Biology subjects

Gilfillan, G. D.

Publications and source records attributed to Gilfillan, G. D..

5 recordsLinked to original sources

bioRxiv2025

Longitudinal analysis of the hand microbiome in response to chlorine-based antiseptic use during a military field exercise

Hand hygiene is essential for infection control, yet the impact of frequent antiseptic use on the skin microbiome, which is crucial for skin barrier function and pathogen exclusion, remains underexplored, especially in field conditions. In high-risk military settings, there is a need for safe, multipurpose antiseptics that avoid the drawbacks of alcohol-based options, including skin irritation, flammability, and unsuitability for wound application. We conducted a longitudinal study during the Norwegian-led military exercise Cold Response 2022 to assess the effects of repeated use of stabilized hypochlorous acid, a non-alcoholic antiseptic, on the hand microbiome of soldiers in a field environment. Participants used either the chlorine-based antiseptic (n = 20) or standard hygiene practices, mainly alcohol-based sanitizers (n = 19), for 10 days. Skin swabs from hands and untreated forearms were collected at baseline, post-intervention, and three weeks after discontinuation, and analyzed using 16S rRNA sequencing. Overall, our data revealed that field exposure accounted for more variation in bacterial composition than antiseptic use. When comparing alpha and beta diversity trajectories between the two antiseptic groups, there was minimal divergence during active field use, but a significant post-treatment increase in alpha diversity associated with the use of chlorine-based antiseptic. In contrast, untreated forearms showed no such group-level differences. These findings suggest that antiseptic-driven microbiome shifts are most apparent during recovery, with non-alcoholic formulations supporting faster recolonization after treatment. Stabilized hypochlorous acid represents a promising alternative to standard alcohol-based antiseptics for military personnel. IMPORTANCEEffective hand hygiene reduces pathogen transmission, but its influence on the skin microbiome has rarely been studied. Our research emphasizes the importance of longitudinal assessments by identifying greater antiseptic-driven differences occurring after cessation of treatment than during repeated use. Service members frequently use antiseptics in challenging environments, highlighting the operational need for a non-alcoholic, multipurpose product that can be safely used on both intact skin and wounds. Our findings suggest that a chlorine-based non-alcoholic antiseptic permits faster recovery of bacterial diversity after perturbation, informing product selection and hygiene policies in defense and other high-risk settings.

microbiology↗

bioRxiv2020

An extension to: Systematic assessment of commercially available low-input miRNA library preparation kits

High-throughput sequencing has emerged as the favoured method to study microRNA (miRNA) expression, but biases introduced during library preparation have been reported. To assist researchers choose the most appropriate library preparation kit, we recently compared the performance of six commercially-available kits on synthetic miRNAs and human RNA, where library preparation was performed by the vendors. We hereby supplement this study with data from two further commonly used kits (NEBNext, NEXTflex) whose manufacturers initially declined to participate. As before, performance was assessed with respect to sensitivity, reliability, titration response and differential expression. Despite NEXTflex employing partially-randomised adapter sequences to minimise bias, we reaffirm that biases in miRNA abundance are kit-specific, complicating the comparison of miRNA datasets generated using different kits.

molecular biology↗

bioRxiv2019

Systematic assessment of commercially available low-input miRNA library preparation kits

High-throughput sequencing is increasingly favoured to assay the presence and abundance of micro RNAs (miRNAs) in biological samples, even from low RNA amounts, and a number of commercial vendors now offer kits that allow miRNA sequencing from sub-nanogram (ng) inputs. However, although biases introduced during library preparation have been documented, the relative performance of current reagent kits has not been investigated in detail. Here, six commercial kits capable of handling <100ng total RNA input were used for library preparation, performed by kit manufactures, on synthetic miRNAs of known quantities and human biological total RNA samples. We compared the performance of miRNA detection sensitivity, reliability, titration response and the ability to detect differentially expressed miRNAs. In addition, we assessed the use of unique molecular identifiers sequence (UMI) tags in one kit. We observed differences in detection sensitivity and ability to identify differentially expressed miRNAs between the kits, but none were able to detect the full repertoire of expected miRNAs. The reliability within the replicates of all kits was good, while larger differences were observed between the kits, although none could accurately quantify the majority of miRNAs. UMI tags, at least within the input ranges tested, offered little advantage to improve data utility. In conclusion, biases in miRNA abundance are heavily influenced by the kit used for library preparation, suggesting that comparisons of datasets prepared by different procedures should be made with caution. This article is intended to assist researchers select the most appropriate kit for their experimental conditions.

bioinformatics↗

bioRxiv2019

Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2.

Pioneer transcription factors (PTF) can recognize their binding sites on nucleosomal DNA and trigger chromatin opening for recruitment of other non-pioneer transcription factors. However, critical properties of PTFs are still poorly understood, such as how these transcription factors selectively recognize cell type-specific binding sites and under which conditions can they can initiate chromatin remodelling. Here we show that early endoderm binding sites of the paradigm PTF Foxa2 are epigenetically primed by low levels of active chromatin modifications in embryonic stem cells (ESC). Priming of these binding sites is supported by preferential recruitment of Foxa2 to endoderm binding sites compared to lineage-inappropriate binding sites, when ectopically expressed in ESCs. We further show that binding of Foxa2 is required for chromatin opening during endoderm differentiation. However, increased chromatin accessibility was only detected on binding sites which are synergistically bound with other endoderm transcription factors. Thus, our data suggest that binding site selection of PTFs is directed by the chromatin environment and that chromatin opening requires collaboration of PTFs with additional transcription factors.

genomics↗

bioRxiv2017

A Novel Ultra High-Throughput 16S rRNA Amplicon Sequencing Library Preparation Method On The Illumina HiSeq Platform

BackgroundAdvances in sequencing technologies and bioinformatics have made the analysis of microbial communities almost routine. Nonetheless, the need remains to improve on the techniques used for gathering such data, including increasing throughput while lowering cost, and benchmarking the techniques so that potential sources of bias can be better characterized.\n\nResultsWe present a triple-index amplicon sequencing strategy that uses a two-stage PCR protocol. The strategy was extensively benchmarked through analysis of a mock community in order to assess biases introduced by sample indexing, number of PCR cycles, and template concentration. We further evaluated the method through re-sequencing of a standardized environmental sample. Finally, we evaluated our protocol on a set of fecal samples from a small cohort of healthy adults, demonstrating good performance in a realistic experimental setting. Between-sample variation was mainly related to batch effects, such as DNA extraction, while sample indexing was also a significant source of bias. PCR cycle number strongly influenced chimera formation and affected relative abundance estimates of species with high GC content. Libraries were sequenced using the Illumina HiSeq and MiSeq platforms to demonstrate that this protocol is highly scalable to sequence thousands of samples at a very low cost.\n\nConclusionsHere, we provide the most comprehensive study of performance and bias inherent to a 16S rRNA gene amplicon sequencing method to date. Triple-indexing greatly reduces the number of long custom DNA oligos required for library preparation, while the inclusion of variable length heterogeneity spacers minimizes the need for PhiX spike-in. This design results in a significant cost reduction of highly multiplexed amplicon sequencing. The biases we characterize highlight the need for highly standardized protocols. Reassuringly, we find that the biological signal is a far stronger structuring factor than the various sources of bias.

microbiology↗