Biology subjects

Ryan, F. J.

Publications and source records attributed to Ryan, F. J..

8 recordsLinked to original sources

bioRxiv2026

OpusTaxa: A Unified Workflow for Taxonomic Profiling, Assembly, and Functional Analysis of Shotgun Metagenomes

Shotgun metagenomics has become a cornerstone of microbiome research, yet the complexity of existing workflows remains a major barrier for life scientists without dedicated bioinformatics support. Manual database setup, detailed sample sheet preparation, and management of software dependencies can make routine analysis difficult and time-consuming. Cross-study comparisons are further hampered by inconsistent processing pipelines, database versions, and profiling strategies, limiting reproducibility and the potential for large-scale meta-analyses. We present OpusTaxa, an open-source Snakemake workflow that provides end-to-end processing of short paired-end shotgun metagenomic data with minimal configuration. Users provide either FASTQ files or Sequence Read Archive accessions; OpusTaxa automatically downloads required databases, performs quality control, removes host reads, and executes taxonomic profiling, metagenome assembly, and functional analysis. All analysis modules can be independently toggled, and per-sample outputs are automatically merged into harmonised, cross-sample tables ready for downstream exploration. Across two public datasets, we demonstrate how OpusTaxa can be used to compare consistency across complementary taxonomic profilers and to estimate microbial load in addition to standard metagenomic workflows. AvailabilityOpusTaxa is freely available at https://github.com/yenkaiC/OpusTaxa. Documentation, test data, and example configurations are included in the repository.

bioinformatics↗

bioRxiv2025

Bladder mucosal afferents detect UTI and aid pathogen clearance

The bladder is innervated by a complex network of sensory neurons that detect and transmit mechanical and chemical signals to the central nervous system, regulating both urine storage and voiding, as well as mediating sensations of bladder fullness and pain. While stretch-sensitive afferents within the bladder wall are known to monitor filling, the contribution of stretch-insensitive afferents that reside within the bladder mucosa to bladder sensation and function remains unclear. Here, we establish a novel mouse model of selective bladder mucosal afferent denervation using intravesical instillation of resiniferatoxin (RTX) to define the functional roles of these fibres in health and disease. We assessed the impact of mucosal denervation on sensory nerve activity and bladder function in healthy mice and in a model of urinary tract infection (UTI) induced by acute bacterial challenge with uropathogenic E. coli. We show that mucosa-innervating afferents do not influence bladder distension responses or voiding function under healthy conditions. In contrast, during UTI, these afferents become hypersensitive and serve as critical drivers of infection-induced pelvic pain and urinary frequency, responses that contribute to enhanced bacterial clearance. Together, these findings identify bladder mucosal afferents as key sensors of pathogenic challenge and reveal a previously unrecognised mechanism that drives behavioural responses to reduce the burden and extent of UTI.

neuroscience↗

bioRxiv2024

TaxSEA: an R package for rapid interpretation of differential abundance analysis output.

Microbial communities are essential regulators of ecosystem function, with their composition commonly assessed through DNA sequencing. Most current tools focus on detecting changes among individual taxa (e.g., species or genera), however in other omics fields, such as transcriptomics, enrichment analyses like Gene Set Enrichment Analysis (GSEA) are commonly used to uncover patterns not seen with individual features. Here, we introduce TaxSEA, an R package for taxon set enrichment analysis. TaxSEA integrates taxon sets from five public microbiota databases (BugSigDB, MiMeDB, GutMGene, mBodyMap, and GMRepoV2) to assess whether disease signatures, metabolite producers, or previously reported associations are enriched or depleted in a metagenomic dataset of interest. In-silico assessments show TaxSEA is accurate across a range of set sizes. When applied to differential abundance analysis output from Inflammatory Bowel Disease and Type 2 Diabetes metagenomic data, TaxSEA outperforms current tools and can rapidly identify changes in functional groups corresponding to known associations. We also show that TaxSEA is robust to the choice of differential abundance (DA) analysis package. In summary, TaxSEA enables researchers to efficiently contextualize their findings within the broader microbiome literature, facilitating rapid interpretation and advancing understanding of microbiome-host and environmental interactions.

