Recently, several EU countries, including the Republic of Ireland, have struggled to meet legally binding commitments to reduce ammonia emissions. Some farmers readily embrace abatement measures, whereas others reject them and it could be argued that farmers’ technology rejection decisions have been studied in less detail within the literature. However, understanding why some farmers reject recommended farming practices holds critical information that helps to inform policy, tailor government support schemes, and reduce pro-innovation biases. This study builds on the Grounded Theory method, data collected from focus group discussions with dairy and beef cattle farmers across eight key farming regions, and inductive thematic analysis. Three main themes, six subthemes and 26 codes were defined. The adoption of recommended bovine farming methods was hindered by affordability, compatibility, usability, availability, and information-related barriers. Participants also expressed frustration with unfair pressure to reduce agricultural emissions along with insufficient recognition of the environmental benefits provided by well-managed grasslands, the contributions cattle production makes to global food production, and the sustainability progress they have already achieved. We recommend that future reforms of the EU Common Agricultural Policy adopt a coordinated policy approach. It should simultaneously target all the nitrogen-related farm environmental issues and fully consider the local farmers perspectives in policy design and implementation. The reforms should include accessible support schemes for small-scale farm owners and more effective efforts to raise awareness about the causes and consequences of farm ammonia3 emissions, available abatement methods, and the correction of misinformation.
Plasmid-encoded mobile colistin resistance ( mcr ) genes have raised concern due to dissemination potential. While mcr variants are reported across One Health compartments, they remain unreported in grass. This study characterises a novel mcr variant ( mcr-13.1 ), detected in Escherichia coli isolated from the grass phylosphere within an agricultural grassland. The two mcr -positive isolates were clonal copies isolated at timepoints eight weeks apart. They belonged to the serotype O17:H18 and were of the sequence type ST394. The E. coli were phenotypically susceptible to β-lactams, aminoglycosides, quinolones, sulphonamides, phenicols, tetracyclines, diaminopyrimidine and colistin (Minimum Inhibitory Concentration (MIC) = 0.5 µg/mL). The mcr-13.1 gene was encoded on an IncFIB plasmid. This plasmid was transferable by conjugation but the colistin MIC of the E. coli J53 transconjugant did not change (0.5 µg/mL). Further, cloned pUC19:: mcr-13.1 did not alter the colistin MIC for E. coli DH5α (0.25 µg/mL). The translated amino acid sequence showed highest homology (82 %) to MCR-10.2 and MCR-10.4. Our findings identify grass as a previously unrecognised reservoir for E. coli carrying mobile mcr genes, reports the identification of the novel mcr-13.1 variant from this niche and demonstrates the importance of genomic screening in identifying mcr genes that would otherwise remain undetected. ### Competing Interest Statement The authors have declared no competing interest. The assembled sequences for Ec\_018 and Ec\_325 have been deposited in the NCBI GenBank and are publicly available under the accession numbers GCA\_056783495.1 (Ec\_018) and GCA\_056783455.1 (Ec\_325). The assemblies can be accessed at: Joint Programming Initiative on Antimicrobial Resistance Department of Agriculture Food and the Marine, https://ror.org/008gjgb19
Early life introduction of potentially allergenic foods such as peanuts is important for the prevention of food allergy. We hypothesized that peanut consumption may indirectly influence the immune system via effects on gut microbiota composition and metabolism. In vitro human fecal fermentations with peanuts were performed. Changes in taxa and metabolism were measured using 16S rRNA gene sequencing and untargeted metabolomics respectively. Ten Bifidobacterium strains were cultured in vitro in the presence of peanuts and human peripheral blood mononuclear cells (PBMCs) were used to assess culture supernatant immunomodulatory effects. Fecal samples were sequenced from children at 12 months (n = 343) using whole genome metagenomic sequencing. An online questionnaire was used to collect dietary data. Human fecal bioreactor fermentation of peanut flour, previously subjected to in vitro simulated gastrointestinal digestion, resulted in significant production of short-chain fatty acids (SCFA), associated with increased relative abundance of Megasphaera and bifidobacteria. 188 metabolites were significantly altered following peanut fermentation. Bifidobacterium longum subspecies longum strain 160 efficiently metabolized peanut associated with secretion of indole-3-lactic acid (ILA). Following growth on peanuts, bifidobacterial supernatants enhanced IL-10 secretion, but reduced TNF-alpha and IL-5 secretion from stimulated PBMCs. Peanut consumption by 12-month-old children was associated with significant changes in gut microbiota composition including increased levels of Prevotella buccae, Megasphaera micronuciformis and Blautia wexlerae. Peanuts are metabolized by microbes generating immunoregulatory metabolites such as SCFAs and ILA. These metabolites may represent one potential mechanism underlying the allergy-protective effects of early peanut consumption, which requires further validation in high-risk allergy cohorts.
Background Metagenomic next-generation sequencing (mNGS) is an untargeted approach that enables detection of pathogens directly from samples without prior knowledge of their genetic sequences. In the context of pandemic preparedness and One Health surveillance, there is a pressing need for validated viral mNGS workflows that perform reliably across diverse hosts sample types and pre-analytical conditions. Results The study designed and evaluated two mNGS workflows, one for swabs and one for complex tissue matrices, using a reference repository of clinical and post-mortem samples. The panel comprised swabs and tissue samples positive for 19 DNA and RNA viruses (including 12 species) from nine host species and nine anatomical sites, encompassing a range of transport media, storage temperatures and processing timelines. Quality control metrics were embedded throughout nucleic acid extraction, library preparation and sequencing to monitor performance and support interpretation. Overall, 89.5% of 19 known DNA and RNA viruses were detected, including from samples with low nucleic acid concentrations (< 1 ng/µl) and variable integrity and purity. The workflows identified viral co-infections that had not been detected by prior targeted testing, as well as Phocid herpesvirus 7 (PHV7) for which no complete reference genome was initially available. Conclusions These results demonstrate that the validated swab and tissue mNGS workflows are sufficiently robust and sensitive for deployment in investigations of suspected viral disease of unknown aetiology and for early detection of emerging viral threats at the animal–human interface.
Common scab, caused by Streptomyces spp., is worldwide an important skin disease of potato, capable of significant reductions in marketable value. Resistant varieties developed through phenotypic selection have been the most effective strategy thus far. Previous studies on the genetics of resistance have identified only minor-effect QTLs. In the current study, we explored the value of historical data for genetic analysis, derived from 52 sources. Based on partial replication of the 3500+ varieties, generalized (entry-mean) heritability was estimated at 0.66. For a subset of 292 varieties with genome-wide markers, the genomic (narrow-sense) heritability was only 0.10. The historical data was combined with a contemporary US dataset spanning 6 environments and 416 varieties. Genome-wide association studies identified four QTLs, which together explained 7.3
