Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range
Open accessAbstract
Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was determined in 742 samples from 32 animal species and 35 countries, to estimate if this was influenced by diet, host species, or geography. Similar bacteria and archaea dominated in nearly all samples, while protozoal communities were more variable. The dominant bacteria are poorly characterised, but the methanogenic archaea are better known and highly conserved across the world. This universality and limited diversity could make it possible to mitigate methane emissions by developing strategies that target the few dominant methanogens. Differences in microbial community compositions were predominantly attributable to diet, with the host being less influential. There were few strong co-occurrence patterns between microbes, suggesting that major metabolic interactions are non-selective rather than specific.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Members of the methanogen clades Methanobrevibacter gottschalkii and Methanobrevibacter ruminantium were found in nearly all samples and accounted for 74% of the archaea.
“Members of the methanogen clades Methanobrevibacter gottschalkii and Methanobrevibacter ruminantium were found in nearly all samples and accounted for 74% of the archaea.”
From Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future (2018) · cites this paper as Henderson et al., 2015
A global comparison study of the rumen microbiome in 742 samples across 32 species identified that 30 of the most abundant bacterial groups were present in over 90% of the samples.
“A recent global comparison study of the rumen microbiome in 742 samples across 32 species from various geographical locations (Henderson et al., 2015), identified that 30 of the most abundant bacterial groups were present in over 90% of the samples.”
From Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future (2018) · cites this paper as Henderson et al., 2015
The composition of the rumen microbiome is mainly driven by diet.
“This study also concluded that the composition of the rumen microbiome was mainly driven by the diet (Henderson et al., 2015).”
From Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future (2018) · cites this paper as Henderson et al., 2015
Diet is the main driver for rumen microbiome composition.
“Whilst Henderson et al. (2015) postulated that diet was the main driver for rumen microbiome composition, they also identified some differences in the relative abundance of certain bacterial populations across ruminant species.”
From Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future (2018) · cites this paper as Henderson et al., 2015
Differences in rumen and camelid foregut volume, physiology as well as feeding frequencies were suggested as a reason for the proportionally higher abundance of unclassified Veillonellaceae in camelids, deer and sheep compared to cattle.
“For example, differences in rumen and camelid foregut volume, physiology as well as feeding frequencies, was suggested as a reason for the proportionally higher abundance of unclassified Veillonellaceae in camelids, deer and sheep compared to cattle (Henderson et al., 2015).”
From Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future (2018) · cites this paper as Henderson et al., 2015
Differences in the relative abundance of certain bacterial populations exist across ruminant species.
“they also identified some differences in the relative abundance of certain bacterial populations across ruminant species.”
From Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future (2018) · cites this paper as Henderson et al., 2015
Rumen physiology is a potential factor that influences the rumen microbiome.
“The physiology of the rumen has also been highlighted as a potential factor that influences the rumen microbiome.”
From Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future (2018) · cites this paper as Henderson et al., 2015
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669 · see citing works
QIIME allows analysis of high-throughput community sequencing data
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.303 · Cited by 34,887 · see citing works
Search and clustering orders of magnitude faster than BLAST
Edgar, R. C. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq461 · Cited by 20,617 · see citing works