bioinformatics↗

bioRxiv2022

Peroxisomal β-oxidation enzyme, DECR2, regulates lipid metabolism and promotes treatment resistance in advanced prostate cancer

Peroxisomes are central metabolic organelles that have key roles in fatty acid homeostasis, including {beta}-oxidation, and emerging evidence has linked aberrant peroxisome metabolism to cancer development and progression. While targeting mitochondrial {beta}-oxidation in prostate cancer (PCa) has gained significant attention in recent years, the contribution of peroxisomal {beta}-oxidation (perFAO) to PCa tumorigenesis is comparatively unexplored. Herein, we explored the therapeutic efficacy of targeting perFAO in PCa cells and clinical prostate tumours, and subsequently identified peroxisomal 2,4-dienoyl CoA reductase 2 (DECR2), as a key therapeutic target. DECR2 is markedly upregulated in clinical PCa, most notably in metastatic castrate-resistant PCa. Depletion of DECR2 significantly suppressed proliferation, migration, and 3D growth of a range of CRPC and enzalutamide-resistant PCa cell lines, and inhibited LNCaP tumour growth and proliferation in vivo. Using transcriptomic and lipidomic analyses, we determined that DECR2 influences cell cycle progression and lipid metabolism to enable tumour cell proliferation. We further demonstrated a novel role for perFAO in driving resistance to standard-of-care androgen receptor pathway inhibition, using genetic and pharmacological approaches to alter DECR2/perFAO in treatment-resistant PCa cells. Our findings highlight a need to focus on peroxisomes to suppress tumour cell proliferation and reveal new therapeutic targets for advanced, treatment-resistant PCa.

cancer biology↗

bioRxiv2019

The human gut virome is highly diverse, stable and individual-specific

The human gut contains a vast array of viruses, mostly bacteriophages. The majority remain uncharacterised and their roles in shaping the gut microbiome and in impacting on human health remain poorly understood. Here we performed a longitudinal focused metagenomic study of faecal bacteriophage populations in healthy adults. Our results reveal high temporal stability and individual specificity of bacteriophage consortia which correlates with the bacterial microbiome. We report the existence of a stable, numerically predominant individual-specific persistent personal virome. Clustering of bacteriophage genomes and de novo taxonomic annotation identified several groups of crAss-like and Microviridae bacteriophages as the most stable colonizers of the human gut. CRISPR-based host prediction highlighted connections between these stable viral communities and highly predominant gut bacterial taxa such as Bacteroides, Prevotella and Faecalibacterium. This study provides insights into the structure of the human gut virome and serves as an important baseline for hypothesis-driven research.

microbiology↗

bioRxiv2019

Autochthonous faecal virome transplantation (FVT) reshapes the murine microbiome after antibiotic perturbation

BackgroundIt has become increasingly apparent that establishing and maintaining a complex and diverse gut microbiome is fundamental to human health. There are growing efforts to identify methods that can modulate and influence the microbiome, especially in individuals who due to disease or circumstance have experienced a disruption in their native microbiome. Faecal microbial transplantation (FMT) is one method that restores diversity to the microbiome of an individual by introducing microbes from a healthy donor. FMT introduces a complete microbiome into the recipient, including the bacteriome, archaeome, mycome and virome. In this study we investigated whether transplanting an autochthonous faecal virome consisting primarily of bacteriophages could impact a bacteriome disrupted by antibiotic treatment (Faecal Virome Transplantation; FVT).\n\nResultsFollowing disruption of the bacteriome by penicillin and streptomycin, test mice (n=8) received a bacteria free, faecal transplant, while Control mice (n=8) received a heated and nuclease treated control. The bacteriomes (as determined via 16S rRNA sequencing) of mice that received an FVT, in which bacteriophages predominate, separated from those of the Control mice as determined by principle co-ordinate analysis (PCoA), and contained differentially abundant taxa that reshaped the bacteriome profile such that it more closely resembled that of the pre-treatment mice. Similarly, metagenomic sequencing of the virome confirmed that the bacteriophages present in the gut of treatment and Control mice differed over time in both abundance and diversity, with transplanted phages seen to colonise the FVT mice.\n\nConclusionsAn autochthonous virome transplant impacts on the bacteriome and virome of mice following antibiotic treatment. The virome, consisting mainly of bacteriophages, reshapes the bacteriome such that it more closely resembles the pre-antibiotic state. To date, faecal transplants have largely focussed on transferring living microbes, but given that bacteriophage are inert biological entities incapable of colonising in the absence of a sensitive host they could form a viable alternative that may have fewer safety implications and that could be delivered as a robust formulation.

