Biology subjects

Lawther, K.

Publications and source records attributed to Lawther, K..

3 recordsLinked to original sources

bioRxiv2026

GeneFior: A back to basics and transparent multi-tool approach tosequence detection

The detection of sequences of interest, such as antimicrobial resistance genes, directly from genomic and metagenomic sequencing data has become routine, enabled by curated reference databases and rapid in silico sequence search tools. Yet most workflows depend on prior assembly, an inherently lossy process in which a substantial proportion of reads fail to assemble or are collapsed into consensus sequences, causing low-abundance variants and nucleotide-level diversity to be systematically obscured. The tools used to interrogate the resulting assemblies compound this further, clustering reference sequences at arbitrary identity thresholds, imposing hidden parameter defaults, and reducing intermediate alignment evidence to summarised outputs that cannot be critically evaluated or reproduced. Here we present GeneFior, a transparent, multitool workflow integrating BLAST, DIAMOND, Bowtie2, BWA, and Minimap2 to search both DNA and protein sequences against any user-supplied reference database. By enforcing genecentric identity and coverage thresholds at both the read and gene level, GeneFior reduces false positives while retaining sensitivity to genuine, low-abundance variants, including those differing at single-nucleotide resolution. Crucially, by exposing all alignment parameters, preserving intermediate outputs, and generating cross-tool consensus detection matrices, GeneFior makes the influence of tool choice, database selection, and parameter configuration on reported gene profiles directly observable and reproducible.

bioinformatics↗

bioRxiv2025

Struvite fertiliser offers a sustainable solution for recycling of phosphorus for crop growth without altering the soil resistome.

BackgroundThe reserves of rock phosphate, used to produce fertilisers, are being exhausted by the ever-increasing pressure to meet the food demands of a growing world population. Sustainable alternatives are urgently needed, and struvite, a renewable phosphorus fertiliser recovered from waste streams such as animal manure, offers a promising solution. However, other manure-derived fertilisers have been associated with the promotion of antimicrobial resistance (AMR) in soil, raising concerns about whether struvite might pose similar risks. Despite this, the impact of struvite on the soil resistome remains poorly understood. MethodsThis study assesses the AMR risk associated with Xiamen struvite (XIA), produced from piggery wastewater, compared with two commercial fertilisers: Crystal Green (CG) and Triple Super Phosphate (TSP), and an untreated control soil. Following a three-month fertilisation period, rhizospheric soils were analysed using mass spectrometry to investigate antimicrobial residues in the soil, and shotgun metagenomics and culture-based assays, and bacterial isolate characterisation to identify bacterial AMR linked to the treatments. Notably, this is the first study to apply culturing methods to investigate struvites impact on AMR. Results and conclusionsWhile XIA struvite soil fertilisation led to an increase in total culturable bacterial load, (CFU/g), there was no evidence of antimicrobial residues detected in soil, as confirmed by mass spectrometry. Metagenomic profiling further revealed no significant alterations to antimicrobial resistance genes (ARGs) across all treatments, including CG, TSP, and untreated controls. Culture-based analysis supported these findings, with tetracycline-resistant bacteria undetected and only minimal resistance observed to erythromycin, florfenicol, and neomycin. Although resistance levels to amoxicillin, streptomycin, and trimethoprim were higher in XIA-treated soils, this appeared to reflect a broader increase in microbial load rather than selective enrichment of resistant strains. These data suggest that piggery-derived struvite does not impose a clear AMR risk in soil and performs similarly to conventional fertilisers. While it appears to increase total bacterial load, there is no evidence of selective enrichment for AMR bacteria. However, variability in antimicrobial and ARG content across studies highlights the need for standardised production specifications for struvites to ensure safety and consistency. This study provides the most comprehensive assessment to date of struvites AMR implications, supporting its potential as a safe, sustainable fertiliser and contributing valuable insights to inform regulatory guidance.

microbiology↗

bioRxiv2025

Dietary inclusion of Asparagopsis taxiformis significantly reduces methane emissions in dairy ruminants by mechanistically altering vitamin B12 coenzyme production and other methanogenesis precursor pathways.

Ruminant products are consumed widely on a global level due to their high protein and micronutrient density. However, ruminant production is a major source of greenhouse gas emissions, particularly with respect to methane (CH), with ruminants contributing 33% of all anthropogenic CH emissions. CH is produced due to the natural fermentative processes undertaken by the complex rumen microbiome, primarily via the utilisation of hydrogen by rumen archaea to form CH. Previous studies have shown that feeding the red seaweed Asparagopsis taxiformis (ASP) to ruminants can reduce CHemissions from beef cattle by up to 80% (Roque et al., 2021). Nevertheless, the mechanism of action of this seaweed in terms of effects on the rumen microbiome is largely unknown, which is the main focus of this study. Six Nordic Red cows at 122 {+/-} 13.7 (mean {+/-} SD) days in milk were divided into 3 blocks by milk yield in Latin square design and fed grass silage and a commercial concentrate (60:40) either with or without 0.5% ASP on an organic matter basis. Rumen fluid was collected 19 days into each experimental period, with a holistic approach using both assembly and read mapping based approaches to interrogate taxonomic, functional, and ecological shifts applied to metagenomic data. We show that ASP reduces methane production not only through direct inhibition of methanogens but also by disrupting cobamide-dependent metabolic pathways and redirecting carbon flow toward pyruvate and propionate rather than acetate and methane. For the first time, specific enzymes involved in vitamin B12 (cobamide) biosynthesis are identified as suppressed by ASP, and microbial taxa contributing to these functional changes are elucidated showing both niche displacement and resilience within the rumen microbiome. These findings offer new mechanistic insight into how red seaweed supplementation modulates the rumen microbiome, supporting its potential role in sustainable ruminant production.

genomics↗