Applied Microbiology and Biotechnology

, Volume 101, Issue 15, pp 6205–6216 | Cite as

Effect of urea-supplemented diets on the ruminal bacterial and archaeal community composition of finishing bulls

  • Zhenming Zhou
  • Qingxiang Meng
  • Shengli Li
  • Lan Jiang
  • Hao Wu
Environmental biotechnology


In this study, we evaluated the effects of urea-supplemented diets on the ruminal bacterial and archaeal communities of finishing bulls using sequencing technology. Eighteen bulls were fed a total mixed ration based on maize silage and concentrate (40:60) and randomly allocated to one of three experimental diets: a basal diet with no urea (UC, 0%), a basal diet supplemented with low urea levels (UL, 0.8% dry matter (DM) basis), and a basal diet supplemented with high urea levels (UH, 2% DM basis). All treatments were iso-nitrogenous (14% crude protein, DM basis) and iso-metabolic energetic (ME = 11.3 MJ/kg, DM basis). After a 12-week feeding trial, DNA was isolated from ruminal samples and used for 16S rRNA gene amplicon sequencing. For bacteria, the most abundant phyla were Firmicutes (44.47%) and Bacteroidetes (41.83%), and the dominant genera were Prevotella (13.17%), Succiniclasticum (4.24%), Butyrivibrio (2.36%), and Ruminococcus (1.93%). Urea supplementation had no effect on most phyla (P > 0.05), while there was a decreasing tendency in phylum TM7 with increasing urea levels (P = 0.0914). Compared to UC, UH had lower abundance of genera Butyrivibrio and Coprococcus (P = 0.0092 and P = 0.0222, respectively). For archaea, the most abundant phylum was Euryarchaeota (99.81% of the sequence reads), and the most abundant genus was Methanobrevibacter (90.87% of the sequence reads). UH increased the abundance of genus Methanobrevibacter and Methanobacterium (P = 0.0299 and P = 0.0007, respectively) and decreased the abundance of vadinCA11 (P = 0.0151). These findings suggest that urea-supplemented diets were associated with a shift in archaeal biodiversity and changes in the bacterial community in the rumen.


Urea Ruminal bacterial community Ruminal archaeal community Sequencing Finishing bulls 



This work was supported by grant from the National Natural Science Foundation of China (31672449 and 31372335), the China Agricultural Research System (CARS-38), and the Special Fund for Agro-scientific Research in the Public Interest (201503134).

Compliance with ethical standards

Conflict of interest

The authors all declare that they have no conflict of interest.

Human and animal rights

This article does not contain any studies with human participants performed by any of the authors. Experiments were performed in strict accordance with the Regulations for the Administration of Affairs Concerning Experimental Animals (The State Science and Technology Commission of P. R. China, 1988). All animal procedures were approved by the China Agricultural University’s Animal Welfare and Ethical Committee (Permit No. DK1066).

Supplementary material

253_2017_8323_MOESM1_ESM.pdf (419 kb)
ESM 1 (PDF 418 kb)


