Prospecting Novel Microbiomes for Antibiotic Compounds using Metagenomics and Genome Mining

There has been a void in the discovery and development of new antibiotic classes over the past four decades due, in part, to the traditional bioprospecting pipeline becoming inefficient from high compound rediscovery rates and high costs. The need for new antibiotic classes is urgent as antimicrobial drug resistant infections are now a major public health concern. Strategies such as exploring novel environments, use of next-generation sequencing, and metagenomics may reduce rediscovery rates and costs which could help accelerate lead discovery and encourage greater participation in bioprospecting. Whole genome-sequencing and analysis was used to characterise four bacterial strains (Y1-4) isolated from raw honey that were shown to have antibiotic activity. The isolates were identified as Bacillus and were closely related but distinctive strains with variations amongst their secondary metabolite profiles. All isolates contained a gene cluster homologous to AS- 48, a circular bacteriocin produced by Enterococcus faecalis, which has broad-spectrum antibiotic activity. To date, no example of this bacteriocin has been reported in Bacillus. This work demonstrated the value of whole-microbial genome sequencing for dereplication. A pipeline for the low-cost sequencing and assembly of bacterial genomes using Oxford Nanopore MinION was developed in order to produce contiguous and accurate genome assemblies for taxonomic and bioprospecting analysis. The pipeline developed used a combination of Nanopore draft assembly by Canu and polishing with RACON and Nanopolish, with final polishing with Illumina reads using Pilon. The Nanopore-only assembly of Streptomyces coelicolor A3(2) produced was contiguous and covered 98.9 % of reference. AntiSMASH analysis identified the full secondary metabolite profile of the genome through homology searches. However, indel rates were high (66.82 per 100 kbp) causing fragmented gene annotations which limited secondary metabolite structure prediction. Illumina read polishing reduced indels (2.03 per 100 kbp) and enabled accurate structure prediction from the identified biosynthetic pathways. This demonstrates that Nanopore sequencing can provide a viable dereplication strategy by detection of known biosynthetic pathways. Additionally, supplementation with Illumina sequencing can allow for structure prediction of biosynthetic pathways which could inform chemical extraction strategies for novel pathways. Nanopore sequencing was further utilised to characterise an antibiotic producing isolate (KB16) active against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus from the hot spring of the Roman Baths, UK. Genomic analysis showed KB16 to be highly related to Streptomyces canus and to contain 26 putative secondary metabolite gene clusters - some of which were potentially novel. One of the gene clusters was identified as encoding the antibiotic albaflavenone. Attempts to chemically identify the antibiotic produced by KB16 showed that it may produce multiple antimicrobial compounds. These findings demonstrate the value in prospecting underexplored environments such as the Roman Baths for microbially-derived antimicrobial leads. A PCR screen was used to amplify NRPS and PKS gene fragments from a human oral metagenome. Analysis of the fragments suggested that some are from uncharacterised gene clusters. Nanopore shotgun metagenomic sequencing was used to profile the water of the Roman Baths which revealed a diverse microbiome of species with reported metabolic characteristics that are in keeping with the known geochemistry of the waters and aligned with 16S rRNA analysis. Further analysis also identified putative heavy metal resistance genes which can be a co-marker for their metabolism and aligned with the chemical properties of the water. These findings demonstrate the potential value in these sites for bioprospecting whilst also giving insight that can inform bioprospecting strategies. The investigations also highlight the utility of Nanopore sequencing for taxonomic and functional gene profiling of environmental microbiomes. In combination these findings have all contributed information on novel environments, potential isolate leads, and cost-efficient methodologies to accelerate the discovery of microbially-derived antibiotics

Community benefits or community bribes?:An experimental analysis of strategies for managing community perceptions of bribery surrounding the siting of renewable energy projects

The provision of financial incentives to local communities by energy developers has attracted cynicism across many localities, with some suggesting such community benefits are akin to “bribery.” The current study used an experimental design embedded within a community postal survey to explore whether potentially damaging effects of bribery rhetoric upon local support for a wind farm can be overcome through (a) portraying community benefits as a policy requirement (rather than a discretionary gesture by developers), and/or (b) the deployment of different discursive strategies by developers to manage their stake in the outcome of the project. Participants told about community benefits as being a policy requirement showed significantly higher support for the wind farm, an effect that was mediated by heightened perceptions of individually and collectively favorable outcomes from the development. We discuss our results in relation to their implications for government policy approaches to promoting renewable energy supply

Rapid Implementation of a Novel Embedded Senior Medical Student Program, as a Response to the Educational Challenges of COVID-19

As with many OECD countries, graduating medical students have been choosing specialist careers at a greater rate than ever before. Generalism in the form of family (general practice) and more generalist medical specialties have been trending down resulting in distributional geographic challenges. With the advent of COVID-19 in March 2020, medical schools and in particular the Joint Medical Program situated in a regional and rural area in NSW Australia had the unique opportunity to rethink the penultimate year curriculum when the previous rapid rotation model through numerous medical specialities became untenable. The need to vision a new practical pragmatic curriculum spurred a rapid revaluation of assessment, placement length and model with a pivot to an “embedded senior student placement” agnostic of discipline and supported by a competency-based learning portfolio. This article explores the barriers and enablers and identifies the potential elements of this type of placement which can be adapted to community and smaller rural sites. The positive student and supervisor experience also enabled an employment model to be woven into the students learning and ensured on hand medical student workforce for hospitals throughout the rural footprint. The capacity of these placements to celebrate variation in experience and support students to learn on the job have now caused a revision of the penultimate year with expectation of gains in students’ satisfaction and in employability. It has also opened up options to deliver and increase the inherent value of generalist placements with likely long term workforce benefit

Are three contact efforts really reflective of a repeated high-intensity effort bout?

The use of 3 or more efforts (running and contact), separated by short recovery periods, is widely used to define a 'repeated high-intensity effort' (RHIE) bout in rugby league. It has been suggested that due to fatigue, players become less effective after RHIE bouts; however, there is little evidence to support this. This study determined whether physical performance is reduced after performing 1, 2, or 3 efforts with minimal recovery. Twelve semiprofessional rugby league players (age: 24.5 ± 2.9 years) competed in 3 'off-side' small-sided games (2 × 10-minute halves) with a contact bout performed every 2 minutes. The rules of each game were identical except for the number of contact efforts performed in each bout. Players performed 1, 2, or 3 × 5-second wrestling bouts in the single-, double- and triple-contact game, respectively. Movement demands of each game were monitored using global positioning system units. From the first to the second half, there were trivial reductions in relative distance during the single-contact game (ES -0.13 ± 0.12), small reductions during the double-contact game (ES -0.47 ± 0.24), and moderate reductions during the triple-contact game (ES -0.74 ± 0.27). These data show that running intensity is progressively reduced as the number of contact efforts per bout is increased. Targeting defensive players and forcing them to perform 2 or more consecutive contact efforts is likely to lead to greater reductions in running intensity. Conditioning performing multiple contact efforts while maintaining running intensity should therefore be incorporated into training for contact team sports