Establishment of ruminal bacterial community in dairy calves from birth to weaning is sequential
Abstract
AIM: Establishment of ruminal bacterial community in dairy calves. METHODS AND RESULTS: Rumen bacterial community was analysed on 6 calves bred according to commercial practices from day one to weaning at day 83 of age, using 454 16S rRNA-based pyrosequencing. Samples taken at day 1 did not produce amplicons. Analysis of data revealed a three-stage implantation process with a progressive but important shift of composition. At day 2, the bacterial community was mainly composed of Proteobacteria (70%) and Bacteroidetes (14%), and Pasteurellaceae was the dominant family (58%). The bacterial community abruptly changed between days 2 and 3, and until day 12, dominant genera were Bacteroides (21%), Prevotella (11%), Fusobacterium (5%) and Streptococcus (4%). From 15 to 83 days, when solid food intake rapidly increased, Prevotella became dominant (42%) and many genera strongly decreased or were no longer detected. A limited number of bacteria genera correlated with feed intake, rumen volatile fatty acids and enzymatic activities. CONCLUSION: The ruminal bacterial community is established before intake of solid food, but solid food arrival in turn shapes this community. SIGNIFICANCE AND IMPACT OF THE STUDY: This study provides insight into the establishment of calves' rumen bacterial community and suggests a strong effect of diet.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
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?
The maturation stage of rumen microbial establishment is characterized by progressively increasing solid feed intake and a distribution of main bacterial phyla and other microbial groups comparable to that in adult animals.
“iii) maturation stage in which solid feed intake progressively increases and the distribution of main bacterial phyla and other microbial groups is comparable to that in adult animals.”
From Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future (2018) · cites this paper as Rey et al., 2014
The transitional stage of rumen microbial establishment occurs 3-15 days during the transition from colostrum to milk.
“(ii) transitional stage (3–15 days) during the transition from colostrum to milk,”
From Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future (2018) · cites this paper as Rey et al., 2014
The dynamics of gut microbial community establishment in young ruminants occurs in three successive steps.
“The dynamics of the gut microbial community establishment in young ruminants occurs in three successive steps (Rey et al., 2014; Abecia et al., 2017):”
From Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future (2018) · cites this paper as Rey et al., 2014
Cites
UCHIME improves sensitivity and speed of chimera detection
Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C., & Knight, R. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr381 · Cited by 15,114 · see citing works
Multidimensional Scaling by Optimizing Goodness of Fit to a Nonmetric Hypothesis
Kruskal, J. B. (1964) · Psychometrika · doi:10.1007/bf02289565 · Cited by 7,270 · see citing works
Pruesse, E., Quast, C., Knittel, K., Fuchs, B. M., Ludwig, W., Peplies, J., & Glöckner, F. O. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm864 · Cited by 6,682 · see citing works
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
Cole, J., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R. J., Kulam-Syed-Mohideen, A., Mcgarrell, D., Marsh, T., Garrity, G., et al. (2008) · Nucleic Acids Res. · doi:10.1093/nar/gkn879 · Cited by 4,940 · see citing works
Evolution of mammals and their gut microbes
Ley, R. E., Hamady, M., Lozupone, C., Turnbaugh, P. J., Ramey, R. R., Bircher, J. S., Schlegel, M. L., Tucker, T. A., Schrenzel, M. D., Knight, R., et al. (2008) · Science · doi:10.1126/science.1155725 · Cited by 3,747 · see citing works
Multivariate analyses in microbial ecology
Ramette, A. (2007) · FEMS Microbiology Ecology · doi:10.1111/j.1574-6941.2007.00375.x · Cited by 1,930 · see citing works
Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution
Zilber-Rosenberg, I., & Rosenberg, E. (2008) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2008.00123.x · Cited by 1,739 · see citing works
The Ruminant Animal: Digestive Physiology and Nutrition
Church, D. C. (1988) · Medical Entomology and Zoology · Cited by 1,386 · see citing works
Comparative Analysis of Human Gut Microbiota by Barcoded Pyrosequencing
Andersson, A. F., Lindberg, M., Jakobsson, H. E., Bäckhed, F., Nyrén, P., & Engstrand, L. G. (2008) · PLoS ONE · doi:10.1371/journal.pone.0002836 · Cited by 1,037 · see citing works
Exploring the bovine rumen bacterial community from birth to adulthood
Jami, E., Israel, A., Kotser, A., & Mizrahi, I. (2013) · The ISME Journal · doi:10.1038/ismej.2013.2 · Cited by 963 · see citing works
Short pyrosequencing reads suffice for accurate microbial community analysis
Liu, Z., Lozupone, C., Hamady, M., Bushman, F. D., & Knight, R. D. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm541 · Cited by 692 · see citing works
Mode and place of delivery, gastrointestinal microbiota, and their influence on asthma and atopy
van Nimwegen, F. A., Penders, J., Stobberingh, E. E., Postma, D. S., Koppelman, G. H., Kerkhof, M., Reijmerink, N. E., Dompeling, E., van den Brandt, P. A., Ferreira, I., et al. (2011) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2011.07.027 · Cited by 493 · see citing works
The Anatomy of Domestic Animals.