  1. Aguiar AD, Vendramini JM, Arthington JD, Sollenberger LE, DiLorenzo N, Hersom MJ (2015) Performance of beef cows and calves fed different sources of rumen-degradable protein when grazing stockpiled limpograss pastures. J Anim Sci 93:1923–1932. doi: 10.2527/jas.2014-8599 CrossRefPubMedGoogle Scholar
  2. Belanche A, de la Fuente G, Newbold CJ (2015) Effect of progressive inoculation of fauna-free sheep with holotrich protozoa and total-fauna on rumen fermentation, microbial diversity and methane emissions. FEMS Microbiol Ecol 91:1–10. doi: 10.1093/femsec/fiu026 CrossRefGoogle Scholar
  3. Bourg BM, Tedeschi LO, Wickersham TA, Tricarico JM (2012) Effects of a slow-release urea product on performance, carcass characteristics, and nitrogen balance of steers fed steam-flaked corn. J Anim Sci 90:3914–3923. doi: 10.2527/jas.2011-4832 CrossRefPubMedGoogle Scholar
  4. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336. doi: 10.1038/nmeth.f.303 CrossRefPubMedPubMedCentralGoogle Scholar
  5. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R (2011) Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci U S A 108(Suppl 1):4516–4522. doi: 10.1073/pnas.1000080107 CrossRefPubMedGoogle Scholar
  6. Ceconi I, Ruiz-Moreno MJ, DiLorenzo N, DiCostanzo A, Crawford GI (2015) Effect of slow-release urea inclusion in diets containing modified corn distillers grains on total tract digestibility and ruminal fermentation in feedlot cattle. J Anim Sci 93:4058–4069. doi: 10.2527/jas.2014-8299 CrossRefPubMedGoogle Scholar
  7. Cherdthong A, Wanapat M, Rakwongrit D, Khota W, Khantharin S, Tangmutthapattharakun G, Kang S, Foiklang S, Phesatcha K (2014) Supplementation effect with slow-release urea in feed blocks for Thai beef cattle—nitrogen utilization, blood biochemistry, and hematology. Trop Anim Health Prod 46:293–298. doi: 10.1007/s11250-013-0485-1 CrossRefPubMedGoogle Scholar
  8. De Barbieri I, Hegarty RS, Silveira C, Gulino LM, Oddy VH, Gilbert RA, Klieve AV, Ouwerkerk D (2015) Programming rumen bacterial communities in newborn Merino lambs. Small Rumin Res 129:48–59. doi: 10.1016/j.smallrumres.2015.05.015 CrossRefGoogle Scholar
  9. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194–2200. doi: 10.1093/bioinformatics/btr381 CrossRefPubMedPubMedCentralGoogle Scholar
  10. Hanada A, Kurogi T, Giang NM, Yamada T, Kamimoto Y, Kiso Y, Hiraishi A (2014) Bacteria of the candidate phylum TM7 are prevalent in acidophilic nitrifying sequencing-batch reactors. Microbes Environ 29:353–362. doi: 10.1264/jsme2.ME14052 CrossRefPubMedPubMedCentralGoogle Scholar
  11. He X, McLean JS, Edlund A, Yooseph S, Hall AP, Liu SY, Dorrestein PC, Esquenazi E, Hunter RC, Cheng G, Nelson KE, Lux R, Shi W (2015) Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle. Proc Natl Acad Sci U S A 112:244–249. doi: 10.1073/pnas.1419038112 CrossRefPubMedGoogle Scholar
  12. Henderson G, Cox F, Ganesh S, Jonker A, Young W, Global Rumen Census Consortium, Janssen PH (2015) Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. Sci Rep 5:14567. doi: 10.1038/srep14567 CrossRefPubMedPubMedCentralGoogle Scholar
  13. Jewell KA, McCormick CA, Odt CL, Weimer PJ, Suen G (2015) Ruminal bacterial community composition in dairy cows is dynamic over the course of two lactations and correlates with feed efficiency. Appl Environ Microbiol 81:4697–4710. doi: 10.1128/AEM.00720-15 CrossRefPubMedPubMedCentralGoogle Scholar
