Understanding microbiomes of the ruminant holobiont

Project Information

HoloRuminant

Grant agreement ID: 101000213

DOI

10.3030/101000213

EC signature date 6 May 2021

Start date 1 October 2021

End date 30 September 2026

Funded under

• SOCIETAL CHALLENGES - Food security, sustainable agriculture and forestry, marine, maritime and inland water research, and the bioeconomy

Total cost

€ 10 895 021,00

EU contribution

€ 9 724 763,75

Coordinated by

INSTITUT NATIONAL DE RECHERCHE POUR L'AGRICULTURE, L'ALIMENTATION ET L'ENVIRONNEMENT
France

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

Open Research Data Pilot (2)

HoloRuminant Data Management Plan (update at M18)

HoloRuminant Data Management Plan update at M18

HoloRuminant Data Management Plan

Documents, reports (1)

Communication toolkit and project identity

Publications

Peer reviewed articles (22)

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

Author(s): Yang, H., Heirbaut, S., Jing, X. et al.
Published in: Journal of Animal Science and Biotechnology, 2022, ISSN 1674-9782
Publisher: BioMed Central
DOI: 10.1186/s40104-022-00738-8

Public acceptance of microbiome management strategy in dairy calves: a European survey on colostrum, probiotic provision and prolonged cow-calf contact

Author(s): A. Ait Sidhoum, A. Stygar, F. Bedoin, J.K. Niemi
Published in: animal, Issue 19, 2025, Page(s) 101380, ISSN 1751-7311
Publisher: Cambridge University Press
DOI: 10.1016/j.animal.2024.101380

Protozoal populations drive system-wide variation in the rumen microbiome

Author(s): Carl M. Kobel, Andy Leu, Arturo Vera-Ponce de León, Ove Øyås, Wanxin Lai, Ianina Altshuler, Live H. Hagen, Rasmus D. Wollenberg, Mads T. Søndergaard, Cassie R. Bakshani, William G. T. Willats, Laura Nicoll, Simon J. McIlroy, Torgeir R. Hvidsten, Oliver Schmidt, Chris Greening, Gene W. Tyson, Rainer Roehe, Velma T. E. Aho, Phillip B. Pope
Published in: Nature Communications, Issue 16, 2025, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-025-61302-2

Metabolic capabilities of key rumen microbiota drive methane emissions in cattle

Author(s): Wanxin Lai, Antton Alberdi, Andy Leu, Arturo V. P. de Leon, Carl M. Kobel, Velma T. E. Aho, Rainer Roehe, Phil B. Pope, Torgeir R. Hvidsten
Published in: mSystems, Issue 10, 2025, ISSN 2379-5077
Publisher: American Society for Microbiology
DOI: 10.1128/msystems.00601-25

A Comprehensive Review: Bovine Respiratory Disease, Current Insights into Epidemiology, Diagnostic Challenges, and Vaccination

Author(s): Stephanie O’Donoghue, Sinéad M. Waters, Derek W. Morris, Bernadette Earley
Published in: Veterinary Sciences, Issue 12, 2025, Page(s) 778, ISSN 2306-7381
Publisher: MDPI AG
DOI: 10.3390/vetsci12080778

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

Author(s): H. Yang, S. Heirbaut, J. Jeyanathan, X.P. Jing, N. De Neve, L. Vandaele, V. Fievez
Published in: Journal of Dairy Science, 2022, ISSN 0022-0302
Publisher: American Dairy Science Association
DOI: 10.3168/jds.2021-21115