(1915) · JAMA · doi:10.1001/jama.1915.02570420070047 · Cited by 395 · see citing works
Pitta, D., Pinchak, W. E., Dowd, S. E., Osterstock, J. B., Gontcharova, V., Youn, E., Dorton, K. L., Yoon, I., Min, B. R., Fulford, J. D., et al. (2009) · Microbial Ecology · doi:10.1007/s00248-009-9609-6 · Cited by 369 · see citing works
Characterization of the rumen microbiota of pre-ruminant calves using metagenomic tools.
Li, R. W., Connor, E., Li, C.-J., Baldwin, R., & Sparks, M. E. (2012) · Environmental Microbiology · doi:10.1111/j.1462-2920.2011.02543.x · Cited by 353 · see citing works
Curtis, T. P., & Sloan, W. T. (2004) · Current Opinion in Microbiology · doi:10.1016/j.mib.2004.04.010 · Cited by 321 · see citing works
A High-Throughput DNA Sequence Aligner for Microbial Ecology Studies
Schloss, P. D. (2009) · PLoS ONE · doi:10.1371/journal.pone.0008230 · Cited by 320 · see citing works
Zened, A., Combes, S., Cauquil, L., Mariette, J., Klopp, C., Bouchez, O., Meynadier, A., & Enjalbert, F. (2012) · FEMS Microbiology Ecology · doi:10.1111/1574-6941.12011 · Cited by 271 · see citing works
Self-citationHernandez-Sanabria, E., Goonewardene, L. A., Wang, Z., Durunna, O. N., Moore, S. S., & Guan, L. L. (2012) · Applied and Environmental Microbiology · doi:10.1128/aem.05114-11 · Cited by 207 · see citing works
Establishment of the Microflora and Anaerobic Fungi in the Rumen of Lambs
Fonty, G., Gouet, P., Jouany, J. P., & Sénaud, J. (1987) · Microbiology · doi:10.1099/00221287-133-7-1835 · Cited by 206 · see citing works
Development of bacterial and bifidobacterial communities in feces of newborn babies
Favier, C. F., de Vos, W. M., & Akkermans, A. D. L. (2003) · Anaerobe · doi:10.1016/j.anaerobe.2003.07.001 · Cited by 194 · see citing works
The role of the intestinal microbiota in enteric infection
Sekirov, I., & Finlay, B. B. (2009) · The Journal of Physiology · doi:10.1113/jphysiol.2009.172742 · Cited by 188 · see citing works
Ruminal Microbial Development in Conventionally or Early-Weaned Calves
Anderson, K. L., Nagaraja, T. G., Morrill, J. L., Avery, T. B., Galitzer, S. J., & Boyer, J. E. (1987) · Journal of Animal Science · doi:10.2527/jas1987.6441215x · Cited by 182 · see citing works
Studies on the Composition of the Ruminal Flora and Fauna of Young Calves
Bryant, M. P., Small, N., Bouma, C., & Robinson, I. M. (1958) · Journal of Dairy Science · doi:10.3168/jds.s0022-0302(58)91160-3 · Cited by 159 · see citing works
Cai, Y., & Sun, Y. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr349 · Cited by 156 · see citing works
Agarwal, N., Kamra, D. N., Chaudhary, L. C., Agarwal, I. S., SAHOO, A., & Pathak, N. N. (2002) · Letters in Applied Microbiology · doi:10.1046/j.1472-765x.2002.01092.x · Cited by 149 · see citing works
Establishment of hydrogen-utilizing bacteria in the rumen of the newborn lamb
Morvan, B., Dore, J. M., Rieu-Lesme, F., Foucat, L. ̄., Fonty, G., & Gouet, P. (1994) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.1994.tb06775.x · Cited by 134 · see citing works
High Rate of Transfer of Staphylococcus aureus from Parental Skin to Infant Gut Flora
Lindberg, E., Adlerberth, I., Hesselmar, B., Saalman, R., Strannegård, I., Åberg, N., & Wold, A. E. (2004) · Journal of Clinical Microbiology · doi:10.1128/jcm.42.2.530-534.2004 · Cited by 108 · see citing works
Wu, S., Baldwin, R. L., Li, W., Li, C., Connor, E. E., & Li, R. W. (2012) · Metagenomics · doi:10.4303/mg/235571 · Cited by 103 · see citing works
Michelland, R. J., Dejean, S., Combes, S., Fortun‐Lamothe, L., & Cauquil, L. (2009) · Molecular Ecology Resources · doi:10.1111/j.1755-0998.2009.02609.x · Cited by 99 · see citing works
Self-citationRey, M., Enjalbert, F., & Monteils, V. (2012) · Journal of Dairy Science · doi:10.3168/jds.2011-4902 · Cited by 93 · see citing works
Self-citationColonization of microorganisms in the rumen of young calves.