microbiology↗

bioRxiv2018

Choice of assembly software has a critical impact on virome characterisation

BackgroundThe viral component of microbial communities play a vital role in driving bacterial diversity, facilitating nutrient turnover and shaping community composition. Despite their importance, the vast majority of viral sequences are poorly annotated and share little or no homology to reference databases. As a result, investigation of the viral metagenome (virome) relies heavily on de novo assembly of short sequencing reads to recover compositional and functional information. Metagenomic assembly is particularly challenging for virome data, often resulting in fragmented assemblies and poor recovery of viral community members. Despite the essential role of assembly in virome analysis and difficulties posed by these data, current assembly comparisons have been limited to subsections of virome studies or bacterial datasets.\n\nDesignThis study presents the most comprehensive virome assembly comparison to date, featuring 16 metagenomic assembly approaches which have featured in human virome studies. Assemblers were assessed using four independent virome datasets, namely; simulated reads, two mock communities, viromes spiked with a known phage and human gut viromes.\n\nResultsAssembly performance varied significantly across all test datasets, with SPAdes (meta) performing consistently well. Performance of MIRA and VICUNA varied, highlighting the importance of using a range of datasets when comparing assembly programs. It was also found that while some assemblers addressed the challenges of virome data better than others, all assemblers had limitations. Low read coverage and genomic repeats resulted in assemblies with poor genome recovery, high degrees of fragmentation and low accuracy contigs across all assemblers. These limitations must be considered when setting thresholds for downstream analysis and when drawing conclusions from virome data.

bioinformatics↗

bioRxiv2018

Biology and taxonomy of crAss-like bacteriophages, the most abundant virus in the human gut

CrAssphage is yet to be cultured even though it represents the most abundant virus in the gut microbiota of humans. Recently, sequence based classification was performed on distantly related crAss-like phages from multiple environments, leading to the proposal of a familial level taxonomic group [Yutin N, et al. (2018) Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut. Nat Microbiol 3(1):38-46]. Here, we assembled the metagenomic sequencing reads from 702 human faecal virome/phageome samples and obtained 98 complete circular crAss-like phage genomes and 145 contigs [≥]70kb. In silico comparative genomics and taxonomic analysis was performed, resulting in a classification scheme of crAss-like phages from human faecal microbiomes into 4 candidate subfamilies composed of 10 candidate genera. Moreover, laboratory analysis was performed on faecal samples from an individual harbouring 7 distinct crAss-like phages. We achieved propagation of crAss-like phages in ex vivo human faecal fermentations and visualised Podoviridae virions by electron microscopy. Furthermore, detection of a crAss-like phage capsid protein could be linked to metagenomic sequencing data confirming crAss-like phage structural annotations.\n\nSignificanceCrAssphage is the most abundant biological entity in the human gut, but it remains uncultured in the laboratory and its host(s) is unknown. CrAssphage was not identified in metagenomic studies for many years as its sequence is so different from anything present in databases. To this day, it can only be detected from sequences assembled from metagenomics or viromic datasets (crAss - cross Assembly). In this study, we identified 243 new crAss-like phages from human faecal metagenomic studies. Taxonomic analysis of these crAss-like phages highlighted their extensive diversity within the human microbiome. We also present the first propagation of crAssphage in faecal fermentations and provide the first electron micrographs of this extraordinary bacteriophage.

microbiology↗