Nutritional ecology of the ruminant
Soest, P. J. V. (1995) · Choice Reviews Online · doi:10.5860/choice.32-4505 · Cited by 7,714 · see citing works
Nutritional Ecology of the Ruminant
Soest, P. J. V. (1994) · Cornell University Press eBooks · doi:10.7591/9781501732355 · Cited by 7,331 · see citing works
McDonald, D. T., Price, M. N., Goodrich, J. K., Nawrocki, E. P., DeSantis, T. Z., Probst, A. J., Andersen, G. L., Knight, R. D., & Hugenholtz, P. (2011) · The ISME Journal · doi:10.1038/ismej.2011.139 · Cited by 5,010 · see citing works
Interactions Between the Microbiota and the Immune System
Hooper, L. V., Littman, D. R., & Macpherson, A. J. (2012) · Science · doi:10.1126/science.1223490 · Cited by 4,173 · see citing works
Hungate, R. E. (2013) · Elsevier eBooks · doi:10.1016/c2013-0-12555-x · Cited by 3,060 · see citing works
Inferring Correlation Networks from Genomic Survey Data
Friedman, J., & Alm, E. J. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002687 · Cited by 2,688 · see citing works
Hofmann, R. R. (1989) · Oecologia · doi:10.1007/bf00378733 · Cited by 1,812 · see citing works
Bellerophon: a program to detect chimeric sequences in multiple sequence alignments
Huber, T., Faulkner, G. J., & Hugenholtz, P. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth226 · Cited by 1,532 · see citing works
Electron transfer in syntrophic communities of anaerobic bacteria and archaea
Stams, A. J. M., & Plugge, C. M. (2009) · Nature Reviews Microbiology · doi:10.1038/nrmicro2166 · Cited by 1,441 · see citing works
Rubel, F., & Kottek, M. (2010) · Meteorologische Zeitschrift · doi:10.1127/0941-2948/2010/0430 · Cited by 1,093 · see citing works
Factors That Alter Rumen Microbial Ecology
Russell, J. B., & Rychlik, J. L. (2001) · Science · doi:10.1126/science.1058830 · Cited by 954 · see citing works
Williams, A. G., & Coleman, G. S. (1991) · Cited by 675 · see citing works
Structure of the Archaeal Community of the Rumen
Janssen, P. H., & Kirs, M. (2008) · Applied and Environmental Microbiology · doi:10.1128/aem.02812-07 · Cited by 655 · see citing works
Self-citationPotential role of the bovine rumen microbiome in modulating milk composition and feed efficiency
Jami, E., White, B. A., & Mizrahi, I. (2014) · PLoS ONE · doi:10.1371/journal.pone.0085423 · Cited by 588 · see citing works
Weimer, P. J. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00296 · Cited by 487 · see citing works
Status of the phylogenetic diversity census of ruminal microbiomes
Kim, M., Morrison, M., & Yu, Z. (2011) · FEMS Microbiology Ecology · doi:10.1111/j.1574-6941.2010.01029.x · Cited by 407 · see citing works
Ruminants, climate change and climate policy
Ripple, W. J., Smith, P., Haberl, H., Montzka, S. A., McAlpine, C., & Boucher, D. H. (2014) · Nature Climate Change · doi:10.1038/nclimate2081 · Cited by 390 · see citing works
Miller, T. L., & Wolin, M. J. (1985) · Archives of Microbiology · doi:10.1007/bf00423270 · Cited by 363 · see citing works
Paul, K., Nonoh, J. O., Mikulski, L., & Brune, A. (2012) · Applied and Environmental Microbiology · doi:10.1128/aem.02193-12 · Cited by 346 · see citing works
Henderson, G., Cox, F., Kittelmann, S., Miri, V. H., Zethof, M., Noel, S. J., Waghorn, G. C., & Janssen, P. H. (2013) · PLoS ONE · doi:10.1371/journal.pone.0074787 · Cited by 328 · see citing works
Self-citationVisualising associations between paired ‘omics’ data sets
González, I., Cao, K. L., Davis, M. J., & Dejean, S. (2012) · BioData Mining · doi:10.1186/1756-0381-5-19 · Cited by 316 · see citing works
Carberry, C. A., Kenny, D. A., Han, S., McCabe, M. S., & Waters, S. M. (2012) · Applied and Environmental Microbiology · doi:10.1128/aem.07759-11 · Cited by 311 · see citing works
Self-citationWilliams, A. G., & Coleman, G. S. (1992) · Brock/Springer series in contemporary bioscience · doi:10.1007/978-1-4612-2776-2 · Cited by 304 · see citing works
Newbold, C. J., Lassalas, B., & Jouany, J. P. (1995) · Letters in Applied Microbiology · doi:10.1111/j.1472-765x.1995.tb01048.x · Cited by 296 · see citing works
Borrel, G., Parisot, N., Harris, H. M. B., Peyretaillade, É., Gaci, N., Tottey, W., Bardot, O., Raymann, K., Gribaldo, S., Peyret, P., et al. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-679 · Cited by 294 · see citing works
Two different bacterial community types are linked with the low-methane emission trait in sheep.
