Skip to main content

Research Repository

Advanced Search

All Outputs (35)

Impact of commercial gut health interventions on caecal metagenome and broiler performance (2025)
Journal Article
Pangga, G., Star-Shirko, B., Psifidi, A., Xia, D., Corcionivoschi, N., Kelly, C., Hughes, C., Lavery, U., Richmond, A., Ijaz, U., & Gundogdu, O. (2025). Impact of commercial gut health interventions on caecal metagenome and broiler performance. Microbiome, 13(1), https://doi.org/10.1186/s40168-024-02012-7

BackgroundMaintaining gut health is a persistent and unresolved challenge in the poultry industry. Given the critical role of gut health in chicken performance and welfare, there is a pressing need to identify effective gut health intervention (GHI)... Read More about Impact of commercial gut health interventions on caecal metagenome and broiler performance.

Identification of DNA methylation markers for age and Bovine Respiratory Disease in dairy cattle: A pilot study based on Reduced Representation Bisulfite Sequencing (2024)
Journal Article
Attree, E., Griffiths, B., Panchal, K., Xia, D., Werling, D., Banos, G., Oikonomou, G., & Psifidi, A. (in press). Identification of DNA methylation markers for age and Bovine Respiratory Disease in dairy cattle: A pilot study based on Reduced Representation Bisulfite Sequencing. Communications Biology, 7(1), https://doi.org/10.1038/s42003-024-06925-9

Multi-omics analysis reveals regime shifts in the gastrointestinal ecosystem in chickens following anticoccidial vaccination and Eimeria tenella challenge (2024)
Journal Article
Liu, P.-Y., Liaw, J., Soutter, F., Ortiz, J. J., Tomley, F. M., Werling, D., Gundogdu, O., Blake, D. P., & Xia, D. (in press). Multi-omics analysis reveals regime shifts in the gastrointestinal ecosystem in chickens following anticoccidial vaccination and Eimeria tenella challenge. mSystems, https://doi.org/10.1128/msystems.00947-24

Large-scale statistical analysis of Mycobacterium tuberculosis genome sequences identifies compensatory mutations associated with multi-drug resistance (2024)
Journal Article
Billow, N., Phelan, J., Xia, D., Peng, Y., Clark, T. G., & Chang, Y.-M. (in press). Large-scale statistical analysis of Mycobacterium tuberculosis genome sequences identifies compensatory mutations associated with multi-drug resistance. Scientific Reports, https://doi.org/10.1038/s41598-024-62946-8

Tuberculosis (TB), caused by Mycobacterium tuberculosis, has a significant impact on global health worldwide. The development of multi-drug strains that are resistant to the first-line drugs isoniazid and rifampicin threatens public health security.... Read More about Large-scale statistical analysis of Mycobacterium tuberculosis genome sequences identifies compensatory mutations associated with multi-drug resistance.

Chicken caecal enterotypes in indigenous Kadaknath and commercial Cobb chicken lines are associated with Campylobacter abundance and influenced by farming practices (2023)
Journal Article
Hay, M. C., Hinsu, A. T., Koringa, P. G., Pandit, R. J., Liu, P.-Y., Parekh, M. J., Jakhesara, S. J., Dai, X., Crotta, M., Fosso, B., Limon, G., Guitian, J., Tomley, F. M., Xia, D., Psifidi, A., Joshi, C. G., & Blake, D. P. (2023). Chicken caecal enterotypes in indigenous Kadaknath and commercial Cobb chicken lines are associated with Campylobacter abundance and influenced by farming practices. Frontiers in Microbiomes, https://doi.org/10.3389/frmbi.2023.1301609

Immune-mediated hematological disease in dogs is associated with alterations of the fecal microbiota: a pilot study (2023)
Journal Article
Liu, P.-Y., Xia, D., McGonigle, K., Carroll, A. B., Chiango, J., Scavello, H., Martins, R., Mehta, S., Krespan, E., Lunde, E., LeVine, D., Fellman, C. L., Goggs, R., Beiting, D. P., & Garden, O. A. (in press). Immune-mediated hematological disease in dogs is associated with alterations of the fecal microbiota: a pilot study. Animal Microbiome, 5(1), https://doi.org/10.1186/s42523-023-00268-2

Feature Weighted Models (FWM) to address lineage dependency in drug-resistance prediction from Mycobacterium tuberculosis genome sequences (2023)
Journal Article
Chang, Y.-M., Xia, D., & Billows, N. (2023). Feature Weighted Models (FWM) to address lineage dependency in drug-resistance prediction from Mycobacterium tuberculosis genome sequences. Bioinformatics, 39(7), https://doi.org/10.1093/bioinformatics/btad428

Background: Tuberculosis is caused by members of the Mycobacterium tuberculosis complex (MTBC) and is the second leading infectious killer after COVID-19. The evolution of drug-resistance poses a threat to successful treatment and disease eradication... Read More about Feature Weighted Models (FWM) to address lineage dependency in drug-resistance prediction from Mycobacterium tuberculosis genome sequences.

