Biology subjects

Glendinning, L.

Publications and source records attributed to Glendinning, L..

11 recordsLinked to original sources

bioRxiv2026

Longitudinal analysis of vaccine-associated alterations in the faecal microbiota of layer chickens using a vaccination schedule representative of commercial practice

The gut microbiota is crucial for immune development and overall health in chickens. In commercial production, birds routinely receive multiple vaccines during early life. While individual vaccines are known to affect microbial composition, the impact of complex, multi-vaccine programs, as used in the poultry industry, is not well understood. This longitudinal study examined the impact of multiple live and inactivated vaccines, given at commercially relevant times from an early age, on gut microbial diversity and composition in layer chickens. We characterised microbiota profiles using 16S rRNA gene sequencing at pre- and post-vaccination timepoints across different vaccine groups. Overall, microbial diversity remained stable across most vaccines, indicating strong resilience of the gut microbiota to repeated immunological interventions. Differential abundance analyses identified changes in selected bacterial taxa following vaccination, with responses varying among vaccine groups. Notably, these changes were not sustained, as the gut microbial community returned to a stable state after the vaccination schedule. These findings underscore the robustness of the chicken gut ecosystem and lay a foundation for future research into microbiome-vaccine interactions and their implications for poultry health, immunity, and production efficiency.

microbiology↗

bioRxiv2025

Integrative multi-omics analysis of dietary fibre-induced modulations in the composition and function of chicken caecal microbiota

BackgroundThe sustainability of poultry farming faces significant challenges due to rising feed costs and competition with human food sources. Dietary fibre offers a promising, cost-effective alternative due to its beneficial impact on gut health. We utilised a multi-omics approach to understand the influence of soluble inulin and insoluble cellulose dietary fibres on the composition and function of caecal microbiota in broilers. ResultsHigh inulin significantly altered caecal microbial composition and promoted broader microbial metabolic adaptations, while high cellulose had a minimal impact. ConclusionsThese findings will enhance our understanding of how various fibre types and quantities shape gut microbiota, ultimately leading to improved poultry performance.

microbiology↗

bioRxiv2025

Metagenomics reveals fibre fermentation and AMR pathways in red grouse (Lagopus scotica) microbiota

BackgroundThe avian caecal microbiota plays a vital role in host nutrition, enabling non-digestible, fibrous material to be converted into compounds that can be absorbed and used as an energy source by the host. The diet of adult red grouse (Lagopus scotica) is dominated by heather (Calluna vulgaris), which is particularly high in fibre. It is therefore likely that the caecal microbiota plays a key role in enabling grouse to thrive on this diet. In this study, we present the first characterisation of the caecal microbiota of red grouse using modern sequencing methods. ResultsWe performed metagenomic sequencing on caecal content samples from fifteen red grouse from three upland estates in Scotland. From this data, we constructed and characterised twelve high-quality, species-level metagenome assembled genomes (MAGs). Eleven of these MAGs could not be assigned a taxonomic label at species level, indicating that they may be novel species. MAGs belonged to diverse taxa (5 phyla) and several encoded genes and pathways for the digestion of fibres, including cellulose, hemi-cellulose, xylooligosaccharides and pectin. Several MAGs also contained antimicrobial resistance genes, predominantly related to vancomycin resistance. ConclusionsThis study is the first to reconstruct commensal microbial genomes from red grouse. The caeca contain diverse, often novel, microbial taxa capable of fermenting various fibres, potentially aiding in the digestion of the red grouses high-fibre diet. Further research is necessary to explore how these bacteria support red grouse nutrition and health.

microbiology↗

bioRxiv2025

Interleukin 10 controls the balance between tolerance, pathogen elimination and immunopathology in birds.

