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18 results on '"Eckenberger, Julia"'

2. Targeted isolation of bacteria with potential to competitively excludeStaphylococcus aureusin the upper respiratory tract of pigs

Author

Vlasblom, Abel A., primary, Patel, Shriram, additional, Lawlor, Peadar G., additional, Claesson, Marcus J., additional, Crespo-Piazuelo, Daniel, additional, Eckenberger, Julia, additional, Huseyin, Chloe Elizabeth, additional, Elend, Christian, additional, Wagenaar, Jaap A, additional, Zomer, Aldert L., additional, and Duim, Birgitta, additional

Published
2024
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6. Machine learning approaches in microbiome research: challenges and best practices

Author

Papoutsoglou, Georgios, primary, Tarazona, Sonia, additional, Lopes, Marta B., additional, Klammsteiner, Thomas, additional, Ibrahimi, Eliana, additional, Eckenberger, Julia, additional, Novielli, Pierfrancesco, additional, Tonda, Alberto, additional, Simeon, Andrea, additional, Shigdel, Rajesh, additional, Béreux, Stéphane, additional, Vitali, Giacomo, additional, Tangaro, Sabina, additional, Lahti, Leo, additional, Temko, Andriy, additional, Claesson, Marcus J., additional, and Berland, Magali, additional

Published
2023
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10. Low-Molecular-Weight Seaweed-Derived Polysaccharides Lead to Increased Faecal Bulk but Do Not Alter Human Gut Health Markers

Author

Bannon, Ciara D., primary, Eckenberger, Julia, additional, Snelling, William John, additional, Huseyin, Chloe Elizabeth, additional, Allsopp, Philip, additional, Strain, Conall, additional, Ramnani, Priya, additional, Chitarrari, Roberto, additional, Grant, John, additional, Hotchkiss, Sarah, additional, Philp, Kevin, additional, Campbell, Ross, additional, Tuohy, Kieran Michael, additional, Claesson, Marcus J., additional, Ternan, Nigel George, additional, Dooley, James S. G., additional, Sleator, Roy D., additional, Rowland, Ian, additional, and Gill, Chris I. R., additional

Published
2021
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11. Additional file 6 of Japanese quail (Coturnix japonica) as a novel model to study the relationship between the avian microbiome and microbial endocrinology-based host-microbe interactions

Author

Lyte, Joshua M., Keane, James, Eckenberger, Julia, Anthony, Nicholas, Sandip Shrestha, Marasini, Daya, Daniels, Karrie M., Caputi, Valentina, Donoghue, Annie M., and Lyte, Mark

Abstract

Additional file 5: Supplemental Table 3. Title of data (Plasma neurohormonal plasticity to handling stress is similar between low (LS) and high (HS) stress responsive Japanese quail). Description of data. (Plasma plasticity to handling stress is similar between low (LS) and high (HS) stress-responsive Japanese quail).

Published
2021
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12. Additional file 16 of Japanese quail (Coturnix japonica) as a novel model to study the relationship between the avian microbiome and microbial endocrinology-based host-microbe interactions

Author

Lyte, Joshua M., Keane, James, Eckenberger, Julia, Anthony, Nicholas, Sandip Shrestha, Marasini, Daya, Daniels, Karrie M., Caputi, Valentina, Donoghue, Annie M., and Lyte, Mark

Abstract

Additional file 15: Supplemental Table 6. Title of data (Correlation metrics for significant associations from the high stress ensemble network). Description of data. (Statistical scores from the Conet Analysis (Pearson, Spearman, Bray Curtis, Kullback-Liebler and Mutual Information) that support inclusion of an edge in the high stress ensemble network. qvalues (Adjusted pvalues) for each edge in the high stress ensemble network from the Conet, Spearman and Pearson networks are also presented).

Published
2021
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13. Additional file 4 of Japanese quail (Coturnix japonica) as a novel model to study the relationship between the avian microbiome and microbial endocrinology-based host-microbe interactions

Author

Lyte, Joshua M., Keane, James, Eckenberger, Julia, Anthony, Nicholas, Sandip Shrestha, Marasini, Daya, Daniels, Karrie M., Caputi, Valentina, Donoghue, Annie M., and Lyte, Mark

Abstract

Additional file 3: Supplemental Table 1. Title of data (Liver neurohormonal plasticity to handling stress is similar between low (LS) and high (HS) stress responsive Japanese quail). Description of data. (Liver plasticity to handling stress is similar between low (LS) and high (HS) stress-responsive Japanese quail).

