Data sharing considerations to maximize the use of pathogen biological and genomics resources data for public health.

Public sector data associated with health are a highly valuable resource with multiple potential end-users, from health practitioners, researchers, public bodies, policy makers, and industry. Data for infectious disease agents are used for epidemiological investigations, disease tracking and assessing emerging biological threats. Yet, there are challenges in collating and re-using it.

Mobility and growth in confined spaces are important mechanisms for the establishment of in the rhizosphere.

The rhizosphere hosts complex and abundant microbiomes whose structure and composition are now well described by metagenomic studies. However, the dynamic mechanisms that enable micro-organisms to establish along a growing plant root are poorly characterized. Here, we studied how a motile bacterium utilizes the microhabitats created by soil pore space to establish in the proximity of plant roots.

Vacuolar localisation of anthocyanin pigmentation in microgreen cotyledons of basil, cabbage and mustard greens does not impact on colonisation by Shiga-toxigenic Escherichia coli O157:H7.

Microgreens, the immature plants harvested after a few weeks of growth, are perceived as a heathy, nutritious food ingredient but may be susceptible to colonisation by human pathogens including Shiga-toxigenic Escherichia coli (STEC). Some microgreen cultivars accumulate anthocyanins or secrete essential oils which, when extracted or purified, have been reported to inhibit bacterial growth. Therefore, the impact of anthocyanins on bacterial colonisation by STEC (Sakai) was compared for three species that have pigmented cultivars: basil (Ocimum basilicum L.

The UK Crop Microbiome Cryobank: a utility and model for supporting Phytobiomes research.

Plant microbiomes are the microbial communities essential to the functioning of the phytobiome-the system that consist of plants, their environment, and their associated communities of organisms. A healthy, functional phytobiome is critical to crop health, improved yields and quality food. However, crop microbiomes are relatively under-researched, and this is associated with a fundamental need to underpin phytobiome research through the provision of a supporting infrastructure.

Plant species-dependent transmission of Escherichia coli O157:H7 from the spermosphere to cotyledons and first leaves.

The colonization of six edible plant species: alfalfa, broccoli, coriander, lettuce, parsley and rocket, by the human pathogen Shigatoxigenic Escherichia coli was investigated following two modes of artificial inoculation of seeds, by soaking or watering. The frequency and extent of colonization of cotyledons depended on the mode of inoculation, with three, rapidly germinating species being successfully colonized after overnight soaking, but slower germinating species requiring prolonged exposure to bacteria by watering of the surrounding growth media. Separate analysis of the cotyledons and leaves from individual plants highlighted that successful colonization of the true leaves was also species dependent.

Phylogeny and potential virulence of cryptic clade species complex isolates derived from an arable field trial.

Analysis of taxonomy has expanded into a species-complex with the identification of divergent cryptic clades. A key question is the evolutionary trajectory of these clades and their relationship to isolates of clinical or veterinary importance. Since they have some environmental association, we screened a collection of isolated from a long-term spring barley field trial for their presence.

Genomic data of an environmental isolate shows high resemblance to K-12 reference strain MG1655.

species exhibits a high genomic diversification from evolution, mobile genetic elements and recombination. An environmental isolate, 'JHI_5025' from a crop trial appeared to be clonally related to the historical reference isolate K-12 strain 'MG1655', warranting further genomic analysis. Their genomes share an average nucleotide identity of 99.

Plant-environment microscopy tracks interactions of with plant roots across the entire rhizosphere.

Our understanding of plant-microbe interactions in soil is limited by the difficulty of observing processes at the microscopic scale throughout plants' large volume of influence. Here, we present the development of three-dimensional live microscopy for resolving plant-microbe interactions across the environment of an entire seedling growing in a transparent soil in tailor-made mesocosms, maintaining physical conditions for the culture of both plants and microorganisms. A tailor-made, dual-illumination light sheet system acquired photons scattered from the plant while fluorescence emissions were simultaneously captured from transparent soil particles and labeled microorganisms, allowing the generation of quantitative data on samples ∼3,600 mm in size, with as good as 5 µm resolution at a rate of up to one scan every 30 min.

High-resolution 3D mapping of rhizosphere glycan patterning using molecular probes in a transparent soil system.

Rhizospheres are microecological zones at the interface of roots and soils. Interactions between bacteria and roots are critical for maintaining plant and soil health but are difficult to study because of constraints inherent in working with underground systems. We have developed an rhizosphere imaging system based on transparent soils and molecular probes that can be imaged using confocal microscopy.

The role of l-arabinose metabolism for 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 micro-organisms such as via pectin and hemicellulose degrading enzymes. However, not all plant-associated microbes encode cell-wall-degrading enzymes, yet can metabolize l-arabinose, raising questions about their use of and access to the glycan in plants.

Microbial cancer therapeutics: A promising approach.

The success of conventional cancer therapeutics is hindered by associated dreadful side-effects of antibiotic resistance and the dearth of antitumor drugs' selectivity and specificity. Hence, the conceptual evolution of anti-cancerous therapeutic agents that selectively target cancer cells without impacting the healthy cells or tissues, has led to a new wave of scientific interest in microbial-derived bioactive molecules. Such strategic solutions may pave the way to surmount the shortcomings of conventional therapies and raise the potential and hope for the cure of wide range of cancer in a selective manner.

