Biology subjects

Cuber, P.

Publications and source records attributed to Cuber, P..

7 recordsLinked to original sources

bioRxiv2026

City life: airborne DNA metagenomic biodiversity monitoring reveals dynamic changes across time and space

Airborne environmental DNA can capture biodiversity across the tree of life, but low sample biomass makes rapid, untargeted detection technically challenging. We combined 45-min air collection, nanopore sequencing and real-time taxonomic analysis in a shotgun metagenomic workflow capable of producing results within 3 hours. Across 77 samples from 13 London sites, including a year of weekly sampling at the Natural History Museum Wildlife Garden, we detected 1,916 species spanning bacteria, fungi, plants and animals. Communities varied spatially and seasonally, shifting from plant dominance in spring to ascomycete dominance in summer and basidiomycete dominance in late autumn and winter. Plant read abundance increased with upwind vegetation, linking airborne signals to surrounding habitat. Detection of catalogued garden plants depended on reference availability, dispersal biology, plant size and proximity to the collector. Together, these findings establish airborne shotgun metagenomics as a platform for rapid, repeated and scalable biodiversity assessment across space and time.

ecology↗

bioRxiv2026

Metagenomic analysis of the effects of European bison Bison bonasus (Linnaeus, 1758) presence on soil community structure and function in West Blean and Thornden Woods, Kent

The reintroduction of extinct or endangered species to restore ecosystem function is an essential aspect of rewilding. The Wilder Blean Project at West Blean and Thornden Woods in Canterbury, UK, is committed to rewilding natural processes and enhancing biodiversity in one of England's oldest and largest areas of ancient woodland. The introduction of European bison (Bison bonasus) is an important part of the project. However, how the reintroduction of large herbivores influences local biodiversity and ecosystem functions during the early stages of rewilding remains poorly understood. Soil samples were collected from the same sampling sites before and two years after bison were reintroduced and profiled by metagenomic sequencing using Oxford Nanopore Technologies sequencing platforms. The results showed that the alpha diversity of soil organisms did not change significantly before and after the introduction of European bison, while beta diversity showed modest shifts in community composition. The relative abundance of some nitrogen-fixing and photosynthetic microbial genera showed declines in the 2024 Bison Area, while the mycorrhizal fungus genus Rhizophagus was significantly less abundant than in the 2024 Control Area. Despite relatively stable taxonomic diversity, functional composition differed significantly between the 2022 and 2024 Bison areas and among the 2024 rewilding treatments, revealing a decoupling between taxonomic diversity and functional composition. Amino acid synthesis pathways and carbon metabolism pathways were significantly enriched. These findings highlight the potential of long-read Oxford Nanopore metagenomics to reveal functional shifts that may not be apparent from taxonomic diversity alone. Although these early-stage responses cannot yet predict long-term rewilding trajectories, continued longitudinal monitoring integrating microbial, soil physicochemical, and ecosystem-level measurements will be essential to determine the persistence and ecological significance of these functional shifts.

ecology↗

bioRxiv2026

Comprehensive analysis of air and surface hospital microbiomes uncovers potential hotspots and avenues for transmission of diverse pathogens linked to hospital-acquired infections

Fomite-mediated and airborne transmission pathways play a significant role in the dissemination of healthcare associated pathogens, contributing to the burden of hospital-acquired infections (HAIs). Effective infection prevention and control therefore require robust surveillance approaches capable of capturing the complexity of air and surface microbial communities present in healthcare settings. However, to date such approaches are not widely employed. In this study we used a rapid and low-biomass optimized metagenomic workflow to detect clinically relevant pathogens, characterise genetic signatures such as antimicrobial resistance and virulence determinants, and profile the wider airborne microbiome, including unculturable taxa) essential for HAI surveillance. Air samples were collected from multiple clinical and non-clinical areas across three multi-storey healthcare units within a UK hospital, alongside to surface samples from a haematology/oncology ward with a documented history of outbreaks. Following DNA extraction and enrichment optimised for low-biomass samples, sequencing was performed using the Oxford Nanopore Technologies MinIon long-read platform. Metagenomics data were analysed using an in-house developed bioinformatics pipeline. Metagenomic profiling revealed high bacterial taxonomic diversity across sampled environments, with limited overlap between the airborne and surface communities. Approximately 0.3% of bacterial reads harboured a large variety of antimicrobial resistance genes (ARGs), virulence factors (VFs) and mobile genetics elements (MGEs) across different hospital sample groups. Notably, critical and emerging pathogens were detected across ten wards and were associated with clinically significant resistance determinants, including multiple blaOXA subtypes, vanA gene clusters, and multidrug efflux pumps conferring resistance to eight important classes of antibiotics, including carbapenems, cephalosporins, penams, and vancomycin. In addition, several plasmid replicons implemented in horizontal gene transfer (HGT) were identified within these pathogens, indicating an increased potential for the emergence and dissemination of multi-drug resistance within hospital associated microbial communities. Our findings highlight the importance of using rapid metagenomics-based methodologies for environmental surveillance in healthcare settings. Correspondingly, this study revealed that hospital air and surface microbiomes comprise complex and dynamic microbial communities that harbour diverse of ARGs and VFs with the potential for rapid transmission across the surface-air interface, particularly in high-risk/vulnerable patient areas where outbreaks are more likely to occur.

