Schubert, H. | Search bioRxiv

bioRxiv2017

Evaluation of Metrics for Benchmarking Antimicrobial Use in the United Kingdom Dairy Industry

The issue of antimicrobial resistance is of global concern across human and animal health. In 2016 the UK government committed to new targets for reducing antimicrobial use (AMU) in livestock. However, though a number of metrics for quantifying AMU are defined in the literature, all give slightly different interpretations.\n\nThis paper reviews a selection of metrics for AMU in the dairy industry: total mg, total mg/kg, daily dose and daily course metrics. Although the focus is on their application to the dairy industry, the metrics and issues discussed are relevant across livestock sectors.\n\nIn order to be used widely, a metric should be understandable and relevant to the veterinarians and farmers who are prescribing and using antimicrobials. This means that clear methods, assumptions (and possible biases), standardised values and exceptions should be published for all metrics. Particularly relevant are assumptions around the number and weight of cattle at risk of treatment and definitions of dose rates and course lengths; incorrect assumptions can mean metrics over- or under-represent AMU.\n\nThe authors recommend that the UK dairy industry work towards UK-specific metrics using UK-specific medicine dose and course regimens as well as cattle weights in order to monitor trends nationally.

epidemiology↗

bioRxiv2017

Eelgrass leaf surface microbiomes are locally variable and highlycorrelated with epibiotic eukaryotes

Eelgrass (Zostera marina) is a marine foundation species essential for coastal ecosystem services around the northern hemisphere. Like all macroscopic organisms, it possesses a microbiome which may play critical roles in modulating the interaction of eelgrass with its environment. For example, its leaf surface microbiome could inhibit or attract eukaryotic epibionts which may overgrow the eelgrass leading to reduced primary productivity and subsequent eelgrass meadow decline. We used amplicon sequencing of the 16S and 18S rRNA genes of prokaryotes and eukaryotes to assess the leaf surface microbiome (prokaryotes) as well as eukaryotic epibionts in-and outside lagoons on the German Baltic Sea coast. Bacterial microbiomes varied substantially both between sites inside lagoons and between open coastal and lagoon sites. Water depth, leaf area and biofilm chlorophyll a concentration explained a large amount of variation in both bacterial and eukaryotic community composition. Communities of bacterial and eukaryotic epibionts were highly correlated, and network analysis revealed disproportionate co-occurrence between a limited number of eukaryotic taxa and several bacterial taxa. This suggests that eelgrass leaf surface biofilms are a mosaic of the microbiomes of several eukaryotes, in addition to that of the eelgrass itself, and underlines that eukaryotic microbial diversity should be taken into account in order to explain microbiome assembly and dynamics in aquatic environments.

microbiology↗