Characterisation of Canine Intestinal MicroRNA Expression in Inflammatory Bowel Disease and T-Cell Lymphoma (2023)
Journal Article
Williams, J., Werling, D., Davison, L., Hiron, T., & Xia, D. (in press). Characterisation of Canine Intestinal MicroRNA Expression in Inflammatory Bowel Disease and T-Cell Lymphoma. Journal of Comparative Pathology, https://doi.org/10.1016/j.jcpa.2023.03.186

Differentiating between canine inflammatory bowel disease and intestinal T-cell lymphoma via histopathological examination of endoscopically-derived intestinal biopsies can be challenging and involves an invasive procedure requiring specialised equip... Read More about Characterisation of Canine Intestinal MicroRNA Expression in Inflammatory Bowel Disease and T-Cell Lymphoma.

Differential expression of microRNAs in the caecal content and faeces of broiler chickens experimentally infected with Eimeria (2022)
Journal Article
Williams, J., Blake, D., & Xia, D. (2022). Differential expression of microRNAs in the caecal content and faeces of broiler chickens experimentally infected with Eimeria. Avian Pathology, https://doi.org/10.1080/03079457.2022.2076581

Differential expression of microRNAs in the caecal content and faeces of broiler chickens experimentally infected with Eimeria

Evidence of altered fatty acid metabolism in dogs with naturally occurring valvular heart disease and congestive heart failure (2022)
Journal Article
Wilshaw, J., Boswood, A., Chang, Y., Sands, C., Camuzeaux, S., Lewis, M., Xia, D., & Connolly, D. (2022). Evidence of altered fatty acid metabolism in dogs with naturally occurring valvular heart disease and congestive heart failure. Metabolomics, 18(6), https://doi.org/10.1007/s11306-022-01887-7

Introduction Myxomatous mitral valve disease (MMVD) is the most common cardiac condition in adult dogs. The disease progresses over several years and affected dogs may develop congestive heart failure (HF). Research has shown that myocardial metaboli... Read More about Evidence of altered fatty acid metabolism in dogs with naturally occurring valvular heart disease and congestive heart failure.

The translocator protein (TSPO) is prodromal to mitophagy loss in neurotoxicity (2021)
Journal Article
Frison, M., Faccenda, D., Abeti, R., Rigon, M., Strobbe, D., England-Rendon, B., Cash, D., Barnes, K., Sadeghian, M., Sajic, M., Wells, L., Xia, D., Giunti, P., Smith, K., Mortiboys, H., Turkheimer, F., & Campanella, M. (2021). The translocator protein (TSPO) is prodromal to mitophagy loss in neurotoxicity. Molecular Psychiatry, 26(7), 2721-2739. https://doi.org/10.1038/s41380-021-01050-z

Dysfunctional mitochondria characterise Parkinson's Disease (PD). Uncovering etiological molecules, which harm the homeostasis of mitochondria in response to pathological cues, is therefore pivotal to inform early diagnosis and therapy in the conditi... Read More about The translocator protein (TSPO) is prodromal to mitophagy loss in neurotoxicity.

Bioinformatic Analysis of the Campylobacter jejuni Type VI Secretion System and Effector Prediction (2021)
Journal Article
Robinson, L., Liaw, J., Omole, Z., Xia, D., van Vliet, A., Corcionivoschi, N., Hachani, A., & Gundogdu, O. (2021). Bioinformatic Analysis of the Campylobacter jejuni Type VI Secretion System and Effector Prediction. Frontiers in Microbiology, 12, https://doi.org/10.3389/fmicb.2021.694824

The Type VI Secretion System (T6SS) has important roles relating to bacterial antagonism, subversion of host cells, and niche colonisation. Campylobacter jejuni is one of the leading bacterial causes of human gastroenteritis worldwide and is a commen... Read More about Bioinformatic Analysis of the Campylobacter jejuni Type VI Secretion System and Effector Prediction.

Accuracy of history, physical examination, cardiac biomarkers, and biochemical variables in identifying dogs with stage B2 degenerative mitral valve disease (2021)
Journal Article
Wilshaw, J., Rosenthal, S., Wess, G., Dickson, D., Bevilacqua, L., Dutton, E., Deinert, M., Abrantes, R., Schneider, I., Oyama, M., Gordon, S., Elliott, J., Xia, D., & Boswood, A. (2021). Accuracy of history, physical examination, cardiac biomarkers, and biochemical variables in identifying dogs with stage B2 degenerative mitral valve disease. Journal of Veterinary Internal Medicine, 35(2), 755-770. https://doi.org/10.1111/jvim.16083

Background Treatment is indicated in dogs with preclinical degenerative mitral valve disease (DMVD) and cardiomegaly (stage B2). This is best diagnosed using echocardiography; however, relying upon this limits access to accurate diagnosis. Objectives... Read More about Accuracy of history, physical examination, cardiac biomarkers, and biochemical variables in identifying dogs with stage B2 degenerative mitral valve disease.