  14. Jin D, Zhao S, Wang P, Zheng N, Bu D, Beckers Y, Wang J (2016) Insights into abundant rumen ureolytic bacterial community using rumen simulation system. Front Microbiol 7:1006. doi: 10.3389/fmicb.2016.01006 PubMedPubMedCentralGoogle Scholar
  15. Kittelmann S, Seedorf H, Walters WA, Clemente JC, Knight R, Gordon JI, Janssen PH (2013) Simultaneous amplicon sequencing to explore co-occurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities. PLoS One 8:e47879. doi: 10.1371/journal.pone.0047879 CrossRefPubMedPubMedCentralGoogle Scholar
  16. Koenig KM, McGinn SM, Beauchemin KA (2013) Ammonia emissions and performance of backgrounding and finishing beef feedlot cattle fed barley-based diets varying in dietary crude protein concentration and rumen degradability. J Anim Sci 91:2278–2294. doi: 10.2527/jas.2012-5651 CrossRefPubMedGoogle Scholar
  17. Lin B, Henderson G, Zou CX, Cox F, Liang XW, Janssen PH, Attwood GT (2015) Characterization of the rumen microbial community composition of buffalo breeds consuming diets typical of dairy production systems in southern China. Anim Feed Sci Tech 207:75–84. doi: 10.1016/j.anifeedsci.2015.06.013 CrossRefGoogle Scholar
  18. Lozupone C, Knight R (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71:8228–8235. doi: 10.1128/AEM.71.12.8228-8235.2005 CrossRefPubMedPubMedCentralGoogle Scholar
  19. Magoc T, Salzberg SL (2011) FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27:2957–2963. doi: 10.1093/bioinformatics/btr507 CrossRefPubMedPubMedCentralGoogle Scholar
  20. Martinez-Fernandez G, Abecia L, Martin-Garcia AI, Ramos-Morales E, Denman SE, Newbold CJ, Molina-Alcaide E, Yanez-Ruiz DR (2015) Response of the rumen archaeal and bacterial populations to anti-methanogenic organosulphur compounds in continuous-culture fermenters. FEMS Microbiol Ecol 91:fiv079. doi: 10.1093/femsec/fiv079 CrossRefPubMedGoogle Scholar
  21. McCabe MS, Cormican P, Keogh K, O’Connor A, O’Hara E, Palladino RA, Kenny DA, Waters SM (2015) Illumina MiSeq phylogenetic amplicon sequencing shows a large reduction of an uncharacterised succinivibrionaceae and an increase of the Methanobrevibacter gottschalkii clade in feed restricted cattle. PLoS One 10:e0133234. doi: 10.1371/journal.pone.0133234 CrossRefPubMedPubMedCentralGoogle Scholar
  22. Paul SS, Deb SM, Dey A, Somvanshi SP, Singh D, Rathore R, Stiverson J (2015) 16S rDNA analysis of archaea indicates dominance of Methanobacterium and high abundance of Methanomassiliicoccaceae in rumen of Nili-Ravi buffalo. Anaerobe 35:3–10. doi: 10.1016/j.anaerobe.2015.06.002 CrossRefPubMedGoogle Scholar
  23. Paz HA, Anderson CL, Muller MJ, Kononoff PJ, Fernando SC (2016) Rumen bacterial community composition in holstein and jersey cows is different under same dietary condition and is not affected by sampling method. Front Microbiol 7:1206. doi: 10.3389/fmicb.2016.01206 CrossRefPubMedPubMedCentralGoogle Scholar
  24. Singh KM, Patel AK, Shah RK, Reddy B, Joshi CG (2015) Potential functional gene diversity involved in methanogenesis and methanogenic community structure in Indian buffalo (Bubalus bubalis) rumen. J Appl Genet 56:411–426. doi: 10.1007/s13353-015-0270-0 CrossRefPubMedGoogle Scholar
