The Quadram Institute is a centre for food and health research, combining Quadram Institute Bioscience (formerly the Institute of Food Research), the Norfolk and Norwich University Hospitals’ endoscopy centre and aspects of the University of East Anglia’s Norwich Medical School and the Faculty of Science. It is located on the outskirts of Norwich, England, United Kingdom and is a member of the Norwich Research Park.The Institute is housed in a purpose-built facility on the Norwich Research Park that opened in 2018. Its founding partners are Quadram Institute Bioscience, University of East Anglia, Norfolk and Norwich University Hospital and the Biotechnology and Biological Sciences Research Council. The institute combines research teams from the partners with a regional gastrointestinal endoscopy unit and a clinical trials facility. The first patients were treated in the endoscopy unit in December 2018.
Third-generation long-read sequencing technologies, significantly improve metagenome assemblies. Highly accurate PacBio HiFi reads can yield hundreds of near-complete metagenome-assembled genomes (MAGs) from a single sample. Recently, the accuracy of the more cost-effective Oxford Nanopore Technologies (ONT) platform has increased to a per-base error rate of 1-2%. However, current metagenome assemblers are optimized for HiFi and do not scale to the large data sets that ONT enables. We present nanoMDBG, an evolution of metaMDBG, which supports the latest ONT reads through an error correction pre-processing step in minimizer-space. Across a range of ONT datasets, including a large 400 Gbp soil sample, nanoMDBG reconstructs up to twice as many high-quality MAGs as the next best ONT assembler, metaFlye, while requiring a third of the CPU time and memory. Critically, the latest ONT technology can now produce comparable MAG construction results as those obtained using PacBio HiFi at the same sequencing depth.
Archaea are an important group of soil organisms that play key roles in carbon and nitrogen cycling, particularly in nitrification (ammonia oxidation) and methanogenesis. However, there are knowledge gaps regarding their importance in ecosystem processes relative to other microbial groups and how they may be impacted by land-use and environmental changes. Here, by carrying out a continental-scale sample collection and utilising archaeaspecific primers for metabarcoding and shotgun metagenomics, we aimed to decipher the structure and function of archaeal communities across various land-use types in Europe. Metagenomic data reveal that land-use intensification increases the relative abundance of archaea, whereas bacteria and eukaryotes show no increase. Alongside this, ammonia oxidising archaea (AOA) increase as a proportion of the total metabarcoding reads, from 1 % of archaea in coniferous woodland to >90 % in croplands. Functional gene profiles reveal that land-use intensification shifts archaeal communities from adaptive metabolic pathways in forests to specialised, ammonia-oxidising microbes in fertiliser-enriched cropland soils. Our data suggest that land-use intensification may shift archaeal communities toward greater dependence on external nitrogen inputs, with potential consequences for soil fertility and greenhouse gas emissions.
Trimethoprim is a clinically important antibiotic used for the routine treatment of urinary tract infections as a cost-effective first-line choice for treatment. A unique feature of the drug is that it can have bacteriostatic or bactericidal effects depending upon the metabolites available in the environment. Bacteriostatic activity requires the absence of nucleoside from the growth media. Conversely, bactericidal activity requires the presence of a nucleoside and the amino acids glycine and methionine. Mechanistically, bacteriostatic action does not appear to be dependent upon protein or RNA synthesis, whereas protein synthesis does not appear to be essential for bactericidal activity. Instead, this is likely due to the inhibition of DNA synthesis and the triggering of programmed cell death, involving the suicide module mazEF. In summary, trimethoprim has a complex mechanism of action that should be considered when researching the antibiotic and informing growth media design to test susceptibility.
AIMS:This project aimed to investigate production of the inhibitory neurotransmitter γ-aminobutyric acid (GABA) from potential probiotic strains. We studied production in co-cultures and faecal fermentations and examined the effect of selected strains on the faecal microbiome composition and metabolome in vitro. METHODS AND RESULTS:Strains of intestinally derived Bifidobacterium adolescentis and Lactiplantibacillus plantarum from fermented cereals were grown singly, in co-culture and in faecal fermentations designed to simulate colonic conditions. Isolates synthesized varying amounts of GABA in vitro; GABA production could be increased by co-culture, lactic acid, or reduced pH but was decreased in the presence of high buffering. In faecal fermentations, selected strains inoculated singly or in combination persisted over 24 h and increased the GABA concentration without causing major disruptions in the microbiome or metabolome. Bifidobacterium adolescentis supplementation increased short-chain fatty acids acetate and propionate, and L. plantarum was associated with increased succinate levels, while all treatments exhibited a reduction in Escherichia compared to the controls. CONCLUSIONS:GABA production from these lactic acid bacteria is strain-specific and the combination of these two species shows potential for future next-generation probiotic development.
Challenges in transporting one-day-old chicks long distances impact logistics, costs, and animal welfare in the quail industry. Transporting fertilized eggs for hatching as an alternative is viable since the quality of eggs can be assessed after transportation. In this study, we propose a new methodology that includes concept equipment for real-time grading of quail eggs according to their freshness level. By calculating the proportion of the segmented air cell size via a thermal imaging machine vision system calibrated with standard methods, the Haugh unit (HU), and the pH of albumen, our proposed method revealed that when the proportion of the thermographic air cell size was less than 3 % of the total egg area, there was significant evidence of high freshness quality; conversely, relative areas above 15 % indicated lack of optimal freshness conditions correlated with the HU (rs =-0.61) and the pH of albumen (rs = 0.57). The F1 scores of the thermal imaging machine vision system trained on the YOLOv8x-segmentation and Mask R-CNN deep learning object detection algorithms were 71.9 % and 77.8 %, respectively, on the sorting testing dataset. This study contributes to the field by proposing an innovative method for grading the freshness level of quail eggs in real time as a fast, noncontact and nondestructive alternative to supply the related industry and alleviate the animal welfare constraints associated with the transportation of avian living cargo.