Effective mucosal immunity in the intestine involves a fine balance between tolerance of the microbiome, recognition and elimination of pathogens, and inflammatory tissue injury. The anti-inflammatory cytokine IL10 regulates these processes in the intestines of mice and humans; the anti-inflammatory activity of IL10 is also conserved in birds. To determine the function of IL10 in avian mucosal immunity, we generated germ line modifications of the chicken IL10 locus to abolish or reduce IL10 expression. In vitro analysis of macrophage response to lipopolysaccharide confirmed the loss of IL10 protein expression, the lack of dosage compensation in heterozygotes, and prevention of autocrine inhibition of nitric oxide production in homozygous IL10 knockout macrophages. IL10-deficiency significantly altered the composition of the caecal microbiome, but unlike IL10-deficient mice and humans, IL10-deficient chickens did not exhibit spontaneous colitis. Following experimental challenge with Salmonella enterica serovar Typhimurium or Campylobacter jejuni in IL10-deficient chickens, enhanced clearance of the pathogens was associated with elevated transcription of pro-inflammatory genes and increased infiltration of inflammatory cells into gut mucosa. In IL10-deficient chickens challenged with the parasite Eimeria tenella, pathogen clearance was accelerated but caecal lesions were more severe and weight gain was compromised. Neither the heterozygous IL10 knockout nor a homozygous IL10 enhancer mutation had a major effect on pathogen clearance or inflammation in any of the challenge models. Our findings highlight the intrinsic compromise in mucosal immune response and have important implications for the development of strategies to combat avian and zoonotic pathogens in poultry.

immunology↗

bioRxiv2024

Determining the culturability of the bovine rumen bacterial and archaeal microbiota

Ruminants play an important part in global food security, but also emit methane which contributes to global warming. Microbes in the rumen strongly influence the energy retention efficiency from the hosts plant-based diet and produce methane as a by-product. While thousands of novel microbial genomes have been assembled from metagenome sequence data, their culturability is ill-defined. Here different media were used to isolate microbes from rumen fluid. 34 genera were grown, and the majority belonged to the phylum Bacillota (75.28% {+/-} 6.34), Bacteroidota (19.99% {+/-} 4.85), Pseudomonadota (2.46% {+/-} 2.01), and Actinomycetota (2.09% {+/-} 1.07). The most abundant genera were Selenomonas (28.08% {+/-} 11.71), Streptococcus (22.67% {+/-} 6.06), Prevotella (18.71% {+/-} 4.02), and unclassified Lachnospiraceae (11.50% {+/-} 2.54). When comparing the mean relative abundance of these genera between media, 31 were significantly enriched on at least one medium. The composition of the source rumen fluid was vastly different to those cultured. Bacteroidota (52.53% {+/-} 5.10) predominated, with by Bacillota (41.00% {+/-} 3.96), the archaeal Euryarchaeota (5.12% {+/-} 1.94), Pseudomonadota (1.22% {+/-} 0.78), and Actinomycetota (0.12% {+/-} 0.08) comprising the rest. The most abundant genera were Prevotella (29.13% {+/-} 4.16), Butyrivibrio (18.21% {+/-} 2.08), Succiniclasticum (15.57% {+/-} 5.03), unclassified Bacteroidetes (13.91% {+/-} 1.67), and unclassified Prevotellaceae (9.50% {+/-} 2.01). These data further emphasise the importance of using defined media to selectively enrich for different microbial taxa. This is essential to understand the complex workings of the rumen microbes to enhance digestion efficiency and reduce the loss of energy as methane.

microbiology↗

bioRxiv2024

Infectious bronchitis virus vaccination, but not the presence of XCR1, is correlated with large differences in chicken caecal microbiota