Minato, H., Otsuka, M., Shirasaka, S., ITABASHI, H., & Mitsumori, M. (1992) · The Journal of General and Applied Microbiology · doi:10.2323/jgam.38.447 · Cited by 88 · see citing works
Evaluation of the RDP Classifier Accuracy Using 16S rRNA Gene Variable Regions
Vilo, C., & Dong, Q. (2012) · Metagenomics · doi:10.4303/mg/235551 · Cited by 83 · see citing works
Spatial and temporal variations of the bacterial community in the bovine digestive tract
Michelland, R. J., Monteils, V., Zened, A., Combes, S., Cauquil, L., Gidenne, T. N., Hamelin, J., & Fortun‐Lamothe, L. (2009) · Journal of Applied Microbiology · doi:10.1111/j.1365-2672.2009.04346.x · Cited by 42 · see citing works
Self-citationMartin, C., Michalet-Doreau, B., Fonty, G., & Williams, A. G. (1993) · Current Microbiology · doi:10.1007/bf01692880 · Cited by 36 · see citing works
Michelland, R. J., Monteils, V., Combes, S., Cauquil, L., Gidenne, T. N., & Fortun‐Lamothe, L. (2011) · Canadian Journal of Microbiology · doi:10.1139/w11-053 · Cited by 15 · see citing works
Self-citationMonteils, V., Rey, M., Cauquil, L., Meynadier, A., Silberberg, M., & Combes, S. (2011) · Livestock Science · doi:10.1016/j.livsci.2011.05.008 · Cited by 12 · see citing works
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
Weimer, P. J. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00296 · Cited by 487 · see citing works
Huws, 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
Manipulating rumen microbiome and fermentation through interventions during early life: a review
Yáñez-Ruiz, D. R., Abecia, L., & Newbold, C. J. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.01133 · Cited by 336 · see citing works
Development and physiology of the rumen and the lower gut: Targets for improving gut health
Steele, M. A., Penner, G. B., Chaucheyras‐Durand, F., & Guan, L. L. (2016) · Journal of Dairy Science · doi:10.3168/jds.2015-10351 · Cited by 302 · see citing works
Jewell, K. A., McCormick, C. A., Odt, C. L., Weimer, P. J., & Suen, G. (2015) · Applied and Environmental Microbiology · doi:10.1128/aem.00720-15 · Cited by 281 · see citing works
Malmuthuge, N., Griebel, P. J., & Guan, L. L. (2015) · Frontiers in Veterinary Science · doi:10.3389/fvets.2015.00036 · Cited by 281 · see citing works
Furman, O., Shenhav, L., Sasson, G., Kokou, F., Honig, H. H., Jacoby, S., Hertz, T., Cordero, O. X., Halperin, E., & Mizrahi, I. (2020) · Nature Communications · doi:10.1038/s41467-020-15652-8 · Cited by 233 · see citing works
McCann, J. C., Wickersham, T. A., & Loor, J. J. (2014) · Bioinformatics and Biology Insights · doi:10.4137/bbi.s15389 · Cited by 227 · see citing works
Malmuthuge, N., Liang, G., & Guan, L. L. (2019) · Genome biology · doi:10.1186/s13059-019-1786-0 · Cited by 219 · see citing works
Malmuthuge, N., & Guan, L. L. (2017) · Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology · doi:10.1186/s40104-016-0135-3 · Cited by 204 · see citing works
Meale, S. J., Li, S., Azevedo, P. A., Derakhshani, H., Plaizier, J. C., Khafipour, E., & Steele, M. A. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00582 · Cited by 197 · see citing works
The Road Not Taken: The Rumen Microbiome, Functional Groups, and Community States
Moraïs, S., & Mizrahi, I. (2019) · Trends in Microbiology · doi:10.1016/j.tim.2018.12.011 · Cited by 166 · see citing works
From pre- to postweaning: transformation of the young calf's gastrointestinal tract
Meale, S. J., Chaucheyras-Durand, F., Berends, H., Guan, L. L., & Steele, M. A. (2017) · Journal of Dairy Science · doi:10.3168/jds.2016-12474 · Cited by 163 · 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
Lignocellulose degradation by rumen bacterial communities: New insights from metagenome analyses