Kittelmann, S., Pinares-Patiño, C. S., Seedorf, H., Kirk, M. R., Ganesh, S., McEwan, J. C., & Janssen, P. H. (2014) · PLoS ONE · doi:10.1371/journal.pone.0103171 · Cited by 277 · see citing works
Self-citationSuen, G., Weimer, P. J., Stevenson, D. M., Aylward, F. O., Boyum, J., Deneke, J., Drinkwater, C., Ivanova, N., Mikhailova, N., Chertkov, O., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0018814 · Cited by 233 · see citing works
Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows
Godoy‐Vitorino, F., Goldfarb, K. C., Karaöz, U., Leal, S. J., García-Amado, M. A., Hugenholtz, P., Tringe, S. G., Brodie, E., & Domínguez-Bello, M. G. (2011) · The ISME Journal · doi:10.1038/ismej.2011.131 · Cited by 207 · see citing works
Pope, P. B., Mackenzie, A. K., Gregor, I., Smith, W. J. M., Sundset, M. A., McHardy, A. C., Morrison, M., & Eijsink, V. G. H. (2012) · PLoS ONE · doi:10.1371/journal.pone.0038571 · Cited by 201 · see citing works
Self-citationType material in the NCBI Taxonomy Database
Federhen, S. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1127 · Cited by 185 · see citing works
Hackmann, T. J., & Spain, J. N. (2010) · Journal of Dairy Science · doi:10.3168/jds.2009-2071 · Cited by 174 · see citing works
Determining the culturability of the rumen bacterial microbiome
Creevey, C. J., Kelly, W. J., Henderson, G., & Leahy, S. C. (2014) · Microbial Biotechnology · doi:10.1111/1751-7915.12141 · Cited by 173 · see citing works
Self-citationVitamin B12-dependent propionate production by the ruminal bacterium Prevotella ruminicola 23
Strobel, H. J. (1992) · Applied and Environmental Microbiology · doi:10.1128/aem.58.7.2331-2333.1992 · Cited by 169 · see citing works
Seedorf, H., Kittelmann, S., Henderson, G., & Janssen, P. H. (2014) · PeerJ · doi:10.7717/peerj.494 · Cited by 168 · see citing works
Self-citationPaillard, D., McKain, N., Chaudhary, L. C., Walker, N. D., Pizette, F., Koppova, I., McEwan, N. R., Kopečný, J., Vercoe, P. E., Louis, P., et al. (2006) · Antonie van Leeuwenhoek · doi:10.1007/s10482-006-9121-7 · Cited by 164 · see citing works
Estimates of animal methane emissions
Johnson, D. E., & Ward, G. M. (1996) · Environmental Monitoring and Assessment · doi:10.1007/bf00394046 · Cited by 160 · see citing works
Do Rumen Bacteroidetes Utilize an Alternative Mechanism for Cellulose Degradation?
Naas, A. E., Mackenzie, A. K., Mravec, J., Schückel, J., Willats, W. G. T., Eijsink, V. G. H., & Pope, P. B. (2014) · mBio · doi:10.1128/mbio.01401-14 · Cited by 153 · see citing works
Self-citationUden, P. C., Rounsaville, T. R., Wiggans, G. R., et al. (1982) · British Journal Of Nutrition · doi:10.1079/bjn19820117 · Cited by 148 · see citing works
Ríus, A. G., Kittelmann, S., Macdonald, K. A., Waghorn, G. C., Janssen, P. H., & Sikkema, E. (2012) · Journal of Dairy Science · doi:10.3168/jds.2012-5392 · Cited by 141 · see citing works
Self-citationCHARACTERISTICS OF TWO NEW GENERA OF ANAEROBIC CURVED RODS ISOLATED FROM THE RUMEN OF CATTLE
Bryant, M. P., & Small, N. (1956) · Journal of Bacteriology · doi:10.1128/jb.72.1.22-26.1956 · Cited by 139 · see citing works
Pectin-fermenting Bacteria Isolated from the Bovine Rumen
Dehority, B. A. (1969) · Journal of Bacteriology · doi:10.1128/jb.99.1.189-196.1969 · Cited by 132 · see citing works
Kittelmann, S., & Janssen, P. H. (2010) · FEMS Microbiology Ecology · doi:10.1111/j.1574-6941.2010.01022.x · Cited by 122 · see citing works
Self-citationKenters, N., Henderson, G., Jeyanathan, J., Kittelmann, S., & Janssen, P. H. (2011) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2010.10.011 · Cited by 108 · see citing works
Seedorf, H., Kittelmann, S., & Janssen, P. H. (2014) · Applied and Environmental Microbiology · doi:10.1128/aem.03018-14 · Cited by 69 · see citing works
