The Natural Products Atlas 2.0: a database of microbially-derived natural products

Within the natural products field there is an increasing emphasis on the study of compounds from microbial sources. This has been fuelled by interest in the central role that microorganisms play in mediating both interspecies interactions and host-microbe relationships. To support the study of natural products chemistry produced by microorganisms we released the Natural Products Atlas, a database of known microbial natural products structures, in 2019. This paper reports the release of a new version of the database which includes a full RESTful application programming interface (API), a new website framework, and an expanded database that includes 8128 new compounds, bringing the total to 32 552. In addition to these structural and content changes we have added full taxonomic descriptions for all microbial taxa and have added chemical ontology terms from both NP Classifier and ClassyFire. We have also performed manual curation to review all entries with incomplete configurational assignments and have integrated data from external resources, including CyanoMetDB. Finally, we have improved the user experience by updating the Overview dashboard and creating a dashboard for taxonomic origin. The database can be accessed via the new interactive website at https://www.npatlas.org.

Arterial stiffness increase from adolescence to young adulthood is accelerated by smoking and alcohol use

Background

Smoking tobacco and drinking alcohol are associated with increased arterial stiffness, a critical intermediate endpoint for cardiovascular disease, in adults and in teenagers. The relationship between these risky behaviours and changes in arterial stiffness from late adolescence to early adulthood is not known.

Purpose

To investigate associations between smoking and drinking habits and the change in arterial stiffness between ages 17 and 24 using a large population-based cohort.

Methods

Participants underwent repeated measurements of arterial stiffness (carotid-femoral pulse wave velocity (cfPWV)), anthropometrics, resting blood pressure and blood biomarkers, at ages 17 and 24 years. Participants were grouped and scored by alcohol (never, medium intensity (MI): ≤4 drinks on a typical day of drinking, high intensity (HI): >5) and smoking (never, past, MI, <10 cigarettes a day HI, ≥10) exposure at both clinics. Average scores between clinics were taken (scores 0–5) and composite alcohol (never, MI, HI) and smoking (never, past, MI, HI) groups were created. Multivariable regression analysis was performed to investigate associations between smoking/drinking habits and change in cfPWV from 17 to 24 years (ΔPWV). Associations were adjusted for age, gender, and socioeconomic status (model 1). Model 2 was additionally adjusted for body mass index, systolic blood pressure, LDL cholesterol, glucose, and C-reactive protein at age 24. Data are presented as means (95% confidence intervals).

Results

1,655 participants (1,013 females and 642 males) had cfPWV recorded at both ages. cfPWV increased from 17 to 24 years in both women (ΔPWV 0.56m/s (0.50, 0.62), p<0.001) and men (0.65m/s (0.56, 0.74), p<0.001). There was a 0.05m/s (0.00, 0.10) increase in ΔPWV per 1 unit increase in average alcohol score (p=0.039). Compared to never drinkers, ΔPWV increased by 0.18m/s (−0.03, 0.38) in MI (p=0.09), and 0.21m/s (−0.01, 0.41) in HI drinkers (p=0.055). There was no association between ΔPWV and average smoking score (β=0.03m/s (−0.03, 0.08), p=0.4). Compared to never smokers, HI smokers had a slightly greater ΔPWV (0.17m/s (−0.08, 0.42), p=0.18). After stratifying by sex, this difference was evident in women (0.32m/s (0.04, 0.60), p=0.028) while no association was seen in men (−0.12m/s (−0.59, 0.35), p=0.6). No differences were found between never-smokers and ex-smokers (difference = 0.04m/s (−0.08, 0.16), p=0.5). Adjustment for potential confounders (model 2) did not attenuate these associations. Figure shows estimated marginal means for ΔPWV between (a) alcohol and (b) smoking groups from model 1. Error bars represent 95% confidence intervals.

Conclusion

Smoking and alcohol use in young adulthood is associated with an accelerated increase in arterial stiffness, with evidence of a graded adverse association for alcohol. Our findings also suggest that adverse effects of smoking in youth may be reversible with smoking cessation.

Funding Acknowledgement

Type of funding sources: Foundation. Main funding source(s): British Heart Foundation

Comparative Metabologenomics Analysis of Polar Actinomycetes

Biosynthetic and chemical datasets are the two major pillars for microbial drug discovery in the omics era. Despite the advancement of analysis tools and platforms for multi-strain metabolomics and genomics, linking these information sources remains a considerable bottleneck in strain prioritisation and natural product discovery. In this study, molecular networking of the 100 metabolite extracts derived from applying the OSMAC approach to 25 Polar bacterial strains, showed growth media specificity and potential chemical novelty was suggested. Moreover, the metabolite extracts were screened for antibacterial activity and promising selective bioactivity against drug-persistent pathogens such as Klebsiella pneumoniae and Acinetobacter baumannii was observed. Genome sequencing data were combined with metabolomics experiments in the recently developed computational approach, NPLinker, which was used to link BGC and molecular features to prioritise strains for further investigation based on biosynthetic and chemical information. Herein, we putatively identified the known metabolites ectoine and chrloramphenicol which, through NPLinker, were linked to their associated BGCs. The metabologenomics approach followed in this study can potentially be applied to any large microbial datasets for accelerating the discovery of new (bioactive) specialised metabolites.