The chicken immune system and microbiota play vital roles in maintaining gut homeostasis and protecting against pathogens. In mammals, XCR1+ conventional dendritic cells (cDCs) are located in the gut-draining lymph nodes and play a major role in gut homeostasis. These cDCs sample antigens in the gut luminal contents and limit the inflammatory response to gut commensal microbes by generating appropriate regulatory and effector T-cell responses. We hypothesised that these cells play similar roles in sustaining gut homeostasis in chickens, and that chickens lacking XCR1 were likely to contain a dysbiotic caecal microbiota. Here we compare the caecal microbiota of chickens that were either heterozygous or homozygous XCR1 knockouts, that had or had not been vaccinated for infectious bronchitis virus (IBV). We used short-read (Illumina) and long-read (PacBio HiFi) metagenomic sequencing to reconstruct 670 high-quality, strain-level metagenome assembled genomes. We found no significant differences between alpha-diversity or the abundance of specific microbial taxa between genotypes. However, IBV vaccination was found to correlate with significant differences in the richness and beta-diversity of the microbiota, and to the abundance of forty bacterial genera. In conclusion, we found that a lack of XCR1 was not correlated with significant changes in the chicken microbiota, but IBV vaccination was. Data SummaryThe raw sequencing data for this project, as well as primary assemblies, putative genome bins and species-level MAGs, are available in the European Nucleotide Archive under project PRJEB64517. Strain-level MAGs are available through Edinburgh DataShare (https://doi.org/10.7488/ds/7678). Impact statementChickens play a vital role in global food systems, with 74 billion chickens killed for meat and 1.6 trillion chicken eggs produced in 2021 alone. The gut microbiota plays a vital role in the health and nutrition of the chicken, contributing to gut homeostasis and the production of nutrients that can be absorbed and used by the host bird. The chicken gut microbiota represents an excellent target to improve pathogen resistance and nutrition, as farmed chickens are not exposed to a maternal hen and thereby develop a low-diversity gut microbiota that negatively impacts their immune development and gut health. In order to develop such microbiota interventions, we first need to understand the fundamental biology behind immune-microbiota interactions. While it is well known that the chicken gut microbiota plays an important role in gut homeostasis, the mechanisms behind this phenomenon are poorly understood. In mammals, XCR1+ conventional dendritic cells have been shown to play a role in maintaining gut homeostasis. In this study we compare the gut microbiota of heterozygous and homozygous XCR1 knockout chickens that did or did not receive infectious bronchitis virus vaccination. We found that the gut microbiota of heterozygous and homozygous XCR1 knockout chickens did not differ significantly, but IBV vaccination did significantly correlate with differences in the microbiota composition.

microbiology↗

bioRxiv2023

Altitude-dependent agro-ecologies impact the microbiome diversity of scavenging indigenous chicken in Ethiopia

Scavenging indigenous village chickens play a vital role in sub-Saharan Africa, sustaining the livelihood of millions of farmers. These chickens are exposed to vastly different environments and feeds compared to commercial chickens. In this study, we analysed the caecal microbiota of 243 Ethiopian village chickens living in different altitude-dependent agro-ecologies. Differences in bacterial diversity were significantly correlated with differences in specific climate factors, topsoil characteristics, and supplemental diets provided by farmers. Microbiota clustered into 3 enterotypes, with one particularly enriched at high altitudes. We assembled 9,977 taxonomically and functionally diverse metagenome-assembled genomes, the vast majority of which were not found in a dataset of previously published chicken microbes, or in the Genome Taxonomy Database. The wide functional and taxonomic diversity of these microbes highlights their importance in the local adaptation of indigenous poultry, and the significant impacts of environmental factors on the microbiota argues for further discoveries in other agro-ecologies.

microbiology↗

bioRxiv2022

Investigating the impact of database choice on the accuracy of metagenomic read classification for the rumen microbiome

Microbiome analysis is quickly moving towards high-throughput methods such as metagenomic sequencing. Accurate taxonomic classification of metagenomic data relies on reference sequence databases, and their associated taxonomy. However, for understudied environments such as the rumen microbiome many sequences will be derived from novel or uncultured microbes that are not present in reference databases. As a result, taxonomic classification of metagenomic data from understudied environments may be inaccurate. To assess the accuracy of taxonomic read classification, this study classified metagenomic data that had been simulated from cultured rumen microbial genomes from the Hungate collection. To assess the impact of reference databases on the accuracy of taxonomic classification, the data was classified with Kraken 2 using several reference databases. We found that the choice and composition of reference database significantly impacted on taxonomic classification results, and accuracy. In particular, NCBI RefSeq proved to be a poor choice of database. Our results indicate that inaccurate read classification is likely to be a significant problem, affecting all studies that use insufficient reference databases. We observe that adding cultured reference genomes from the rumen to the reference database greatly improves classification rate and accuracy. We also demonstrate that metagenome-assembled genomes (MAGs) have the potential to further enhance classification accuracy by representing uncultivated microbes, sequences of which would otherwise be unclassified or incorrectly classified. However, classification accuracy was strongly dependent on the taxonomic labels assigned to these MAGs. We therefore highlight the importance of accurate reference taxonomic information and suggest that, with formal taxonomic lineages, MAGs have the potential to improve classification rate and accuracy, particularly in environments such as the rumen that are understudied or contain many novel genomes.