Gharechahi, J., Vahidi, M. F., Sharifi, G., Ariaeenejad, S., Ding, X., Han, J., & Salekdeh, G. H. (2023) · Environmental Research · doi:10.1016/j.envres.2023.115925 · Cited by 152 · see citing works
Arshad, M. A., Hassan, F., Rehman, M. S.-U., Huws, S., Cheng, Y., & Din, A. U. (2021) · Animal nutrition · doi:10.1016/j.aninu.2021.03.004 · Cited by 144 · see citing works
Mizrahi, I., & Jami, E. (2018) · animal · doi:10.1017/s1751731118001957 · Cited by 147 · see citing works
Saponin-induced shifts in the rumen microbiome and metabolome of young cattle
Wang, B., Ma, M. P., Diao, Q. Y., & Tu, Y. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.00356 · Cited by 140 · see citing works
Rumen microbiota and dietary fat: a mutual shaping
Enjalbert, F., Combes, S., Zened, A., & Meynadier, A. (2017) · Journal of Applied Microbiology · doi:10.1111/jam.13501 · Cited by 139 · see citing works
Self-citationGuzman, C. E., Bereza-Malcolm, L., Groef, B. D., & Franks, A. E. (2015) · PLoS ONE · doi:10.1371/journal.pone.0133048 · Cited by 139 · see citing works
The microbiome of the digestive system of ruminants – a review
Cholewińska, P., Czyż, K., Nowakowski, P., & Wyrostek, A. (2020) · Animal Health Research Reviews · doi:10.1017/s1466252319000069 · Cited by 136 · see citing works
Dias, J., Marcondes, M. I., de Souza, S. M., Silva, B. C. D. M. E., Noronha, M. F., Resende, R. T., Machado, F. S., Mantovani, H. C., Dill‐McFarland, K. A., & Suen, G. (2018) · Applied and Environmental Microbiology · doi:10.1128/aem.02675-17 · Cited by 134 · see citing works
Weaning age influences the severity of gastrointestinal microbiome shifts in dairy calves
Meale, S. J., Li, S. C., Azevedo, P., Derakhshani, H., DeVries, T. J., Plaizier, J. C., Steele, M. A., & Khafipour, E. (2017) · Scientific Reports · doi:10.1038/s41598-017-00223-7 · Cited by 133 · see citing works
Colonization and development of the gut microbiome in calves
Du, Y., Gao, Y., Hu, M., Hou, J., Yang, L., Wang, X., Du, W., Liu, J., & Xu, Q. (2023) · Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology · doi:10.1186/s40104-023-00856-x · Cited by 129 · see citing works
Clemmons, B. A., Voy, B. H., & Myer, P. R. (2018) · Microbial Ecology · doi:10.1007/s00248-018-1234-9 · Cited by 124 · see citing works
Effects of early feeding on the host rumen transcriptome and bacterial diversity in lambs
Wang, W., Li, C., Li, F., Wang, X., Zhang, X., Liu, T., Nian, F., Yue, X., Li, F., Pan, X., et al. (2016) · Scientific Reports · doi:10.1038/srep32479 · Cited by 120 · see citing works
Song, Y., Malmuthuge, N., Steele, M. A., & Guan, L. L. (2017) · FEMS Microbiology Ecology · doi:10.1093/femsec/fix179 · Cited by 115 · see citing works
Li, B., Zhang, K., Li, C., Wang, X., Chen, Y., & Yang, Y. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.02125 · Cited by 113 · see citing works
Firkins, J. L., & Yu, Z. (2015) · Journal of Animal Science · doi:10.2527/jas.2014-8754 · Cited by 110 · see citing works
Synergetic action between the rumen microbiota and bovine health
Zeineldin, M. M., Barakat, R., Elolimy, A. A., Salem, A. Z. M., Elghandour, M. M. M. Y., & Monroy, J. C. (2018) · Microbial Pathogenesis · doi:10.1016/j.micpath.2018.08.038 · Cited by 110 · see citing works
Taxonomic Identification of Ruminal Epithelial Bacterial Diversity during Rumen Development in Goats
Jiao, J., Huang, J., Zhou, C., & Tan, Z. (2015) · Applied and Environmental Microbiology · doi:10.1128/aem.00203-15 · Cited by 108 · see citing works
Exploring the Goat Rumen Microbiome from Seven Days to Two Years
Wang, L., Xu, Q., Kong, F., Yang, Y., Wu, D., Mishra, S., & Li, Y. (2016) · PLoS ONE · doi:10.1371/journal.pone.0154354 · Cited by 107 · see citing works