Self-citationMcAllister, T. A., Meale, S. J., Valle, E., Guan, L., Zhou, M., Kelly, W. J., Henderson, G., Attwood, G. T., & Janssen, P. H. (2015) · Journal of Animal Science · doi:10.2527/jas.2014-8329 · Cited by 66 · see citing works
Self-citationReal-Time PCR Detection of the Effects of Protozoa on Rumen Bacteria in Cattle
Ozutsumi, Y., Tajima, K., Takénaka, A., et al. (2006) · Current Microbiology · doi:10.1007/s00284-005-0266-9 · Cited by 41 · see citing works
Anaerobic Ciliates and Their Methanogenic Endosymbionts
Hackstein, J. H. P. (2010) · Microbiology monographs · doi:10.1007/978-3-642-13615-3_2 · Cited by 39 · see citing works
Tymensen, L. D., & McAllister, T. A. (2012) · Applied and Environmental Microbiology · doi:10.1128/aem.07994-11 · Cited by 39 · see citing works
Self-citationNyonyo, T., Shinkai, T., Tajima, A., & Mitsumori, M. (2012) · Letters in Applied Microbiology · doi:10.1111/lam.12019 · Cited by 34 · see citing works
Self-citationREMARKS ON THE STOMACH AND THE SYSTEMATIC POSITION OF THE TYLOPODA
Bohlken, H. (1960) · Proceedings of the Zoological Society of London · doi:10.1111/j.1469-7998.1960.tb05588.x · Cited by 25 · see citing works
Gastro-enteric methane versus sulphate and volatile fatty acid production
Nollet, L. M. L., & Verstraete, W. (1996) · Environmental Monitoring and Assessment · doi:10.1007/bf00394045 · Cited by 14 · see citing works
Use of genomics and transcriptomics to identify strategies to lower ruminal methanogenesis
McAllister, T. A. (2014) · 2014 ADSA-ASAS-CSAS Joint Annual Meeting · Cited by 10 · see citing works
Self-citation
Flagged first, then by citations
Research works printed but not linked: 3
- Dehority B. A. in Parasitic Protozoa Vol. 3 (eds Kreier J. P. & Baker J. R.) Ch. 1, 1– 42 (Academic Press, Inc., 1993).
- Hackstein J. H. P. in (Endo)symbiotic Methanogenic Archaea Microbiology Monographs 19 (ed. Hackstein J. H. P.) 13– 23 (Springer-Verlag Berlin Heidelberg, 2010).
- GenStat for Windows 14th Edition (Hemel Hempstead, UK, 2011).
Cited by
Sorted by citations
Specific microbiome-dependent mechanisms underlie the energy harvest efficiency of ruminants.
Shabat, S. K. B., Sasson, G., Doron-Faigenboim, A., Durman, T., Yaacoby, S., Berg Miller, M. E., White, B. A., Shterzer, N., & Mizrahi, I. (2016) · The ISME Journal · doi:10.1038/ismej.2016.62 · Cited by 823 · see citing works
Self-citationAmerican Gut: an Open Platform for Citizen-Science Microbiome Research
McDonalda, D., Hyde, E., Debelius, J. W., Morton, J. T., Gonzalez, A., Ackermann, G., Aksenov, A. A., Behsaz, B., Brennan, C., Chen, Y., et al. (2018) · doi:10.1101/277970 · Cited by 878 · see citing works
Prevotella Diversity, Niches and Interactions with the Human Host
Tett, A., Pasolli, E., Masetti, G., Ercolini, D., & Segata, N. (2021) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00559-y · Cited by 748 · see citing works
Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection
Hungate1000 project collaborators, Seshadri, R., Leahy, S. C., Attwood, G. T., Teh, K. H., Lambie, S. C., Cookson, A. L., Eloe-Fadrosh, E. A., Pavlopoulos, G. A., Hadjithomas, M., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4110 · Cited by 624 · see citing works
Self-citationLi, F., Li, C., Chen, Y., Liu, J., Zhang, C., Irving, B., Fitzsimmons, C., Plastow, G., & Guan, L. L. (2019) · Microbiome · doi:10.1186/s40168-019-0699-1 · Cited by 530 · see citing works
The rumen microbiome: balancing food security and environmental impacts
Mizrahi, I., Wallace, R. J., & Moraïs, S. (2021) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00543-6 · Cited by 490 · see citing works
Self-citationHuws, S. A., Creevey, C. J., Oyama, L. B., Mizrahi, I., Denman, S. E., Popova, M., Muñoz-Tamayo, R., Forano, E., Waters, S. M., Hess, M., et al. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.02161 · Cited by 487 · see citing works