genomics↗

bioRxiv2020

Metagenomic analysis of the cow, sheep, reindeer and red deer rumen

The rumen microbiota comprises a community of microorganisms which specialise in the degradation of complex carbohydrates from plant-based feed. These microbes play a highly important role in ruminant nutrition and could also act as sources of industrially useful enzymes. In this study, we performed a metagenomic analysis of samples taken from the ruminal contents of cattle (Bos Taurus), sheep (Ovis aries), reindeer (Rangifer tarandus) and red deer (Cervus elaphus). We constructed 391 metagenome-assembled genomes originating from 16 microbial phyla. We compared our genomes to other publically available microbial genomes and found that they contained 279 novel species. We also found significant differences between the microbiota of different ruminant species in terms of the abundance of microbial taxonomies, carbohydrate-active enzyme genes and KEGG orthologs. However, we found that the vast majority of carbohydrate-active enzymes were present in all of our sample types, which may indicate that there is a core set of these enzymes which are present across ruminants and are independent of diet and environmental conditions. We present a dataset of rumen-derived genomes which in combination with other publicly-available rumen genomes can be used as a reference dataset in future metagenomic studies. Data SummaryThe paired-read fastq files supporting the conclusions of this article are available in the European Nucleotide Archive repository (https://www.ebi.ac.uk/ena/browser/view/PRJEB34458). The RUG fasta files supporting the conclusions of this article are available in the Edinburgh DataShare repository (https://doi.org/10.7488/ds/2640).

microbiology↗

bioRxiv2019

Development of the duodenal, ileal, jejunal and caecal microbiota in chickens

BackgroundThe chicken intestinal microbiota plays a large role in chicken health and productivity and a greater understanding of its development may lead to interventions to improve chicken nutrition, disease resistance and welfare.\n\nResultsIn this study we examine the duodenal, jejunal, ileal and caecal microbiota of chickens from day of hatch to 5 weeks of age (day 1, 3, 7, 14 and week 5). DNA was extracted from intestinal content samples and the V4 region of the 16S rRNA gene was amplified and sequenced. We identify significant differences in microbial community composition, diversity and richness between samples taken from different locations within the chicken intestinal tract. We also characterise the development of the microbiota at each intestinal site over time.\n\nConclusionsOur study builds upon existing literature to further characterise the development of the chicken intestinal microbiota.

microbiology↗

bioRxiv2019

Assembly of hundreds of novel bacterial genomes from the chicken caecum

Chickens are a highly important source of protein for a large proportion of the human population. The caecal microbiota plays a crucial role in chicken nutrition through the production of short chain fatty acids, nitrogen recycling and amino acid production. In this study we sequenced DNA from caecal contents samples taken from 24 chickens belonging to either a fast or slower growing breed consuming either a vegetable-only diet or a diet containing fish meal. We utilised 1.6T of Illumina data to construct 469 draft metagenome-assembled bacterial genomes, including 460 novel strains, 283 novel species and 42 novel genera. We compared our genomes to data from eight EU countries and show that these genomes are abundant within European chicken flocks. We also compared the abundance of our genomes, and the carbohydrate active enzymes they produce, between our chicken groups and demonstrate that there are both breed- and diet-specific microbiomes, as well as an overlapping core microbiome. This data will form the basis for future studies examining the composition and function of the chicken caecal microbiota.

microbiology↗