microbiology↗

bioRxiv2024

CD62L-selected umbilical cord blood universal CAR T cells

Umbilical cord blood (UCB) T cells exhibit distinct naive ontogenetic profiles and may be an attractive source of starting cells for the production of chimeric antigen receptor (CAR) T cells. Pre-selection of UCB-T cells on the basis of CD62L expression was investigated as part of a machine-based manufacturing process, incorporating lentiviral transduction, CRISPR-Cas9 editing, T-cell expansion and depletion of residual TCR{beta} T cells. This provided stringent mitigation against the risk of graft versus host disease (GVHD), and was combined with simultaneous knockout of CD52 to enable persistence of edited T cells in combination with preparative lymphodepletion using Alemtuzumab. Under compliant manufacturing conditions, two cell banks were generated with high levels of CAR19 expression and minimal carriage of TCR{beta} T cells. Sufficient cells were cryopreserved in dose-banded aliquots at the end of each campaign to treat dozens of potential recipients. Molecular characterisation captured vector integration sites and CRISPR editing signatures and functional studies, including in vivo potency studies in humanised mice, confirmed anti-leukaemic activity comparable to peripheral blood-derived universal CAR19 T cells. Machine manufactured UCB derived T cells banks offer an alternative to autologous cell therapies and could help widen access to CAR T cells.

molecular biology↗

bioRxiv2023

Optimizing CRE and PhiC31 mediated recombination in Aedes aegypti

Genetic manipulation of Aedes aegypti is key to developing a deeper understanding of this insects biology, vector-virus interactions and makes future genetic control strategies possible. Despite some advances, this process remains laborious and requires highly skilled researchers and specialist equipment. Here we present two improved methods for genetic manipulation in this species. Use of transgenic lines which express Cre recombinase allowed, by simple crossing schemes, germline or somatic recombination of transgenes, which could be utilized for numerous genetic manipulations. PhiC31 integrase based methods for site-specific integration of genetic elements was also improved, by developing a plasmid which expresses PhiC31 when injected into early embryos, eliminating the need to use costly and unstable mRNA as is the current standard.

bioengineering↗

bioRxiv2022

Comparing the accuracy and efficiency of third generation DNA barcode sequencing: Oxford Nanopore Technologies versus Pacific Biosciences

At times of drastic decrease in biodiversity and loss of species, sometimes referred to as the "sixth mass extinction" or "Holocene extinction", there is a high demand on the development of effective tools for studying and monitoring biodiversity. In the past decade, new promising technologies, such as third generation sequencing (TGS), enabled massive, rapid, and cost-effective data analysis of non-model organisms, accelerating taxonomic identification studies and contributing to conservation applications. Here, we focus on the comparison of the two main TGS providers, Pacific Biosciences (PacBio), and Oxford Nanopore Technologies (ONT), for the purpose of DNA barcoding. For ONT, we also tested selected combinations of different types of flow cells and ligation sequencing kits. Out of five tested combinations (PacBio, ONT Flongle flow cell & SQK-LSK110 kit, R9 flow cell & SQK-LSK109 kit, R9 & SQK-LSK100 kit, and R10 flow cell & Q20+ chemistry kit), ONTs Flongle turned out to be most variable in returning the results, but at the same time the most cost efficient. The highest numbers of successfully sequenced samples were achieved with the ONTs R10 & Q20+ chemistry combination. In terms of library preparation time, ONT protocols are the quickest, whereas regarding cost effectiveness - using Sanger pricing per sample as a cut-off - various technologies become affordable depending on the number of samples used. Although both tested platforms are suitable for DNA barcoding, we further discuss their limitations and applicability to different studies, with a special focus on the price and the number of samples. The pipeline we developed, from whole specimens to final DNA barcode consensuses, can aid planning and budgeting biodiversity studies, maximising the number of specimens sequenced in one run and speeding up the sample processing time.

molecular biology↗

bioRxiv2021

How low can you go? Driving down the DNA input requirements for nanopore sequencing

The requirement for large amounts of purified DNA limits many sequencing experiments, especially when seeking to avoid pre-amplification or when using third generation technology to sequence molecules directly. We wanted to test the limits of current nanopore sequencing input requirements and devised a set of experiments to evaluate extraction and library preparation approaches for low inputs. We found an optimised bead beating approach combined with a magnetic bead protocol, rather than traditional spin columns for DNA extraction, improved both molecule length, integrity score and DNA yield. Through reducing the DNA input to as little as 6.25 % of recommended (25 ng versus 400 ng) and reaction volumes in half, library construction can be completed, and sequencing begun within 20 minutes of sample collection. Applying these approaches, we demonstrated that our pipeline can be used as a cheap and effective method to de novo assemble a genome and identify genes from low quantities and quality of DNA. With our rapid extraction protocol using transportable equipment and low input library construction we were able to generate a de novo assembly from a single insect (Drosophila melanogaster) spanning 125 Mbp / 85 % of the reference genome, over 96.9% complete BUSCO genes, with a contig N50 over 1.2 Mbp, including chromosome arm sized contigs, for a modest consumable cost under {pound}600.

genomics↗