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Peer-reviewed publications

2025

  • Characterisation of the bacterial and archaeal microbiota in fresh colostrum collected from a single, spring-calving dairy herd. Scully S, Earley B, Smith PE, Finnie MSJ, McAloon C, Buckley F, et al. (2025). PLoS One 20(10): e0335718. DOI:10.1371/journal.pone.0335718 (10/25).
  • CompareM2 is a genomes-to-report pipeline for comparing microbial genomes. Kobel, Carl M, Aho, Velma T E, Øyås, Ove, Nørskov-Lauritsen, Niels, Woodcroft, Ben J, Pope, Phillip B. Bioinformatics 2025. ISSN 1367-4811. DOI: 10.1093/bioinformatics/btaf517. (09/25).
  • Metabolic capabilities of key rumen microbiota drive methane emissions in cattle. Lai W, Alberdi A, Leu A, de Leon AVP, Kobel CM, Aho VTE, Roehe R, Pope PB, Hvidsten TR. 0. mSystems 0:e00601-25. DOI: doi.org/10.1128/msystems.00601-25 (09/25).
  • A Comprehensive Review: Bovine Respiratory Disease, Current Insights into Epidemiology, Diagnostic Challenges, and Vaccination. O’Donoghue, S.; Waters, S.M.; Morris, D.W.; Earley, B. Vet. Sci. 2025, 12, 778. DOI: 10.3390/vetsci12080778 (08/25).
  • Response of primary mammary epithelial cells to pathogen challenge in dairy cows with divergent genomic breeding values for udder health. Terhi Iso-Touru, Daniel Fischer, Frank Panitz, Suvi Taponen, Zexi Cai, Goutam Sahana, Ilma Tapio, Johanna Vilkki, Genomics, Volume 117, Issue 5, 2025, 111102, ISSN 0888-7543, DOI: 10.1016/j.ygeno.2025.111102. (08/25).
  • Empowering bioinformatics communities with Nextflow and nf-core. Langer, B.E., Amaral, A., Baudement, MO. et al. Genome Biol 26, 228 (2025). DOI: 10.1186/s13059-025-03673-9 (07/25).
  • Protozoal populations drive system-wide variation in the rumen microbiome. Kobel, C.M., Leu, A., Vera-Ponce de León, A. et al.  Nat Commun 16, 6238 (2025). DOI: 10.1038/s41467-025-61302-2 (07/25).
  • Rumen microbiota associated with feed efficiency in beef cattle are highly influenced by diet composition. Abimael Ortiz-Chura, Karla Fabiola Corral-Jara, Jeremy Tournayre, Gonzalo Cantalapiedra-Hijar, Milka Popova, Diego P. Morgavi, Animal Nutrition, Volume 21, 2025, Pages 378-389, ISSN 2405-6545, DOI: 10.1016/j.aninu.2024.11.027. (06/25).
  • Co-occurring microbial guilds in pig fecal microbiota: key drivers and effects on host performance. Vourlaki, IT., Rio-Lopez, R., Clavell-Sansalvador, A. et al. Genet Sel Evol 57, 27 (2025). DOI: 10.1186/s12711-025-00979-x. (06/25).
  • Duration of dam contact had a long effect on calf rumen microbiota without affecting growth. Voland, L., A. Ortiz-Chura, J. Tournayre, B. Martin, M. Bouchon, A. Nicolao, D. Pomies, D. P. Morgavi, and M. Popova. Front Vet Sci Volume 12 – 2025 | DOI: 10.3389/fvets.2025.1548892 (05/25).
  • Can high-lipid concentrates offset the high enteric methane production caused by high-forage diets fed to lactating dairy cows N. Ayanfe, I. Tapio, S. Ahvenjärvi, M. Rinne, A. Sairanen, A.R. Bayat, Journal of Dairy Science, Volume 0, Issue 0. DOI: 10.3168/jds.2024-26108 (05/25).
  • International Symposium on Ruminant Physiology: The role of rumen microbiome in the development of methane mitigation strategies for ruminant livestock * Waters, S.M. et al. Journal of Dairy Science, Volume 108, Issue 7, 7591 – 7606 DOI: 10.3168/jds.2024-25778
  • Effects of feed additives in the diet of male dairy beef calves on physiological status and rumen microbial fermentation pre- and postweaning. E. Romera-Recio, E. Ramos-Morales, A. Belanche, M. Hassan, P. Romero, A. Gómez, I. Rivelli, N. Llanes, J. Torra, D.R. Yáñez-Ruiz, Animal Feed Science and Technology, Volume 321, 2025, 116243, ISSN 0377-8401, DOI:10.1016/j.anifeedsci.2025.116243. (01/25).
  • Public acceptance of microbiome management strategy in dairy calves: a European survey on colostrum, probiotic provision and prolonged cow-calf contact. A. Ait Sidhoum, A. Stygar, F. Bedoin, J.K. Niemi.  animal, Volume 19, Issue 1, 2025, 101380, ISSN 1751-7311, DOI: 10.1016/j.animal.2024.101380. (01/25).

2024

  • Ruminant microbiome data are skewed and unFAIR, undermining their usefulness for sustainable production improvement. Ortiz-Chura, A., Popova, M. & Morgavi, D.P.  anim microbiome 6, 61 (2024). DOI: 10.1186/s42523-024-00348-x (10/24).
  • Feed additives for methane mitigation: A guideline to uncover the mode of action of antimethanogenic feed additives for ruminants. Belanche, Alejandro et al. Journal of Dairy Science, Volume 108, Issue 1, 375 – 394 DOI: 10.3168/jds.2024-25046 (08/24).
  • Integrating host and microbiome biology using holo-omics. Kobel CM, Merkesvik J, Burgos IMT, et al. Molecular Omics. 2024 Aug;20(7):438-452. DOI: 10.1039/d4mo00017j. PMID: 38963125. (08/24).
  • Health-associated changes of the fecal microbiota in dairy heifer calves during the pre-weaning period. Scully S, Earley B, Smith PE, McAloon C and Waters SM (2024) Front. Microbiol. 15:1359611. DOI: 10.3389/fmicb.2024.1359611 (04/24).
  • Recent Advances in Enteric Methane Mitigation and the Long Road to Sustainable Ruminant Production. Roques S, Martinez-Fernandez G, Ramayo-Caldas Y, et al.  Annual Review of Animal Biosciences. 2024 Feb;12:321-343. DOI: 10.1146/annurev-animal-021022-024931 (02/24).
  • Genes and pathways revealed by whole transcriptome analysis of milk derived bovine mammary epithelial cells after Escherichia coli challenge. Iso-Touru, T., Panitz, F., Fischer, D. et al.  Vet Res 55, 13 (2024). DOI:10.1186/s13567-024-01269-y (02/24).

2022

  • Susceptibility of dairy cows to subacute ruminal acidosis is reflected in both prepartum and postpartum bacteria as well as odd- and branched-chain fatty acids in feces. Yang, H., Heirbaut, S., Jing, X. et al. J Animal Sci Biotechnol 13, 87 (2022). October 5, 2022. DOI:https://doi.org/10.1186/s40104-022-00738-8 (10/22).
  • Subacute ruminal acidosis phenotypes in periparturient dairy cows differ in ruminal and salivary bacteria and in the in vitro fermentative activity of their ruminal microbiota H. Yang S. Heirbaut J. Jeyanathan N. De Neve L. Vandaele V. Fievez. Journal of Dairy Science. February 24, 2022. DOI:https://doi.org/10.3168/jds.2021-21115 (02/22).