Biology subjects

Jones, L. B.

Publications and source records attributed to Jones, L. B..

3 recordsLinked to original sources

bioRxiv2026

NAP: an open-source pipeline for cross-domain microbiome profiling using Nanopore sequencing-derived amplicon data

BackgroundNanopore sequencing offers a cost-effective and portable platform for microbiome analysis, but amplicon-based approaches remain limited by higher sequencing error rates and a lack of workflows tailored to mixed domain ribosomal RNA profiling. While short-read technologies dominate microbial community analysis, their portability and flexibility are constrained. There is therefore a need for robust pipelines designed specifically for cross-domain Nanopore amplicon data. ResultsWe introduce the Nanopore sequencing-based Amplicon Pipeline (NAP; https://github.com/Luke-B-Jones/NAP), an open-source workflow optimised for flexible mixed domain primer sets such as 515Y/926R. NAP performs adaptive quality filtering, chimera removal, centroid generation, BLAST-based taxonomic classification, hierarchical consensus correction, and domain-aware post-processing, outputting decontaminated abundance tables suitable for downstream analysis. Initial validation against two complementary commercial mock communities showed that NAP achieved strong genus-level performance across both low complexity logarithmic and more compositionally complex gut mock communities. Detection was most reliable above ca. 1% relative abundance, and replicate outputs showed strong agreement with expected composition under Bray-Curtis, Jaccard, agreement-plot, and Bland-Altman analyses. Benchmarking of NAPs internal filtering modes showed that the default adaptive setting provided the most robust balance of read quality, retained depth, and downstream taxonomic fidelity across heterogeneous inputs. Direct comparison against QIIME2 and Kraken2/Bracken further showed that NAP most accurately preserved expected community structure, with markedly fewer false positive assignments at genus level and substantially stronger species-level behaviour under the tested conditions. Species-level assignments were informative for some taxa, but remained less robust than genus-level outputs with the default V4-V5 amplicon. ConclusionsNAP provides a robust and flexible workflow for cross-domain Nanopore amplicon profiling, with strongest performance at genus level and competitive species-level behaviour for well resolved taxa. Although analysis of field-derived data was not assessed here, NAP compatibility with portable Nanopore sequencing supports accurate mixed domain microbiome profiling under the tested conditions.

bioinformatics↗

bioRxiv2026

Stress-induced DNA methylome plasticity and transcriptional re-programming in Staphylococcus aureus

Staphylococcus aureus, a major human and livestock pathogen, is the second biggest cause of antimicrobial resistance-associated mortality. Although S. aureus transcriptional regulation has been extensively characterised, the potential role of DNA methylation in S. aureus transcriptional regulation and stress response remains largely undefined. We tackled this gap by combining genome-wide nanopore sequencing-derived DNA methylation data and transcriptomic data, acquired before and during exposure of methicillin-resistant Staphylococcus aureus strain USA300 to clinically relevant oxidative, antibiotic and nitrosative stresses. Stress-induced significant DNA methylation changes were rare, with <0.1% of cytosines/adenines undergoing [≥]20% change in methylation; these changes were enriched within genomic features (protein-coding genes, predicted promoter regions, ncRNAs). Transcription changes reflected metabolic, regulatory and stress-specific pathway adjustments. Many of the stress-induced DNA methylation changes occurred alongside transcription changes, although there was no obvious overarching relationship between the directions of changes in DNA methylation and transcription. Pre-stress treatment methylation entropy tended to be elevated at sites containing a base that underwent stress-induced change in methylation level, identifying focal sites of pre-existing methylome heterogeneity relative to both local and genome-wide backgrounds; the magnitude of the site-specific methylation entropy peak, moreover, correlated with the magnitude of subsequent methylation change. Genome-wide entropy levels were consistent with a finite number of methylation patterns, distinguished by key bases, that could correspond to clinically important S. aureus subpopulations exhibiting persistence, dormancy and immune evasion. These findings support the principle that DNA methylation is an important component of the regulatory machinery underpinning S. aureus adaptability and persistence. ImportanceStaphylococcus aureus survives antibiotic treatment and host immune attack partly through phenotypic diversity, yet the regulatory processes that support this adaptability remain incompletely understood. Here, we integrate genome-wide DNA methylation and transcriptomic profiling to examine how epidemic methicillin-resistant S. aureus USA300 responds to oxidative, antibiotic, and nitrosative stresses. Stress-induced methylation changes were rare but non-random, concentrated in coding and regulatory regions linked to stress defence, metabolism, persistence, virulence, biofilm formation, and host interaction. Sites that underwent stress-induced methylation changes tended to have unusually high pre-stress methylation pattern diversity relative to local and genome-wide pattern diversity. These findings support a model in which an S. aureus population contains a pre-stress repertoire of epigenetic states that stress selectively redistributes via bases that differentiate stable methylation patterns. By revealing a layer of heterogeneity that may support pathogen resilience, this work provides a framework for investigating whether bacterial methylation dynamics can be exploited clinically.

microbiology↗

bioRxiv2020

Lipopolysaccharide administration alters extracellular vesicles in human lung-cancer cells and mice

Extracellular vesicles (EVs) play a fundamental role in cell and infection biology and have the potential to act as biomarkers for novel diagnostic tools. In this study, we explored the in vitro impact of bacterial lipopolysaccharide administration on a cell line that represents a target for bacterial infection in the host. Administration of lipopolysaccharide at varying concentrations to this A549 cell line caused only modest changes in cell death, but EV numbers were significantly changed. After treatment with the highest concentration of lipopolysaccharide, EVs derived from A549 cells packaged significantly less interleukin-6 and lysosomal-associated membrane protein 1. We also examined the impact of lipopolysaccharide administration on exosome biogenesis and cargo composition in BALB/c mice. Serum-isolated EVs from lipopolysaccharide-treated mice showed significantly increased lysosomal-associated membrane protein 1 and toll-like receptor 4 levels compared with EVs from control mice. In summary, this study demonstrated that EV numbers and cargo were altered using these in vitro and in vivo models of bacterial infection.

microbiology↗