Self-citationA heritable subset of the core rumen microbiome dictates dairy cow productivity and emissions
Wallace, R. J., Sasson, G., Garnsworthy, P. C., Tapio, I., Gregson, E., Bani, P., Huhtanen, P., Bayat, A. R., Strozzi, F., Biscarini, F., et al. (2019) · Science Advances · doi:10.1126/sciadv.aav8391 · Cited by 410 · see citing works
Self-citationThe ruminal microbiome associated with methane emissions from ruminant livestock
Tapio, I., Snelling, T. J., Strozzi, F., & Wallace, R. J. (2017) · Journal of Animal Science and Biotechnology · doi:10.1186/s40104-017-0141-0 · Cited by 391 · see citing works
Self-citationAntimicrobial usage and resistance in beef production
Cameron, A., & McAllister, T. A. (2016) · Journal of Animal Science and Biotechnology · doi:10.1186/s40104-016-0127-3 · Cited by 207 · see citing works
Yeoman, C. J., Ishaq, S. L., Bichi, E., Olivo, S. K., Lowe, J., & Aldridge, B. M. (2018) · Scientific Reports · doi:10.1038/s41598-018-21440-8 · Cited by 168 · see citing works
Svartström, O., Alneberg, J., Terrapon, N., Lombard, V., de Bruijn, I., Malmsten, J., Dalin, A.-M., EL Muller, E., Shah, P., Wilmes, P., et al. (2017) · The ISME Journal · doi:10.1038/ismej.2017.108 · Cited by 161 · see citing works
Hassan, F.-U., Arshad, M. A., Ebeid, H. M., Rehman, M. S.-U., Khan, M. S., Shahid, S., & Yang, C. (2020) · Frontiers in Veterinary Science · doi:10.3389/fvets.2020.575801 · Cited by 160 · see citing works
CowPI: a rumen microbiome focussed version of the PICRUSt functional inference software
Wilkinson, T. J., Huws, S. A., Edwards, J. E., Kingston-Smith, A. H., Siu-Ting, K., Hughes, M., Rubino, F., Friedersdorff, M., & Creevey, C. J. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.01095 · Cited by 160 · see citing works
Min, B. R., Solaiman, S., Waldrip, H. M., Parker, D., Todd, R. W., & Brauer, D. (2020) · Animal nutrition · doi:10.1016/j.aninu.2020.05.002 · Cited by 159 · see citing works
Schären, M., Drong, C., Kiri, K., Riede, S., Gardener, M., Meyer, U., Hummel, J., Urich, T., Breves, G., & Dänicke, S. (2017) · Journal of Dairy Science · doi:10.3168/jds.2016-11994 · Cited by 149 · see citing works
Strategies to improve the efficiency of beef cattle production
Terry, S. A., Basarab, J. A., Guan, L. L., & McAllister, T. A. (2021) · Canadian Journal of Animal Science · doi:10.1139/cjas-2020-0022 · Cited by 142 · see citing works
“However, given that the composition of the microbiome is overwhelmingly determined by the nature of the diet (Henderson et al. 2015) and the apparent variation in the rumen microbial indicators associated with RFI, their usefulness is yet to be proven.”
BackgroundInfluentialEdwards, J. E., Forster, R. J., Callaghan, T. M., Dollhofer, V., Dagar, S. S., Cheng, Y., Chang, J., Kittelmann, S., Fliegerova, K., Puniya, A. K., et al. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01657 · Cited by 130 · see citing works
Ikeda-Ohtsubo, W., Brugman, S., Warden, C. H., Rebel, J. M. J., Folkerts, G., & Pieterse, C. M. J. (2018) · Frontiers in Nutrition · doi:10.3389/fnut.2018.00090 · Cited by 115 · see citing works
Auffret, M. D., Stewart, R., Dewhurst, R. J., Duthie, C.-A., Rooke, J. A., Wallace, R. J., Freeman, T. C., Snelling, T. J., Watson, M., & Roehe, R. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.02642 · Cited by 82 · see citing works
Hu, X., Liu, G., Li, Y., Wei, Y., Lin, S., Liu, S., Zheng, Y., & Hu, D. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.01674 · Cited by 69 · see citing works
Ishaq, S. L., AlZahal, O., Walker, N., & McBride, B. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01943 · Cited by 61 · see citing works