Bickhart, D. M., & Weimer, P. J. (2017) · Journal of Dairy Science · doi:10.3168/jds.2017-13328 · Cited by 105 · see citing works
Dynamic progression of the calf’s microbiome and its influence on host health
Amin, N., & Seifert, J. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.01.035 · Cited by 102 · see citing works
Rumen microbial communities influence metabolic phenotypes in lambs
Morgavi, D. P., Rathahao, E., Popova, M., Boccard, J., Nielsen, K. F., & Boudra, H. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.01060 · Cited by 102 · see citing works
Jiao, J., Li, X., Beauchemin, K. A., Tan, Z., Tang, S., & Zhou, C. (2015) · British Journal Of Nutrition · doi:10.1017/s0007114514004413 · Cited by 101 · see citing works
Methodological terminology and definitions for research and discussion of cow-calf contact systems
Širovnik, J., Barth, K., de Oliveira, D., Ferneborg, S., Haskell, M. J., Hillmann, E., Jensen, M. B., Mejdell, C. M., Napolitano, F., Vaarst, M., et al. (2020) · Journal of Dairy Research · doi:10.1017/s0022029920000564 · Cited by 101 · see citing works
Jacometo, C. B., Zhou, Z., Luchini, D. N., Trevisi, E., Corrêa, M. N., & Loor, J. J. (2016) · Journal of Dairy Science · doi:10.3168/jds.2016-11018 · Cited by 99 · see citing works
Kim, Y., Nagata, R., Ohtani, N., ICHIJO, T., Ikuta, K., & Sato, S. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.01575 · Cited by 96 · see citing works
Dietary impacts on rumen microbiota in beef and dairy production
Loor, J. J., Elolimy, A. A., & McCann, J. C. (2016) · Animal Frontiers · doi:10.2527/af.2016-0030 · Cited by 100 · see citing works
Dias, J., Marcondes, M. I., Noronha, M. F., Resende, R. T., Machado, F. S., Mantovani, H. C., Dill‐McFarland, K. A., & Suen, G. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01553 · Cited by 89 · see citing works
Influence of host genetics in shaping the rumen bacterial community in beef cattle
Abbas, W., Howard, J., Paz, H. A., Hales, K. E., Wells, J. E., Kuehn, L. A., Erickson, G. E., Spangler, M. L., & Fernando, S. C. (2020) · Scientific Reports · doi:10.1038/s41598-020-72011-9 · Cited by 89 · see citing works
Dynamic Changes in Fecal Microbial Communities of Neonatal Dairy Calves by Aging and Diarrhea
Kim, E. T., Lee, S.-J., Kim, T.-Y., Lee, H. G., Atikur, R. M., Gu, B., Kim, D. H., Park, B.-Y., Son, J.-K., & Kim, M. (2021) · Animals · doi:10.3390/ani11041113 · Cited by 85 · see citing works
Wang, Y., Cao, P., Wang, L., Zhao, Z., Chen, Y., & Yang, Y. (2017) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-017-8144-5 · Cited by 86 · see citing works
Assessment of Ruminal Bacterial and Archaeal Community Structure in Yak (Bos grunniens)
Zhou, Z., Fang, L., Meng, Q., Li, S., Chai, S., Liu, S., & Schonewille, J. T. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.00179 · Cited by 82 · see citing works
Meale, S. J., Popova, M., Saro, C., Martin, C., Bernard, A., Lagrée, M., Yáñez-Ruíz, D. R., Boudra, H., Duval, S. M., & Morgavi, D. P. (2021) · Scientific Reports · doi:10.1038/s41598-021-82084-9 · Cited by 78 · see citing works
Hu, X., Liu, G., Shafer, A. B. A., Wei, Y., Zhou, J., Lin, S., Wu, H., Zhou, M., Hu, D., & Liu, S. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.00572 · Cited by 78 · see citing works
Alfalfa Intervention Alters Rumen Microbial Community Development in Hu Lambs During Early Life
Yang, B., Le, J., Wu, P., Liu, J., Guan, L. L., & Wang, J. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.00574 · Cited by 77 · see citing works
Impact of selected environmental factors on microbiome of the digestive tract of ruminants
Cholewińska, P., Górniak, W., & Wojnarowski, K. (2021) · BMC Veterinary Research · doi:10.1186/s12917-021-02742-y · Cited by 75 · see citing works