Probing Differences in Gene Essentiality Between the Human and Animal Adapted Lineages of the Mycobacterium tuberculosis Complex Using TnSeq (2021)
Journal Article
Gibson, A., Passmore, I., Faulkner, V., Xia, D., Nobeli, I., Stiens, J., Willcocks, S., Clark, T., Sobkowiak, B., Werling, D., Villarreal-Ramos, B., Wren, B., & Kendall, S. (2021). Probing Differences in Gene Essentiality Between the Human and Animal Adapted Lineages of the Mycobacterium tuberculosis Complex Using TnSeq. Frontiers in Veterinary Science, 8, https://doi.org/10.3389/fvets.2021.760717

Members of the Mycobacterium tuberculosis complex (MTBC) show distinct host adaptations, preferences and phenotypes despite being >99% identical at the nucleic acid level. Previous studies have explored gene expression changes between the members, ho... Read More about Probing Differences in Gene Essentiality Between the Human and Animal Adapted Lineages of the Mycobacterium tuberculosis Complex Using TnSeq.

Probing differences in gene essentiality between the human and animal adapted (2021)
Journal Article
Gibson, A. J., Passmore, I. J., Faulkner, V., Xia, D., Nobeli, I., Stiens, J., Clarke, T. G., Sobkowiak, B., Willcocks, S., Werling, D., Villarreal-Ramos, B., Wren, B. W., & Kendall, S. L. (2021). Probing differences in gene essentiality between the human and animal adapted. Frontiers in Veterinary Science,

Members of the Mycobacterium tuberculosis complex (MTBC) show distinct host adaptations, preferences and phenotypes despite being >99% identical at the nucleic acid level. Previous studies have explored gene expression changes between the members, ho... Read More about Probing differences in gene essentiality between the human and animal adapted.

Controlling the causative agents of coccidiosis in domestic chickens; an eye on the 1 past and considerations for the future 2 (2021)
Journal Article
Attree, E., Sanchez-Arsuaga, G., Jones, M., Xia, D., -Hernandez, M., Blake, D., & Tomley, F. (2021). Controlling the causative agents of coccidiosis in domestic chickens; an eye on the 1 past and considerations for the future 2. CAB Reviews: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources, https://doi.org/10.1186/s43170-021-00056-5

Coccidiosis is a potentially severe enteritis caused by species of obligate intracellular parasites of the genus Eimeria. These parasites cause significant economic losses to the poultry industry, predominantly due to compromised efficiency of produc... Read More about Controlling the causative agents of coccidiosis in domestic chickens; an eye on the 1 past and considerations for the future 2.

Genetic and biological characterisation of three cryptic Eimeria operational taxonomic units that infect chickens (Gallus gallus domesticus) (2021)
Journal Article
Blake, D., Blake, D., Vrba, V., Xia, D., Xia, D., Tomley, F., Danladi Jatau, I., Spiro, S., Nolan, M. J., Underwood, G., & Tomley, F. (2021). Genetic and biological characterisation of three cryptic Eimeria operational taxonomic units that infect chickens (Gallus gallus domesticus). International Journal for Parasitology,

More than 68 billion chickens were produced globally in 2018, emphasising their major contribution to the production of protein for human consumption, and the importance of their pathogens. Protozoan Eimeria species are the most economically signific... Read More about Genetic and biological characterisation of three cryptic Eimeria operational taxonomic units that infect chickens (Gallus gallus domesticus).

Transcriptomic Profiling of In Vitro Tumor-Stromal Cell Paracrine Crosstalk Identifies Involvement of the Integrin Signaling Pathway in the Pathogenesis of Mesenteric Fibrosis in Human Small Intestinal Neuroendocrine Neoplasms (2021)
Journal Article
Laskaratos, F.-M., Levi, A., Schwach, G., Pfragner, R., Hall, A., Xia, D., von Stempel, C., Bretherton, J., Thanapirom, K., Alexander, S., Ogunbiyi, O., Watkins, J., Luong, T. V., Toumpanakis, C., Mandair, D., Caplin, M., & Rombouts, K. (in press). Transcriptomic Profiling of In Vitro Tumor-Stromal Cell Paracrine Crosstalk Identifies Involvement of the Integrin Signaling Pathway in the Pathogenesis of Mesenteric Fibrosis in Human Small Intestinal Neuroendocrine Neoplasms. Frontiers in Oncology, 11, https://doi.org/10.3389/fonc.2021.629665