Biology subjects

Holden, N. J.

Publications and source records attributed to Holden, N. J..

3 recordsLinked to original sources

bioRxiv2026

Motile bacteria collectively transport soil water during host colonisation

Nutrient availability in soil is temporally and spatially heterogeneous, and, as a result, microbial migration is critical for many species. The nature of microbial movement in soil, however, is unknown due to a lack of observations and experimental data. We developed live-imaging and image-analysis techniques to track the movement of single cells through soil to elucidate how Bacillus subtilis utilises pore space during the early root colonisation. The study reveals that the bacterium can modify fluid pathways to create streams, even at low bulk cell density. The phenomenon was influenced by pore structure, distance from the root and the viscosity of the soil solution. By generating macroscopic fluid motion, bacteria may also be able to travel faster and farther than individually, while limiting energy expenditure.

microbiology↗

bioRxiv2026

Stitching genomics data to protein structures: Virulence factors in non-O157 Shiga toxin-producing Escherichia coli

The genetic diversity of the Shiga toxin-producing Escherichia coli (STEC) sub-species group poses major challenges for assigning pathogenic potential, and for accurate diagnostics. Although existing risk-based frameworks work for the predominant serotypes e.g. STEC O157 or O26, they are less useful for more diverse genotypes, with variation in the genetic complement of virulence factors that is responsible for disease outcome. Moreover, genetic diversity occurs at the virulence factor allele level. We investigated the functional potential of genetic variation at a whole genome level and at an allele variant level, based on the premise that genomic variability underlies phenotypic traits including disease outcomes. We analysed 286 non-O157 STEC genomes for their virulence factor complement and determined co-occurrence patterns. Genetic variation in the well-characterized virulence factor intimin (eae) and its receptor (tir) was analyzed at a sequence level, and by modelling the three-dimensional protein-protein complex using AlphaFold3 and homology modelling. Different subtypes of Eae were shown to preserve their interaction with the receptor Tir by retaining the interactions at the protein-protein interface. The study shows that virulence factor characterisation in association with 3-D modelling of protein complexes can aid genomic analysis for risk assessment, and inform on functional mechanisms for pathogenicity.

bioinformatics↗

bioRxiv2021

The role of L-arabinose metabolism for Escherichia coli O157:H7 in edible plants

Arabinose is a major plant aldopentose in the form of arabinans complexed in cell wall polysaccharides or glycoproteins (AGP), but comparatively rare as a monosaccharide. L-arabinose is an important bacterial metabolite, accessed by pectolytic microorganisms such as Pectobacterium atrosepticum via pectin and hemicellulose degrading enzymes. However, not all plant-associated microbes encode cell wall degrading enzymes, yet can metabolise L-arabinose, raising questions about their use of and access to the glycan in plants. Therefore, we examined L-arabinose metabolism in the food-borne pathogen Escherichia coli O157:H7 (isolate Sakai) during its colonisation of plants. L-arabinose metabolism (araBA) and transport (araF) genes were activated at 18 {degrees}C in vitro by L-arabinose and expressed over prolonged periods in planta. Although deletion of araBAD did not impact the colonisation ability of E. coli O157:H7 (Sakai) on plants, araA was induced on exposure to spinach cell wall polysaccharides. Furthermore, debranched and arabinan oligosaccharides induced ara metabolism gene expression in vitro, and stimulated modest proliferation, while immobilised pectin did not. Thus, E. coli O157:H7 (Sakai) can utilise pectin/AGP- derived L-arabinose as a metabolite, but differs fundamentally in ara gene organisation, transport and regulation from the related pectinolytic species P. atrosepticum, reflective of distinct plant- associated lifestyles.

microbiology↗