Published
2021
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14. Additional file 5 of Japanese quail (Coturnix japonica) as a novel model to study the relationship between the avian microbiome and microbial endocrinology-based host-microbe interactions

Author

Lyte, Joshua M., Keane, James, Eckenberger, Julia, Anthony, Nicholas, Sandip Shrestha, Marasini, Daya, Daniels, Karrie M., Caputi, Valentina, Donoghue, Annie M., and Lyte, Mark

Abstract

Additional file 4: Supplemental Table 2. Title of data (Lung neurohormonal plasticity to handling stress is similar between low (LS) and high (HS) stress responsive Japanese quail). Description of data. (Lung plasticity to handling stress is similar between low (LS) and high (HS) stress-responsive Japanese quail).

Published
2021
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15. Japanese quail (Coturnix japonica) as a novel model to study the relationship between the avian microbiome and microbial endocrinology-based host-microbe interactions

Author

Lyte, Joshua M., primary, Keane, James, additional, Eckenberger, Julia, additional, Anthony, Nicholas, additional, Shrestha, Sandip, additional, Marasini, Daya, additional, Daniels, Karrie M., additional, Caputi, Valentina, additional, Donoghue, Annie M., additional, and Lyte, Mark, additional

Published
2021
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16. Ranking microbiome variance in inflammatory bowel disease: a large longitudinal intercontinental study

Author

Clooney, Adam G, primary, Eckenberger, Julia, additional, Laserna-Mendieta, Emilio, additional, Sexton, Kathryn A, additional, Bernstein, Matthew T, additional, Vagianos, Kathy, additional, Sargent, Michael, additional, Ryan, Feargal J, additional, Moran, Carthage, additional, Sheehan, Donal, additional, Sleator, Roy D, additional, Targownik, Laura E, additional, Bernstein, Charles N, additional, Shanahan, Fergus, additional, and Claesson, Marcus J, additional

Published
2020
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17. Ranking microbiome variance in inflammatory bowel disease: a large longitudinal intercontinental study.

Author

Clooney, Adam G., Eckenberger, Julia, Laserna-Mendieta, Emilio, Sexton, Kathryn A., Bernstein, Matthew T., Vagianos, Kathy, Sargent, Michael, Ryan, Feargal J., Moran, Carthage, Sheehan, Donal, Sleator, Roy D., Targownik, Laura E., Bernstein, Charles N., Shanahan, Fergus, and Claesson, Marcus J.

Subjects
INFLAMMATORY bowel diseases, LARGE intestine, CROHN'S disease, LONGITUDINAL method, CLOSTRIDIA, LIFE sciences
Published
2021
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18. The developing pig respiratory microbiome harbors strains antagonistic to common respiratory pathogens.

Author

Vlasblom AA, Duim B, Patel S, Luiken REC, Crespo-Piazuelo D, Eckenberger J, Huseyin CE, Lawlor PG, Elend C, Wagenaar JA, Claesson MJ, and Zomer AL

Abstract

In the global efforts to combat antimicrobial resistance and reduce antimicrobial use in pig production, there is a continuous search for methods to prevent and/or treat infections. Within this scope, we explored the relationship between the developing piglet nasal microbiome and (zoonotic) bacterial pathogens from birth until 10 weeks of life. The nasal microbiome of 54 pigs was longitudinally studied over 16 timepoints on 9 farms in 3 European countries (Germany, Ireland, and the Netherlands) using amplicon sequencing targeting the V3-V4 16S rRNA region as well as the tuf gene for its staphylococcal discrimination power. The piglets' age, the farm, and the litter affected the nasal microbiome, with piglets' age explaining 19% of the variation in microbial composition between samples. Stabilization of the microbiome occurred around 2 weeks post-weaning. Notably, while opportunistic pathogens were ubiquitously present, they did not cause disease. The piglet nasal microbiome often carried species associated with gut, skin, or vagina, which suggests that contact with the vaginal and fecal microbiomes shapes the piglet nasal microbiome. We identified bacterial co-abundance groups of species that were present in the nasal microbiomes in all three countries over time. Anti-correlation between these species and known bacterial pathogens identified species that might be exploited for pathogen reduction. Further experimental evidence is required to confirm these findings. Overall, this study advances our understanding of the piglet nasal microbiome, the factors influencing it, and its longitudinal development, providing insights into its role in health and disease., Importance: Our study on the nasal microbiota development in piglets across farms in three European countries found that the microbiomes developed similarly in all locations. Additionally, we observed that the colonization of porcine pathogens was either positively or negatively associated with the presence of other bacterial species. These findings enhance our knowledge of co-colonizing species in the nasal cavity and the identified microbial interactions that can be explored for the development of interventions to control pathogens in porcine husbandry.

Published
2024
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