Abecia, L., Jiménez, E., Martínez-Fernandez, G., Martín-García, A. I., Ramos-Morales, E., Pinloche, E., Denman, S. E., Newbold, C. J., & Yáñez-Ruiz, D. R. (2017) · PLoS ONE · doi:10.1371/journal.pone.0182235 · Cited by 59 · see citing works
Iqbal, M. W., Zhang, Q., Yang, Y., Li, L., Zou, C., Huang, C., & Lin, B. (2018) · Journal of Applied Animal Research · doi:10.1080/09712119.2017.1394859 · Cited by 53 · see citing works
Self-citationElekwachi, C. O., Wang, Z., Wu, X., Rabee, A., & Forster, R. J. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01814 · Cited by 48 · see citing works
Popova, M., McGovern, E., McCabe, M. S., Martin, C., Doreau, M., Arbre, M., Meale, S. J., Morgavi, D. P., & Waters, S. M. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.00937 · Cited by 48 · see citing works
Self-citationMethanogen diversity in indigenous and introduced ruminant species on the Tibetan plateau
Huang, X. D., Martinez-Fernandez, G., Padmanabha, J., Long, R., Denman, S. E., & McSweeney, C. S. (2016) · Archaea · doi:10.1155/2016/5916067 · Cited by 45 · see citing works
Self-citationMannelli, F., Daghio, M., Alves, S. P., Bessa, R. J. B., Minieri, S., Giovannetti, L., Conte, G., Mele, M., Messini, A., Rapaccini, S., et al. (2019) · Microorganisms · doi:10.3390/microorganisms7070202 · Cited by 33 · see citing works
Golder, H. M., Thomson, J. M., Denman, S. E., McSweeney, C. S., & Lean, I. J. (2018) · Frontiers in Genetics · doi:10.3389/fgene.2018.00062 · Cited by 32 · see citing works
Self-citationCandyrine, S. C. L., Mahadzir, M. F., Garba, S., Jahromi, M. F., Ebrahimi, M., Goh, Y. M., Samsudin, A. A., Sazili, A. Q., Chen, W. L., Ganesh, S., et al. (2018) · PLOS ONE · doi:10.1371/journal.pone.0199840 · Cited by 31 · see citing works
Self-citation
- Authors
- Henderson, G., Cox, F., Ganesh, S., Jonker, A., Young, W., Collaborators, G. R. C., Abecia, L., Angarita, E., Aravena, P., Nora Arenas, G., Ariza, C., Attwood, G. T., Mauricio Avila, J., Avila-Stagno, J., Bannink, A., Barahona, R., Batistotti, M., Bertelsen, M. F., Brown-Kav, A., Carvajal, A. M., Cersosimo, L., Vieira Chaves, A., Church, J., Clipson, N., Cobos-Peralta, M. A., Cookson, A. L., Cravero, S., Cristobal Carballo, O., Crosley, K., Cruz, G., Cerón Cucchi, M., de la Barra, R., De Menezes, A. B., Detmann, E., Dieho, K., Dijkstra, J., dos Reis, W. L. S., Dugan, M. E. R., Hadi Ebrahimi, S., Eythórsdóttir, E., Nde Fon, F., Fraga, M., Franco, F., Friedeman, C., Fukuma, N., Gagić, D., Gangnat, I., Javier Grilli, D., Guan, L. L., Heidarian Miri, V., Hernandez-Sanabria, E., Gomez, A. X. I., Isah, O. A., Ishaq, S., Jami, E., Jelincic, J., Kantanen, J., Kelly, W. J., Kim, S.-H., Klieve, A., Kobayashi, Y., Koike, S., Kopecny, J., Nygaard Kristensen, T., Julie Krizsan, S., LaChance, H., Lachman, M., Lamberson, W. R., Lambie, S., Lassen, J., Leahy, S. C., Lee, S.-S., Leiber, F., Lewis, E., Lin, B., Lira, R., Lund, P., Macipe, E., Mamuad, L. L., Cuquetto Mantovani, H., Marcoppido, G. A., Márquez, C., Martin, C., Martinez, G., Eugenia Martinez, M., Lucía Mayorga, O., McAllister, T. A., McSweeney, C., Mestre, L., Minnee, E., Mitsumori, M., Mizrahi, I., Molina, I., Muenger, A., Muñoz, C., Murovec, B., Newbold, J., Nsereko, V., O’Donovan, M., Okunade, S., O’Neill, B., Ospina, S., Ouwerkerk, D., Parra, D., Pereira, L. G. R., Pinares-Patiño, C., Pope, P. B., Poulsen, M., Rodehutscord, M., Rodriguez, T., Saito, K., Sales, F., Sauer, C., Shingfield, K., Shoji, N., Simunek, J., Stojanović-Radić, Z., Stres, B., Sun, X., Swartz, J., Liang Tan, Z., Tapio, I., Taxis, T. M., Tomkins, N., Ungerfeld, E., Valizadeh, R., van Adrichem, P., Van Hamme, J., Van Hoven, W., Waghorn, G., John Wallace, R., Wang, M., Waters, S. M., Keogh, K., Witzig, M., Wright, A.-D. G., Yamano, H., Yan, T., Yáñez-Ruiz, D. R., Yeoman, C. J., Zambrano, R., Zeitz, J., Zhou, M., Wei Zhou, H., Xia Zou, C., Zunino, P., & Janssen, P. H.
