approaches used to annotate an unknown fragmentation mass spectrum is through the use of in silico predictions. One of the challenges of in silico annotation is the uncertainty around the correct structure among the predicted candidate lists. Here we show how molecular networking can be used to improve the accuracy of in silico predictions through propagation of structural annotations, even when there is no match to a MS/MS spectrum in spectral libraries. This is accomplished through creating a network consensus of re-ranked structural candidates using the molecular network topology and structural similarity to improve in silico annotations. The Network Annotation Propagation (NAP) tool is accessible through the GNPS web-platform https://gnps.ucsd.edu/ProteoSAFe/static/gnps-theoretical.jsp.</p

Chemical interplay and complementary adaptative strategies toggle bacterial antagonism and co-existence.

Bacterial communities are in a continuous adaptive and evolutionary race for survival. In this work we expand our knowledge on the chemical interplay and specific mutations that modulate the transition from antagonism to co-existence between two plant-beneficial bacteria, Pseudomonas chlororaphis PCL1606 and Bacillus amyloliquefaciens FZB42. We reveal that the bacteriostatic activity of bacillaene produced by Bacillus relies on an interaction with the protein elongation factor FusA of P. chlororaphis and how mutations in this protein lead to tolerance to bacillaene and other protein translation inhibitors. Additionally, we describe how the unspecific tolerance of B. amyloliquefaciens to antimicrobials associated with mutations in the glycerol kinase GlpK is provoked by a decrease of Bacillus cell membrane permeability, among other pleiotropic responses. We conclude that nutrient specialization and mutations in basic biological functions are bacterial adaptive dynamics that lead to the coexistence of two primary competitive bacterial species rather than their mutual eradication

The molecular impact of life in an indoor environment

The chemistry of indoor surfaces, and the role of microbes in shaping and responding to that chemistry, are largely unexplored. We found that over one month, people’s presence and activities profoundly reshaped the chemistry of a house. Molecules associated with eating/cooking, bathroom use, and personal care were found throughout the entire house, while molecules associated with medications, outdoor biocides, and microbially-derived compounds were distributed in a location-dependent manner. The house, and its microbial occupants, in turn, also introduced chemical transformations such as oxidation and transformations of foodborne molecules. The awareness of and the ability to observe the molecular changes introduced by people should influence future building designs