Biology subjects

Williamson, E.

Publications and source records attributed to Williamson, E..

4 recordsLinked to original sources

bioRxiv2024

Blanking on Blanks: Few Insect Microbiota Studies Control for Contaminants - A Systematic Review

Research on insect-microbe relationships is booming, with DNA sequencing being the most commonly used method to describe insect microbiota. However, sequencing is vulnerable to contamination, especially when the sample has low microbial biomass. Such low-biomass samples are common across insect taxa, developmental stages, and tissue types. Identifying putative contaminants is essential to distinguish between true microbiota and introduced contaminant DNA. It is therefore important that studies control for contamination, but how often this is done is unknown. To investigate the status quo of contamination control, we undertook a systematic literature review to quantify the prevalence of negative control usage and contamination control across the literature on insect microbiota (specifically bacterial communities) over the past 20 years. Two-thirds of the 243 insect microbiota studies evaluated did not include blanks (negative controls), and only 13.6% of the studies sequenced these blanks to control for contamination in their samples. Our findings highlight a major lack of contamination control in the field of insect microbiota research. This result suggests that a large number of microbes reported in the literature may be contaminants as opposed to insect-associated microbiota, and that more rigorous contamination control is needed to improve research reliability, validity and reproducibility. Based on our findings, we recommend a modified version of the guidelines outlined in the RIDES checklist: Report methodology, Include negative controls, Determine the level of contamination, Explore contamination downstream, and State the amount of off-target amplification. IMPORTANCEOur systematic review reveals a major lack of methodological rigour within the field of research on insect-associated microbiota. The small percentage of studies that control for contamination suggests that a considerable proportion of bacteria reported in the literature could be contaminants. The implication of this finding is that true microbiota may be masked or misrepresented, especially in insects with low microbial biomass.

microbiology↗

bioRxiv2022

A cross-sectional study of the commercial plant-based landscape across the US, UK and Canada.

As plant-based foods comprise an ever-increasing proportion of the diet, understanding the nutritional composition of these products is critical. In this study we assess the nutritional content of all commercial plant-based products across multiple sectors (supermarkets, fast food & sit down restaurants, food delivery companies and manufacturers) in the US, UK and Canada. We identified 3488 unique products. Across all sectors, 45% of main meals had >15g protein, 60% had <10%kcal from saturated fat; 29% had >10g fibre per meal; 86% had <1000mg sodium. At restaurants, meat-based main meals were significantly higher in protein and sodium compared to vegetarian and vegan meals. The meat-based options were also significantly higher in saturated fat than the vegan but not vegetarian options. We conclude that plant-based items tend to be lower in saturated fat and sodium than their meat-based counterparts but improvements are needed to optimise their nutritional composition.

scientific communication and education↗

bioRxiv2020

DNA methylation covariation in human whole blood and sperm: implications for studies of intergenerational epigenetic effects

BackgroundEpidemiological studies suggest that paternal obesity may increase the risk of fathering small for gestational age offspring. Studies in non-human mammals suggest that such associations could be mediated by DNA methylation changes in spermatozoa that influence offspring development in utero. Human obesity is associated with differential DNA methylation in peripheral blood. It is unclear, however, whether this differential DNA methylation is reflected in spermatozoa. We profiled genome-wide DNA methylation using the Illumina MethylationEPIC array in matched human blood and sperm from lean (discovery n=47; replication n=21) and obese (n=22) males to analyse tissue covariation of DNA methylation, and identify whether this covariation is influenced by obesity. ResultsDNA methylation signatures of human blood and spermatozoa are highly discordant, and methylation levels are correlated at only a minority of CpG sites ([~]1%). While at the majority of these sites, DNA methylation appears to be influenced by genetic variation, obesity-associated DNA methylation in blood was not generally reflected in spermatozoa, and obesity did not influence covariation patterns. However, one cross-tissue obesity-specific hypermethylated site (cg19357369; chr4:2429884; P=8.95 x 10-8; beta=0.02) was identified, warranting replication and further investigation. When compared to a wide range of human somatic tissue samples (n=5,917), spermatozoa displayed differential DNA methylation in pathways enriched in transcriptional regulation. ConclusionsHuman sperm displays a unique DNA methylation profile that is highly discordant to, and practically uncorrelated with, that of matched peripheral blood. Obesity only nominally influences sperm DNA methylation, making it an unlikely mediator of intergenerational effects of metabolic traits.

genomics↗

bioRxiv2019

Evaluating a digital sepsis alert in a London multi-site hospital network: a natural experiment using electronic health record data

ObjectiveTo determine the impact of a digital sepsis alert on patient outcomes in a UK multi-site hospital network.\n\nMethodsA natural experiment utlising the phased introduction of a digital sepsis alert into a multi-site hospital network. Sepsis alerts were either visible to clinicans (the intervention group) or running silently and not visible (the control group). Inverse probability of treatment weighted multivariable logistic regression was used to estimate the effect of the intervention on patient outcomes.\n\nOutcomes: In-hospital 30-day mortality (all inpatients), prolonged hospital stay ([≥]7 days) and timely antibiotics ([≤]60 minutes of the alert) for patients who alerted in the Emergency Department.\n\nResultsThe introduction of the alert was associated with lower odds of death (OR:0.76; 95%CI:(0.70, 0.84) n=21,183); lower odds of prolonged hospital stay [≥]7 days (OR:0.93; 95%CI:(0.88, 0.99) n=9988); and in patients who required antibiotics, an increased odds of receiving timely antibiotics (OR:1.71; 95%CI:(1.57,1.87) n=4622).\n\nDiscussionCurrent evidence that digital sepsis alerts are effective is mixed. In this large UK study a digital sepsis alert has been shown to be associated with improved outcomes, including timely antibiotics, which may suggest a causal pathway. It is not known whether the presence of alerting is responsible for improved outcomes, or whether the alert acted as a useful driver for quality improvement initiatives.\n\nConclusionsThese findings strongly suggest that the the introduction of a network-wide digital sepsis alert is associated with improvements in patient outcomes, demonstrating that digital based interventions can be successfully introduced and readily evaluated.\n\nFundingImperial NIHR Biomedical Research Centre: NIHR-BRC-P68711.

epidemiology↗