Cui, Y., Liu, H., Gao, Z., Xu, J., Liu, B., Guo, M., Yang, X., Niu, J., Zhu, X., Ma, S., et al. (2022) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-022-11956-5 · Cited by 77 · see citing works
Fomenky, B., Do, D. N., Talbot, G., Chiquette, J., Bissonnette, N., Chouinard, Y., Lessard, M., & Ibeagha-Awemu, E. (2018) · Scientific Reports · doi:10.1038/s41598-018-32375-5 · Cited by 64 · see citing works
Zhang, Y., Choi, S. H., Nogoy, K. M. C., & Liang, S. (2021) · animal · doi:10.1016/j.animal.2021.100316 · Cited by 72 · see citing works
Zhu, Z., Kristensen, L., Difford, G. F., Poulsen, M., Noel, S. J., Al‐Soud, W. A., Sørensen, S. J., Lassen, J., Løvendahl, P., & Højberg, O. (2018) · Journal of Dairy Science · doi:10.3168/jds.2017-14366 · Cited by 71 · see citing works
Palma‐Hidalgo, J. M., Jiménez, E., Popova, M., Morgavi, D. P., Martín-García, A. I., Yáñez-Ruíz, D. R., & Belanche, A. (2021) · Animal Microbiome · doi:10.1186/s42523-021-00073-9 · Cited by 71 · see citing works
Feeding modes shape the acquisition and structure of the initial gut microbiota in newborn lambs
Bi, Y.-L., Cox, M., Zhang, F., Suen, G., Zhang, N.-F., Tu, Y., & Diao, Q. (2019) · Environmental Microbiology · doi:10.1111/1462-2920.14614 · Cited by 63 · see citing works
Understanding the Diversity and Roles of the Ruminal Microbiome
Keum, G. B., Pandey, S., Kim, E. S., Doo, H., Kwak, J., Ryu, S., Choi, Y., Kang, J., Kim, S., & Kim, H. B. (2024) · The Journal of Microbiology · doi:10.1007/s12275-024-00121-4 · Cited by 75 · see citing works
Biotechnological utilization of animal gut microbiota for valorization of lignocellulosic biomass
Ozbayram, E. G., Kleinsteuber, S., & Nikolausz, M. (2019) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-019-10239-w · Cited by 66 · see citing works
Belanche, A., Yáñez-Ruíz, D. R., Detheridge, A. P., Griffith, G. W., Kingston‐Smith, A. H., & Newbold, C. J. (2019) · Environmental Microbiology · doi:10.1111/1462-2920.14801 · Cited by 65 · see citing works
Ceniti, C., Spina, A. A., Piras, C., Oppedisano, F., Tilocca, B., Roncada, P., Britti, D., & Morittu, V. M. (2023) · Foods · doi:10.3390/foods12152917 · Cited by 64 · see citing works
O’Hara, E., Kelly, A. L., McCabe, M. S., Kenny, D. A., Guan, L. L., & Waters, S. M. (2018) · Scientific Reports · doi:10.1038/s41598-018-33122-6 · Cited by 64 · see citing works
Dynamics and stabilization of the rumen microbiome in yearling Tibetan sheep
Wang, L., Zhang, K., Zhang, C., Feng, Y., Zhang, X., Wang, X., & Wu, G. (2019) · Scientific Reports · doi:10.1038/s41598-019-56206-3 · Cited by 70 · see citing works
A pioneer calf foetus microbiome
Guzman, C. E., Wood, J. L., Egidi, E., Monsant, A. C., Semenec, L., Grommen, S. V. H., Hill‐Yardin, E. L., Groef, B. D., & Franks, A. E. (2020) · Scientific Reports · doi:10.1038/s41598-020-74677-7 · Cited by 64 · see citing works
Effects and immune responses of probiotic treatment in ruminants
Raabis, S. M., Li, W., & Cersosimo, L. M. (2019) · Veterinary Immunology and Immunopathology · doi:10.1016/j.vetimm.2018.12.006 · Cited by 61 · see citing works
Guo, W., Zhou, M., Ma, T., Bi, S., Wang, W., Zhang, Y., Huang, X., Guan, L. L., & Long, R. (2020) · Animal Microbiome · doi:10.1186/s42523-020-00042-8 · Cited by 59 · see citing works
Lyons, T., Boland, T. M., Storey, S., & Doyle, E. M. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01656 · Cited by 60 · see citing works
Li, J. H., Yousif, M., Li, Z. Q., Wu, Z., Li, S. L., Yang, H., Wang, Y. J., & Cao, Z. (2019) · Journal of Dairy Science · doi:10.3168/jds.2018-15506 · Cited by 60 · 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
Characteristics of Bacterial Microbiota in Different Intestinal Segments of Aohan Fine-Wool Sheep