- Affiliations
- AgResearch (NZ)
- Consejo Superior de Investigaciones Científicas (ES)
- University of Concepción (CL)
- Universidad Nacional de Cuyo (AR)
- Universidad de Cundinamarca (CO)
- Universidad Nacional de Colombia (CO)
- Copenhagen Zoo (DK)
- University of Vermont (US)
- University College Dublin (IE)
- Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias (MX)
- University of Aberdeen (GB)
- Cargill (United States) (US)
- Wageningen University & Research (NL)
- Universidade Federal de Viçosa (BR)
- Agriculture and Agri-Food Canada (CA)
- Agricultural University of Iceland (IS)
- National University of San Marcos (PE)
- Hokkaido University (JP)
- ETH Zurich (CH)
- University of Alberta (CA)
- Federal University of Agriculture, Abeokuta (NG)
- Agricultural Research Organization (IL)
- Natural Resources Institute Finland (FI)
- University of Eastern Finland (FI)
- Sunchon National University (KR)
- The University of Queensland (AU)
- Czech Academy of Sciences (CZ)
- Montana State University (US)
- Aarhus University (DK)
- Instituto de Investigaciones Agropecuarias (CL)
- Commonwealth Scientific and Industrial Research Organisation (AU)
- Corporación Colombiana de Investigación Agropecuaria – AGROSAVIA (CO)
- National Agriculture and Food Research Organization (JP)
- University of Ljubljana (SI)
- Cargill (Netherlands) (NL)
- University of Hohenheim (DE)
- University of Nis (RS)
- Chinese Academy of Sciences (CN)
- Teagasc - The Irish Agriculture and Food Development Authority (IE)
- Corresponding author
- Henderson, Gemma
- Janssen, Peter H.
- ORCID
- Henderson, Gemma
- Cox, Faith
- Ganesh, Siva
- Jonker, Arjan
- Young, Wayne
- Abecia, Leticia
- Angarita, Erika
- Attwood, Graeme T.
- Bannink, André
- Bertelsen, Mads F.
- Carvajal, Andres M.
- Cersosimo, Laura
- Cobos-Peralta, Mario A.
- Cookson, Adrian L.
- Cravero, Silvio
- Cruz, Gustavo
- Dieho, Kasper
- Dijkstra, Jan
- Fraga, Martín
- Franco, Francisco
- Fukuma, Naoki
- Gagić, Dragana
- Gangnat, Isabelle
- Guan, Le Luo
- Isah, Olubukola A.
- Ishaq, Suzanne
- Jami, Elie
- Kantanen, Juha
- Kelly, William J.
- Kim, Seon-Ho
- Klieve, Athol
- Kobayashi, Yasuo
- Koike, Satoshi
- Lamberson, William R.
- Lambie, Suzanne
- Lassen, Jan
- Leahy, Sinead C.
- Lee, Sang-Suk
- Leiber, Florian
- Lewis, Eva
- Lin, Bo
- Lund, Peter
- Mamuad, Lovelia L.
- Marcoppido, Gisela Ariana
- Martin, Cécile
- McAllister, Tim A.
- Minnee, Elena
- Mitsumori, Makoto
- Mizrahi, Itzhak
- Muñoz, Camila
- Newbold, John
- Nsereko, Victor
- Ouwerkerk, Diane
- Pereira, Luiz Gustavo Ribeiro
- Pinares-Patiño, Cesar
- Poulsen, Morten
- Rodehutscord, Markus
- Sales, Francisco
- Stojanović-Radić, Zorica
- Sun, Xuezhao
- Tapio, Ilma
- Taxis, Tasia M.
- Tomkins, Nigel
- Ungerfeld, Emilio
- Wang, Min
- Waters, Sinéad M.
- Keogh, Kate
- Yan, Tianhai
- Yeoman, Carl J.
- Zambrano, Ricardo
- Zeitz, Johanna
- Zunino, Pablo
- Janssen, Peter H.