  25. Snelling TJ, Genc B, McKain N, Watson M, Waters SM, Creevey CJ, Wallace RJ (2014) Diversity and community composition of methanogenic archaea in the rumen of Scottish upland sheep assessed by different methods. PLoS One 9:e106491. doi: 10.1371/journal.pone.0106491 CrossRefPubMedPubMedCentralGoogle Scholar
  26. Soro V, Dutton LC, Sprague SV, Nobbs AH, Ireland AJ, Sandy JR, Jepson MA, Micaroni M, Splatt PR, Dymock D, Jenkinson HF (2014) Axenic culture of a candidate division TM7 bacterium from the human oral cavity and biofilm interactions with other oral bacteria. Appl Environ Microbiol 80:6480–6489. doi: 10.1128/AEM.01827-14 CrossRefPubMedPubMedCentralGoogle Scholar
  27. St-Pierre B, Wright AD (2013) Diversity of gut methanogens in herbivorous animals. Animal 7(Suppl 1):49–56. doi: 10.1017/S1751731112000912 CrossRefPubMedGoogle Scholar
  28. Tap J, Furet JP, Bensaada M, Philippe C, Roth H, Rabot S, Lakhdari O, Lombard V, Henrissat B, Corthier G, Fontaine E, Dore J, Leclerc M (2015) Gut microbiota richness promotes its stability upon increased dietary fibre intake in healthy adults. Environ Microbiol 17:4954–4964. doi: 10.1111/1462-2920.13006 CrossRefPubMedGoogle Scholar
  29. Taylor-Edwards CC, Elam NA, Kitts SE, McLeod KR, Axe DE, Vanzant ES, Kristensen NB, Harmon DL (2009) Influence of slow-release urea on nitrogen balance and portal-drained visceral nutrient flux in beef steers. J Anim Sci 87:209–221. doi: 10.2527/jas.2008-0913 CrossRefPubMedGoogle Scholar
  30. Van Soest PJ, Robertson JB, Lewis BA (1991) Methods for dietary fiber, neutral detergent fiber, and nonstarch polysaccharides in relation to animal nutrition. J Dairy Sci 74:3583–3597. doi: 10.3168/jds.S0022-0302(91)78551-2 CrossRefPubMedGoogle Scholar
  31. Wetzels SU, Mann E, Metzler-Zebeli BU, Wagner M, Klevenhusen F, Zebeli Q, Schmitz-Esser S (2015) Pyrosequencing reveals shifts in the bacterial epimural community relative to dietary concentrate amount in goats. J Dairy Sci 98:5572–5587. doi: 10.3168/jds.2014-9166 CrossRefPubMedGoogle Scholar
  32. Whiteley AS, Jenkins S, Waite I, Kresoje N, Payne H, Mullan B, Allcock R, O’Donnell A (2012) Microbial 16S rRNA ion tag and community metagenome sequencing using the ion torrent (PGM) platform. J Microbiol Methods 91:80–88. doi: 10.1016/j.mimet.2012.07.008 CrossRefPubMedGoogle Scholar
  33. Wozny MA, Bryant MP, Holdeman LV, Moore WE (1977) Urease assay and urease-producing species of anaerobes in the bovine rumen and human feces. Appl Environ Microbiol 33:1097–1104PubMedPubMedCentralGoogle Scholar
  34. Yu Z, Morrison M (2004) Improved extraction of PCR-quality community DNA from digesta and fecal samples. BioTechniques 36:808–812PubMedGoogle Scholar
  35. Zhang C, Zhang M, Wang S, Han R, Cao Y, Hua W, Mao Y, Zhang X, Pang X, Wei C, Zhao G, Chen Y, Zhao L (2010) Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice. ISME J 4:232–241. doi: 10.1038/ismej.2009.112 CrossRefPubMedGoogle Scholar
  36. Zhao L, Meng Q, Ren L, Liu W, Zhang X, Huo Y, Zhou Z (2015) Effects of nitrate addition on rumen fermentation, bacterial biodiversity and abundance. Asian-Australas J Anim Sci 28:1433–1441. doi: 10.5713/ajas.15.0091 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2017

Authors and Affiliations

  • Zhenming Zhou
    • 1
  • Qingxiang Meng
    • 1
  • Shengli Li
    • 1
  • Lan Jiang
    • 1
  • Hao Wu
    • 1
  1. 1.State Key Laboratory of Animal Nutrition, College of Animal Science and TechnologyChina Agricultural UniversityBeijingChina

Personalised recommendations