Ma, Y., Deng, X., Yang, X. Y., Wang, J., Li, T., Hua, G., Han, D., Da, L., Li, R., Rong, W., et al. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.874536 · Cited by 58 · see citing works
Yu, S., Zhang, G., Liu, Z., Wu, P., Yu, Z., & Wang, J. (2020) · BMC Microbiology · doi:10.1186/s12866-020-1716-z · Cited by 56 · see citing works
Saro, C., Hohenester, U. M., Bernard, M., Lagrée, M., Martin, C., Doreau, M., Boudra, H., Popova, M., & Morgavi, D. P. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.01273 · Cited by 55 · see citing works
Ma, J., Zhu, Y., Wang, Z., Xiong, Y., Hu, R., Wang, Y., Cao, G., Zou, H., Shah, A. M., Peng, Q., et al. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.600516 · Cited by 55 · see citing works
Li, Z., Wang, X., Zhang, T., Si, H., Nan, W., Xu, C., Guan, L. L., Wright, A. G., & Li, G. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.00004 · Cited by 54 · see citing works
O’Hara, E., Kenny, D. A., McGovern, E., Byrne, C. J., McCabe, M. S., Guan, L. L., & Waters, S. M. (2020) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiz203 · Cited by 54 · see citing works
Wang, Z., Elekwachi, C. O., Jiao, J., Wang, M., Tang, S., Zhou, C., Tan, Z., & Forster, R. J. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.00159 · Cited by 53 · see citing works
Xiao, J., Alugongo, G. M., Li, J., Wang, Y., Li, S., & Cao, Z. (2020) · Animals · doi:10.3390/ani10020188 · Cited by 55 · see citing works
Cui, Z., Wu, S., Li, J., Yang, Q., Chai, S., Wang, L., Wang, X., Zhang, X., Liu, S., & Yao, J. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.00994 · Cited by 51 · see citing works
Wang, Z., Elekwachi, C. O., Jiao, J., Wang, M., Tang, S., Zhou, C., Tan, Z., & Forster, R. J. (2017) · Scientific Reports · doi:10.1038/s41598-017-00500-5 · Cited by 50 · see citing works
Ma, T., O’Hara, E., Song, Y., Fischer, A. J., He, Z., Steele, M. A., & Guan, L. L. (2019) · Journal of Dairy Science · doi:10.3168/jds.2018-16130 · Cited by 55 · see citing works
Cui, Z., Wu, S., Liu, S., Sun, L., Feng, Y., Cao, Y., Chai, S., Zhang, G., & Yao, J. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.00485 · Cited by 50 · see citing works
Lyons, T., Bielak, A., Doyle, E. M., & Kuhla, B. (2018) · Journal of Dairy Science · doi:10.3168/jds.2017-14200 · Cited by 49 · see citing works
Barden, M., Richards, P., Ganda, E., Lenzi, L., Eccles, R. M., Neary, J. M., Oultram, J. W. H., & Oikonomou, G. (2020) · Animal Microbiome · doi:10.1186/s42523-020-00049-1 · Cited by 48 · see citing works
Zuo, W., Yu, Y., Li, X., Xiao, H., Zhang, P., Shen, W., Wan, F., He, J., Tang, S., Tan, Z., et al. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.625857 · Cited by 46 · see citing works
Jiao, J., Wu, J., Zhou, C., Tang, S., Wang, M., & Tan, Z. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.01364 · Cited by 46 · see citing works
Waters, S. M., Roskam, E., Smith, P. E., Kenny, D. A., Popova, M., Eugène, M., & Morgavi, D. P. (2025) · Journal of Dairy Science · doi:10.3168/jds.2024-25778 · Cited by 45 · see citing works
Li, H., Yu, Q., Li, T., Shao, L., Su, M., Zhou, H., & Qu, J. (2020) · Frontiers in Veterinary Science · doi:10.3389/fvets.2020.00609 · Cited by 46 · see citing works
Healthy Cattle Microbiome and Dysbiosis in Diseased Phenotypes
Khalil, A., Batool, A., & Arif, S. (2022) · Ruminants · doi:10.3390/ruminants2010009 · Cited by 44 · see citing works
Zhang, L., Jiang, X. P., Liu, X. B., Zhao, X., Liu, S., Li, Y., & Zhang, Y. (2019) · Journal of Animal Science · doi:10.1093/jas/skz126 · Cited by 44 · see citing works
Abecia, L., Martı́nez, G., Waddams, K. E., Martín-García, A. I., Pinloche, E., Creevey, C. J., Denman, S. E., Newbold, C. J., & Yáñez-Ruíz, D. R. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.02227 · Cited by 43 · see citing works