The rise, fall and resurrection of chemical-induced resistance agents.

Since the discovery that the plant immune system could be augmented for improved deployment against biotic stressors through the exogenous application of chemicals that lead to induced resistance (IR), many such IR-eliciting agents have been identified. Initially it was hoped that these chemical IR agents would be a benign alternative to traditional chemical biocides. However, owing to low efficacy and/or a realization that their benefits sometimes come at the cost of growth and yield penalties, chemical IR agents fell out of favour and were seldom used as crop protection products.

Functional Analysis of Shiga Toxin-Producing Escherichia coli Biofilm Components in Plant Leaves.

Plants represent alternative or secondary hosts for Shiga toxin-producing Escherichia coli (STEC), enabling transmission of the pathogens through the food chain on horticultural crops. This becomes a public health concern for plants that are eaten raw or minimally processed, such as leafy salad and fruits. STEC actively interact with plants as hosts, and so to determine the mechanistic basis to the interaction, it is necessary to assess STEC gene function in planta.

MacConkey broth purple provides an efficient MPN estimation method for Shigatoxigenic Escherichia coli.

MacConkey broth purple provides a more efficient method for Most Probable Number estimation for Shigatoxigenic Escherichia coli (E.coli) than the process of bacterial enrichment in buffered peptone water followed by detection on MacConkey agar, since it is a single-step process that gives comparable results in plant extracts.

O157:H7 F9 Fimbriae Recognize Plant Xyloglucan and Elicit a Response in .

Fresh produce is often a source of enterohaemorrhagic (EHEC) outbreaks. Fimbriae are extracellular structures involved in cell-to-cell attachment and surface colonisation. F9 (Fml) fimbriae have been shown to be expressed at temperatures lower than 37 °C, implying a function beyond the mammalian host.

Framework for Quantification of the Dynamics of Root Colonization by Isolate SBW25.

Colonization of the root surface, or rhizoplane, is one of the first steps for soil-borne bacteria to become established in the plant microbiome. However, the relative contributions of processes, such as bacterial attachment and proliferation is not well characterized, and this limits our ability to comprehend the complex dynamics of microbial communities in the rhizosphere. The work presented here addresses this knowledge gap.

A high-throughput genomic screen identifies a role for the plasmid-borne type II secretion system of Escherichia coli O157:H7 (Sakai) in plant-microbe interactions.

Shiga-toxigenic Escherichia coli (STEC) is often transmitted into food via fresh produce plants, where it can cause disease. To identify early interaction factors for STEC on spinach, a high-throughput positive-selection system was used. A bacterial artificial chromosome (BAC) clone library for isolate Sakai was screened in four successive rounds of short-term (2 h) interaction with spinach roots, and enriched loci identified by microarray.

Dataset of O157: H7 genes enriched in adherence to spinach root tissue.

A high-throughput positive-selection approach was taken to generate a dataset of Shigatoxigenic (STEC) O157:H7 genes enriched in adherence to plant tissue. The approach generates a differential dataset based on BAC clones enriched in the output, after adherence, compared to the inoculum used as the input. A BAC clone library derived from STEC isolate 'Sakai' was used since this isolate is associated with a very large-scale outbreak of human disease from consumption of contaminated fresh produce; white radish sprouts.

Variability in growth responses of non-O157 EHEC isolates in leafy vegetables, sprouted seeds and soil extracts occurs at the isolate level.

Foods of plant origin are recognised as a major source of foodborne pathogens, in particular for Shigatoxigenic Escherichia coli (STEC). Most work for STEC and plant-based fresh produce has focused on the most prevalent outbreak serogroup, O157. However, non-O157 STEC is an emerging hazard, and as such it is important to characterise aspects within this group that reflect their ability to colonise alternative hosts and habitats relevant to horticultural production.

Influence of Plant Species, Tissue Type, and Temperature on the Capacity of Shiga-Toxigenic To Colonize, Grow, and Be Internalized by Plants.

Contamination of fresh produce with pathogenic , including Shiga-toxigenic (STEC), represents a serious risk to human health. Colonization is governed by multiple bacterial and plant factors that can impact the probability and suitability of bacterial growth. Thus, we aimed to determine whether the growth potential of STEC for plants associated with foodborne outbreaks (two leafy vegetables and two sprouted seed species) is predictive of the colonization of living plants, as assessed from growth kinetics and biofilm formation in plant extracts.

O157:H7 transcriptome datasets for comparison of RNA-seq and microarray platforms.

Whole transcriptome analysis to investigate differential gene expression and regulatory adaption can be carried out on two different technological platforms: by probe hybridisation to microarrays or by RNAseq for deep sequencing. Since there are difference in terms of their genome coverage, sensitivity and cost, there is a requirement for robust comparisons to determine the platform of choice. Here, we present datasets for the whole transcriptional response verocytoxigenic (VTEC) obtained from RNA-seq and microarray platforms in response to spinach, together with a comparison between the datasets (available at Array Express: E-MTAB-3249, E-MTAB-4120, E-MTAB-7441).