Biology subjects

Savva, G.

Publications and source records attributed to Savva, G..

3 recordsLinked to original sources

bioRxiv2020

Tape lures swell bycatch on a Mediterranean island harbouring illegal bird trapping

Mediterranean islands are critical for migrating birds, providing shelter and sustenance for millions of individuals each year. Humans have long exploited bird migration through hunting and illegal trapping. On the island of Cyprus, trapping birds during their migratory peak is considered a local tradition, but has long been against the law. Illegal bird trapping is a lucrative business, however, with trappers using tape lures that broadcast species’ vocalizations because it is expected to increase numbers of target species. Yet, by how much the use of song playback increases capture rates remains underappreciated. In particular, it is not known whether song playback of target species affects bycatch rates. Here, we show with the use of playback experiments that song playback is highly effective in luring birds towards trapping sites. We found that playback increases six to eight times the number of individuals of target species captured, but also significantly increases bycatch. Our findings thus show that in contrast to popular belief that tape lures are a selective trapping method, they also lead to increased captures of non-target species, which can include species of conservation concern.View Full Text

zoology↗

bioRxiv2019

AlbaTraDIS: Comparative analysis of large datasets from parallel transposon mutagenesis experiments

BackgroundBacteria have evolved over billions of years to survive in a wide range of environments. Currently, there is an incomplete understanding of the genetic basis for mechanisms underpinning survival in stressful conditions, such as the presence of anti-microbials. Transposon mutagenesis has been proven to be a powerful tool to identify genes and networks which are involved in survival and fitness under a given condition by simultaneously assaying the fitness of millions of mutants, thereby relating genotype to phenotype and contributing to an understanding of bacterial cell biology. A recent refinement of this approach allows the roles of essential genes in conditional stress survival to be inferred by altering their expression. These advancements combined with the rapidly falling costs of sequencing now allows comparisons between multiple experiments to identify commonalities in stress responses to different conditions. This capacity however poses a new challenge for analysis of multiple data sets in conjunction.\n\nResultsTo address this analysis need, we have developed AlbaTraDIS; a software application for rapid large-scale comparative analysis of TraDIS experiments that predicts the impact of transposon insertions on nearby genes. AlbaTraDIS can identify genes which are up or down regulated, or inactivated, between multiple conditions, producing a filtered list of genes for further experimental validation as well as several accompanying data visualisations. We demonstrate the utility of our new approach by applying it to identify genes used by Escherichia coli to survive in a wide range of different concentrations of the biocide Triclosan. AlbaTraDIS automatically identified all well characterised Triclosan resistance genes, including the primary target, fabI. A number of new loci were also implicated in Triclosan resistance and the predicted phenotypes for a selection of these were validated experimentally and results showed high consistency with predictions.\n\nConclusionsAlbaTraDIS provides a simple and rapid method to analyse multiple transposon mutagenesis data sets allowing this technology to be used at large scale. To our knowledge this is the only tool currently available that can perform these tasks. AlbaTraDIS is written in Python 3 and is available under the open source licence GNU GPL 3 from https://github.com/quadram-institute-bioscience/albatradis.

bioinformatics↗

bioRxiv2019

Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients

BackgroundFor long-stay patients on the adult intensive care unit, the gut microbiota plays a key role in determining the balance between health and disease. However, it remains unclear which ICU patients might benefit from interventions targeting the gut microbiota or the pathogens therein.\n\nMethodsWe undertook a prospective observational study of twenty-four ICU patients, in which serial faecal samples were subjected to shotgun metagenomic sequencing, phylogenetic profiling and microbial genome analyses.\n\nResultsTwo-thirds of patients experienced a marked drop in gut microbial diversity (to an inverse Simpsons index of <4) at some stage during their stay in ICU, often accompanied by absence or loss of beneficial commensal bacteria. Intravenous administration of the broad-spectrum antimicrobial agent meropenem was significantly associated with loss of gut microbial diversity, but administration of other antibiotics, including piperacillin-tazobactam, failed to trigger statistically detectable changes in microbial diversity. In three quarters of ICU patients, we documented episodes of gut domination by pathogenic strains, with evidence of cryptic nosocomial transmission of Enterococcus faecium. In some patients we also saw domination of the gut microbiota by commensal organisms, such as Methanobrevibacter smithii.\n\nConclusionsOur results support a role for metagenomic surveillance of the gut microbiota and pave the way for patient-specific interventions that maintain or restore gut microbial diversity in the ICU.

microbiology↗