The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery

Despite rapid evolution in the area of microbial natural products chemistry, there is currently no open access database containing all microbially produced natural product structures. Lack of availability of these data is preventing the implementation of new technologies in natural products science. Specifically, development of new computational strategies for compound characterization and identification are being hampered by the lack of a comprehensive database of known compounds against which to compare experimental data. The creation of an open access, community-maintained database of microbial natural product structures would enable the development of new technologies in natural products discovery and improve the interoperability of existing natural products data resources. However, these data are spread unevenly throughout the historical scientific literature, including both journal articles and international patents. These documents have no standard format, are often not digitized as machine readable text, and are not publicly available. Further, none of these documents have associated structure files (e.g., MOL, InChI, or SMILES), instead containing images of structures. This makes extraction and formatting of relevant natural products data a formidable challenge. Using a combination of manual curation and automated data mining approaches we have created a database of microbial natural products (The Natural Products Atlas, www.npatlas.org) that includes 24 594 compounds and contains referenced data for structure, compound names, source organisms, isolation references, total syntheses, and instances of structural reassignment. This database is accompanied by an interactive web portal that permits searching by structure, substructure, and physical properties. The Web site also provides mechanisms for visualizing natural products chemical space and dashboards for displaying author and discovery timeline data. These interactive tools offer a powerful knowledge base for natural products discovery with a central interface for structure and property-based searching and presents new viewpoints on structural diversity in natural products. The Natural Products Atlas has been developed under FAIR principles (Findable, Accessible, Interoperable, and Reusable) and is integrated with other emerging natural product databases, including the Minimum Information About a Biosynthetic Gene Cluster (MIBiG) repository, and the Global Natural Products Social Molecular Networking (GNPS) platform. It is designed as a community-supported resource to provide a central repository for known natural product structures from microorganisms and is the first comprehensive, open access resource of this type. It is expected that the Natural Products Atlas will enable the development of new natural products discovery modalities and accelerate the process of structural characterization for complex natural products libraries.

The effect of phosphate, sodium chloride, sodium nitrite, storage temperature and pH on the growth of enteropathogenic Escherichia coli in a laboratory medium

The effect of eight phosphates in combination with sodium chloride/nitrite mixtures on growth of mixed strains of enteropathogenic Escherichia coli over a period of 10 weeks at three pH values (5.6, 6.2, 6.8) and at seven temperatures ranging from 10 degrees C to 35 degrees C is reported. All eight phosphates inhibited growth to varying degrees in at least some of the conditions investigated. Instances of inhibition increased with concentration of sodium chloride/nitrite and were more frequent at lower temperatures and pH values.

The function of teichoic acids in cation control in bacterial membranes

1. The effects of teichoic acids on the Mg(2+)-requirement of some membrane-bound enzymes in cell preparations from Bacillus licheniformis A.T.C.C. 9945 were examined. 2. The biosynthesis of the wall polymers poly(glycerol phosphate glucose) and poly(glycerol phosphate) by membrane-bound enzymes is strongly dependent on Mg(2+), showing maximum activity at 10-15mm-Mg(2+). 3. When the membrane is in close contact with the cell wall and membrane teichoic acid, the enzyme systems are insensitive to added Mg(2+). The membrane appears to interact preferentially with the constant concentration of Mg(2+) that is bound to the phosphate groups of teichoic acid in the wall and on the membrane. When the wall is removed by the action of lysozyme the enzymes again become dependent on an external supply of Mg(2+). 4. A membrane preparation that retained its membrane teichoic acid was still dependent on Mg(2+) in solution, but the dependence was damped so that the enzymes exhibited near-maximal activity over a much greater range of concentrations of added Mg(2+); this preparation contained Mg(2+) bound to the membrane teichoic acid. The behaviour of this preparation could be reproduced by binding membrane teichoic acid to membranes in the presence of Mg(2+). Addition of membrane teichoic acid to reaction mixtures also had a damping effect on the Mg(2+) requirement of the enzymes, since the added polymer interacted rapidly with the membrane. 5. Other phosphate polymers behaved in a qualitatively similar way to membrane teichoic acid on addition to reaction mixtures. 6. It is concluded that in whole cells the ordered array of anionic wall and membrane teichoic acids provides a constant reservoir of bound bivalent cations with which the membrane preferentially interacts. The membrane teichoic acid is the component of the system which mediates the interaction of bound cations with the membrane. The anionic polymers in the wall scavenge cations from the medium and maintain a constant environment for the membrane teichoic acid. Thus a function of wall and membrane teichoic acids is to maintain the correct ionic environment for cation-dependent membrane systems.