Kaur, H., Kaur, G., Gupta, T., Mittal, D., & Ali, S. A. (2023) · Biology · doi:10.3390/biology12091200 · Cited by 42 · see citing works
Guo, J., Li, P., Zhang, K., Zhang, L., Wang, X., Li, L., & Zhang, H. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.584742 · Cited by 40 · see citing works
Ruminal Microbiota and Fermentation in Response to Dietary Protein and Energy Levels in Weaned Lambs
Lv, X., Cui, K., Qi, M., Wang, S., Diao, Q., & Zhang, N. (2020) · Animals · doi:10.3390/ani10010109 · Cited by 36 · see citing works
Bu, D., Zhang, X., Ma, L., Park, T., Wang, L., Wang, M., Xu, J., & Yu, Z. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.01403 · Cited by 37 · see citing works
Gómez, D. E., Arroyo, L. G., Poljak, Z., Viel, L., & Weese, J. S. (2017) · The Veterinary Journal · doi:10.1016/j.tvjl.2017.06.009 · Cited by 33 · see citing works
Li, C., Zhang, Q., Wang, G., Niu, X., Wang, W., Li, F., Li, F., & Zhang, Z. (2020) · Animal Biotechnology · doi:10.1080/10495398.2020.1812618 · Cited by 33 · see citing works
The Temporal Dynamics of Rumen Microbiota in Early Weaned Lambs
Wang, S., Chai, J., Zhao, G., Zhang, N., Cui, K., Bi, Y., Ma, T., Tu, Y., & Diao, Q. (2022) · Microorganisms · doi:10.3390/microorganisms10010144 · Cited by 32 · see citing works
Chai, J., Weiss, C. P., Beck, P. A., Zhao, W., Li, Y., & Zhao, J. (2024) · Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology · doi:10.1186/s40104-023-00967-5 · Cited by 31 · see citing works
Xiao, J., Alugongo, G. M., Ji, S., Wu, Z., Dong, S., Li, S., Yoon, I., Chung, R., & Cao, Z. (2018) · Animals · doi:10.3390/ani9010004 · Cited by 31 · see citing works
Júnior, G. F. V., & Bittar, C. M. M. (2021) · Animal Health Research Reviews · doi:10.1017/s1466252321000062 · Cited by 31 · see citing works
Mining ofluxSgenes from rumen microbial consortia by metagenomic and metatranscriptomic approaches
Ghali, I., Shinkai, T., & Mitsumori, M. (2015) · Animal Science Journal · doi:10.1111/asj.12476 · Cited by 28 · see citing works
Jiao, J., Zhou, C., Guan, L. L., McSweeney, C. S., Tang, S., Wang, M., & Tan, Z. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01655 · Cited by 27 · see citing works
- Authors
- Rey, M., Enjalbert, F., Combes, S., Cauquil, L., Bouchez, O., & Monteils, V.
- Affiliations
- École Nationale Vétérinaire de Toulouse (FR)
- Laboratoire de Génétique Cellulaire (FR)
- Corresponding author
- Enjalbert, F.
- Venue
- Journal of Applied Microbiology
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-12-11
- Volume
- 116
- Issue
- 2
- Pages
- 245-257
- ISSN
- 1364-5072 (ISSN-L)
- OpenAlex
- W2154517868
- Cited by
- 314
- References
- 37
- Citations by year
- 2026: 12 · 2025: 30 · 2024: 33 · 2023: 30 · 2022: 30 · 2021: 43 · 2020: 48 · 2019: 23 · 2018: 20 · 2017: 24 · 2016: 9 · 2015: 10 · 2014: 2
- FWCI
- 14.87
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- Locations
- Journal of Applied Microbiology (publishedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Agronomy and Crop Science › Ruminant Nutrition and Digestive Physiology
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Nutrition and Physiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Keywords
- dairy calves, weaning, solid food intake, Prevotella, Bacteroides, Pasteurellaceae, rumen volatile fatty acids, rumen enzymes, 16S rRNA pyrosequencing
- MeSH terms
- Animals, Animals, Newborn, Animals, Suckling, Bacteria, Bacteroides, Cattle, Colostrum, Diet, DNA, Bacterial, DNA, Ribosomal, Fatty Acids, Volatile, Female, Fusobacterium, Male, RNA, Bacterial, RNA, Ribosomal, 16S, Rumen, Streptococcus, Weaning, Pasteurellaceae, Prevotella, Proteobacteria, Bacteroidetes
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