- Venue
- Scientific Reports
- Published
- 2015-10-09
- Volume
- 5
- Issue
- 1
- Pages
- 14567-14567
- ISSN
- 2045-2322 (ISSN-L)
- PMC
- PMC4598811
- OpenAlex
- W1842963151
- Cited by
- 1,682
- References
- 55
- Citations by year
- 2026: 169 · 2025: 157 · 2024: 216 · 2023: 184 · 2022: 207 · 2021: 191 · 2020: 181 · 2019: 129 · 2018: 106 · 2017: 96 · 2016: 45
- FWCI
- 178.65
- Type
- journal article
- Language
- en
- Update notices
- erratum (2016-01-20)
- Open access
- gold
- doi.org
- Locations
- Scientific Reports (publishedVersion, cc-by-sa)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Repository of the University of Ljubljana (University of Ljubljana) (publishedVersion, other-oa)
- Socio-Environmental Systems Modeling (acceptedVersion, cc-by)
- Queensland Department of Agriculture and Fisheries archive of scientific and research publications (Queensland Department of Agriculture and Fisheries) (submittedVersion, cc-by-sa)
- Jukuri (Natural Resources Institute Finland (Luke)) (submittedVersion, cc-by)
- Research at the University of Copenhagen (University of Copenhagen) (submittedVersion, public-domain)
- LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (submittedVersion, cc-by-sa)
- University of Salford Institutional Repository (University of Salford) (submittedVersion, cc-by)
- Americanae (AECID Library) (submittedVersion, other-oa)
- ASEP (submittedVersion, public-domain)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion)
- Figshare (submittedVersion)
- Jukuri (Natural Resources Institute Finland (Luke)) (submittedVersion)
- VBN Forskningsportal (Aalborg Universitet) (submittedVersion, other-oa)
- LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (submittedVersion, cc-by-nc-nd)
- Repository for Publications and Research Data (ETH Zurich) (submittedVersion, cc-by)
- Data Archiving and Networked Services (DANS) (submittedVersion, cc-by)
- ETH Zürich Research Collection (cc-by)
- Funders
- University of Missouri
- Aarhus Universitet
- AgResearch
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria
- Agencia Nacional de Investigación e Innovación
- Montana State University
- Montana Agricultural Experiment Station (MONB00113)
- Universität Hohenheim
- Diamond V
- Rural and Environment Science and Analytical Services Division
- Scottish Government
- Australian Government
- New Zealand Government
- Commonwealth Scientific and Industrial Research Organisation
- Science Foundation Ireland (09/RFP/GEN2447)
- Teagasc
- James Cook University
- University of Queensland
- Chinese Academy of Sciences
- Sunchon National University
- Alberta Livestock and Meat Agency
- DairyNZ
- Ferdowsi University of Mashhad
- Conselho Nacional de Desenvolvimento Científico e Tecnológico
- Rural Development Administration (PJ010906)
- Akademie Věd České Republiky
- Javna Agencija za Raziskovalno Dejavnost RS (and P4-, P4-0097, J1-6732)
- Sveriges Lantbruksuniversitet
- Fundação de Amparo à Pesquisa do Estado de Minas Gerais
- Institut National de la Recherche Agronomique
- Clermont Université
- Univerza v Ljubljani
- Norges Miljø- og Biovitenskapelige Universitet
- Product Board Animal Feed
- Instituto Nacional de Tecnología Agropecuaria
- VetAgro Sup
- Université de Lyon
- Secretaría de Agricultura, Ganadería, Desarrollo Rural, Pesca y Alimentación
- Agroscope
- Topics
- Life Sciences › Agricultural and Biological Sciences › Agronomy and Crop Science › Ruminant Nutrition and Digestive Physiology
- Physical Sciences › Engineering › Building and Construction › Anaerobic Digestion and Biogas Production
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Keywords
- rumen microbiome, ruminant livestock, host species effects, regional variation, core microbiome, methanogenic archaea, rumen protozoa, microbial co-occurrence, methane mitigation, feed degradation
- MeSH terms
- Gastrointestinal Microbiome, Animals, Archaea, Bacteria, Diet, DNA, Bacterial, Geography, Phylogeny, Rumen, Ruminants, Species Specificity, Genetic Variation, DNA, Protozoan, Sequence Analysis, DNA, DNA, Archaeal, Host-Pathogen Interactions, DNA Barcoding, Taxonomic
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