Empowering bioinformatics communities with Nextflow and nf-core

Author(s): Björn E. Langer, Andreia Amaral, Marie-Odile Baudement, Franziska Bonath, Mathieu Charles, Praveen Krishna Chitneedi, Emily L. Clark, Paolo Di Tommaso, Sarah Djebali, Philip A. Ewels, Sonia Eynard, James A. Fellows Yates, Daniel Fischer, Evan W. Floden, Sylvain Foissac, Gisela Gabernet, Maxime U. Garcia, Gareth Gillard, Manu Kumar Gundappa, Cervin Guyomar, Christopher Hakkaart, Friederike Hanssen
Published in: Genome Biology, Issue 26, 2025, ISSN 1474-760X
Publisher: Springer Science and Business Media LLC
DOI: 10.1186/s13059-025-03673-9

Feed additives for methane mitigation: A guideline to uncover the mode of action of antimethanogenic feed additives for ruminants

Author(s): Alejandro Belanche, André Bannink, Jan Dijkstra, Zoey Durmic, Florencia Garcia, Fernanda G. Santos, Sharon Huws, Jeyamalar Jeyanathan, Peter Lund, Roderick I. Mackie, Tim A. McAllister, Diego P. Morgavi, Stefan Muetzel, Dipti W. Pitta, David R. Yáñez-Ruiz, Emilio M. Ungerfeld
Published in: Journal of Dairy Science, Issue 108, 2025, Page(s) 375-394, ISSN 0022-0302
Publisher: American Dairy Science Association
DOI: 10.3168/jds.2024-25046

Rumen microbiota associated with feed efficiency in beef cattle are highly influenced by diet composition

Author(s): Abimael Ortiz-Chura, Karla Fabiola Corral-Jara, Jeremy Tournayre, Gonzalo Cantalapiedra-Hijar, Milka Popova, Diego P. Morgavi
Published in: Animal Nutrition, Issue 21, 2025, Page(s) 378-389, ISSN 2405-6545
Publisher: Elsevier BV
DOI: 10.1016/j.aninu.2024.11.027

Response of Primary Mammary Epithelial Cells to Pathogen Challenge in Dairy Cows with Divergent Genomic Breeding Values for Udder Health

Author(s): Terhi Iso-Touru, Daniel Fischer, Frank Panitz, Suvi Taponen, Zexi Cai, Goutam Sahana, Ilma Tapio, Johanna Vilkki
Published in: Genomics, Issue Volume 117, Issue 5, 2025, ISSN 0888-7543
Publisher: Academic Press
DOI: 10.2139/ssrn.5277413

Can high-lipid concentrates offset the high enteric methane production caused by high-forage diets fed to lactating dairy cows?

Author(s): N. Ayanfe, I. Tapio, S. Ahvenjärvi, M. Rinne, A. Sairanen, A.R. Bayat
Published in: Journal of Dairy Science, Issue 108, 2025, Page(s) 8350-8366, ISSN 0022-0302
Publisher: American Dairy Science Association
DOI: 10.3168/jds.2024-26108

CompareM2 is a genomes-to-report pipeline for comparing microbial genomes

Author(s): Carl M Kobel, Velma T E Aho, Ove Øyås, Niels Nørskov-Lauritsen, Ben J Woodcroft, Phillip B Pope
Published in: Bioinformatics, Issue 41, 2025, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btaf517

Duration of dam contact had a long effect on calf rumen microbiota without affecting growth

Author(s): Laurianne Voland, Abimael Ortiz-Chura, Jeremy Tournayre, Bruno Martin, Matthieu Bouchon, Alessandra Nicolao, Dominique Pomiès, Diego P. Morgavi, Milka Popova
Published in: Frontiers in Veterinary Science, Issue 12, 2025, ISSN 2297-1769
Publisher: Frontiers Media SA
DOI: 10.3389/fvets.2025.1548892

Effects of feed additives in the diet of male dairy beef calves on physiological status and rumen microbial fermentation pre- and postweaning

Author(s): E. Romera-Recio, E. Ramos-Morales, A. Belanche, M. Hassan, P. Romero, A. Gómez, I. Rivelli, N. Llanes, J. Torra, D.R. Yáñez-Ruiz
Published in: Animal Feed Science and Technology, Issue 321, 2025, Page(s) 116243, ISSN 0377-8401
Publisher: Elsevier BV
DOI: 10.1016/j.anifeedsci.2025.116243

International Symposium on Ruminant Physiology: The role of rumen microbiome in the development of methane mitigation strategies for ruminant livestock

Author(s): S.M. Waters, E. Roskam, P.E. Smith, D.A. Kenny, M. Popova, M. Eugène, D.P. Morgavi
Published in: Journal of Dairy Science, Issue 108, 2025, Page(s) 7591-7606, ISSN 0022-0302
Publisher: American Dairy Science Association
DOI: 10.3168/jds.2024-25778

Genes and pathways revealed by whole transcriptome analysis of milk derived bovine mammary epithelial cells after Escherichia coli challenge

Author(s): Terhi Iso-Touru, Frank Panitz, Daniel Fischer, Minna K. Kyläniemi, Suvi Taponen, Jonna Tabell, Anneli Virta, Johanna Vilkki
Published in: Veterinary Research, Issue 55, 2024, ISSN 1297-9716
Publisher: Veterinary research
DOI: 10.1186/s13567-024-01269-y

Ruminant microbiome data are skewed and unFAIR, undermining their usefulness for sustainable production improvement

Author(s): Abimael Ortiz-Chura, Milka Popova, Diego P. Morgavi
Published in: Animal Microbiome, Issue 6, 2024, ISSN 2524-4671
Publisher: National Library of Medicine
DOI: 10.1186/s42523-024-00348-x

Health-associated changes of the fecal microbiota in dairy heifer calves during the pre-weaning period

Author(s): Sabine Scully, Bernadette Earley, Paul E. Smith, Catherine McAloon, Sinéad M. Waters
Published in: Frontiers in Microbiology, Issue 15, 2024, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2024.1359611

Recent Advances in Enteric Methane Mitigation and the Long Road to Sustainable Ruminant Production

Author(s): Simon Roques, Gonzalo Martinez-Fernandez, Yuliaxis Ramayo-Caldas, Milka Popova, Stuart Denman, Sarah J. Meale, Diego P. Morgavi
Published in: Annual Review of Animal Biosciences, Issue 12, 2024, Page(s) 321-343, ISSN 2165-8102
Publisher: Annual Reviews Inc.
DOI: 10.1146/annurev-animal-021022-024931

Characterisation of the bacterial and archaeal microbiota in fresh colostrum collected from a single, spring-calving dairy herd

Author(s): Sabine Scully, Bernadette Earley, Paul E. Smith, Matthew S. J. Finnie, Catherine McAloon, Frank Buckley, David A. Kenny, Sinéad M. Waters
Published in: PLOS One, Issue 20, 2025, Page(s) e0335718, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0335718

Co-occurring microbial guilds in pig fecal microbiota: key drivers and effects on host performance

Author(s): Ioanna-Theoni Vourlaki, Raquel Rio-Lopez, Adrià Clavell-Sansalvador, Lino C. Ramírez-Ayala, Maria Ballester, Juan P. Sanchez, Miriam Piles, Raquel Quintanilla, Angela C. da Fonseca de Oliveira, Leandro Batista Costa, Antoni Dalmau, Yuliaxis Ramayo-Caldas
Published in: Genetics Selection Evolution, Issue 57, 2025, ISSN 1297-9686
Publisher: Springer Science and Business Media LLC
DOI: 10.1186/s12711-025-00979-x

Integrating host and microbiome biology using holo-omics

Author(s): Carl M. Kobel, Jenny Merkesvik, Idun Maria Tokvam Burgos, Wanxin Lai, Ove Øyås, Phillip B. Pope, Torgeir R. Hvidsten, Velma T. E. Aho
Published in: Molecular Omics, Issue 20, 2024, Page(s) 438-452, ISSN 2515-4184
Publisher: Royal Society of Chemistry (RSC)
DOI: 10.1039/d4mo00017j