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Journal of Integrative Agriculture  2019, Vol. 18 Issue (5): 1080-1092    DOI: 10.1016/S2095-3119(18)62120-3
Animal Science · Veterinary Medicine Advanced Online Publication | Current Issue | Archive | Adv Search |
Weaning methods affect ruminal methanogenic archaea composition and diversity in Holstein calves
DONG Li-feng*, MA Jun-nan*, TU Yan, DIAO Qi-yu
Feed Research Institute, Chinese Academy of Agricultural Sciences/Beijing Key Laboratory for Dairy Cow Nutrition/Key Laboratory of Feed Biotechnology, Ministry of Agriculture, Beijing 100081, P.R.China
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The objective of the present study was to examine the effect of different weaning methods on the ruminal methanogenic archaea composition and diversity in Holstein calves.  Thirty-six newborn Holstein bull calves were assigned to 1 of 3 treatments: (1) conventional weaning (d 56) and fed a high proportion of solid feed (CWS); (2) conventional weaning (d 56) and fed a high proportion of liquid feed (CWL); (3) early weaning (d 42) and fed with a high proportion of solid feed (EWS).  High-throughput sequencing of the methyl coenzyme M reductase (mcrA) gene, which encodes the α-subunit of methyl coenzyme M reductase - the enzyme that catalyzes the final step in methanogenesis was used to determine the composition and diversity of rumen methanogens.  No significant difference (P>0.05) was observed for operational taxonomic units (OTUs) or richness indices, but diversity indices increased (P<0.05) for calves fed high dietary solids.  Predominant families across the three treatments were Methanobacteriaceae, Thermoplasmataceae and Methanomassiliicoccaceae.  Calves in the EWS treatment had a higher (P<0.05) relative abundance of Methanobrevibacter sp. strain AbM4 and Methanosphaera stadtmanae, while calves in the CWL treatment had a higher (P<0.05) abundance of Methanosphaera sp. strain SM9.  A positive (P<0.05) relationship was identified between butyrate and Methanobrevibacter sp. strain AbM4.  In conclusion, the composition and diversity of methanogens in the rumen of Holstein calves varied under the different weaning methods.  This study identified a positive relationship between butyrate and Methanobrevibacter sp. strain AbM4, potentially reflecting correlations between ruminal fermentation variables and methanogenesis function.  These in-depth analyses provide further understanding of weaning methods for intensified production systems. 
Keywords:  calf        methyl coenzyme M reductase (mcrA) gene        methanogenic archaea diversity        rumen fermentation        weaning methods
Received: 02 April 2018   Accepted:
Fund: This study was supported by the Key Program for International S&T Cooperation Projects of China (2016YFE0109000), the National Key R&D Program of China (2017YFF0211702), the National Natural Science Foundation of China (41475126 and 31802085), and the Young Scientist Lifting Project, China (2017–2019).
Corresponding Authors:  Correspondence DIAO Qi-yu, Tel/Fax: +86-10-82106055, E-mail:    
About author:  DONG Li-feng, Tel: +86-10-62166878, E-mail:; * These authors contributed equally to this study.

Cite this article: 

DONG Li-feng, MA Jun-nan, TU Yan, DIAO Qi-yu. 2019. Weaning methods affect ruminal methanogenic archaea composition and diversity in Holstein calves. Journal of Integrative Agriculture, 18(5): 1080-1092.

Abecia L, Ramos-Morales E, Martínez-Fernandez G, Arco A, Martín-García A I, Newbold C J, Yáñez-Ruiz D R. 2014. Feeding management in early life influences microbial colonisation and fermentation in the rumen of newborn goat kids. Animal Production Science, 54, 1449–1454.
Amato K R, Yeoman C J, Kent A, Righini N, Carbonero F, Estrada A, Gaskins H R, Stumpf R M, Yildirim S, Torralba M, Gillis M, Wilson B A, Nelson K E, White B A, Leigh S R. 2013. Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes. The ISME Journal, 7, 1344–1353.
Bach A, Ahedo J, Ferrer A. 2010. Optimizing weaning strategies of dairy replacement calves. Journal of Dairy Science, 93, 413–419.
Baldwin R L, McLeod VI K R, Klotz J L, Heitmann R N. 2004. Rumen development, intestinal growth and hepatic metabolism in the pre- and postweaning ruminant. Journal of Dairy Science, 87, E55–E65.
Bodas R, Prieto N, García-González R, Andrés S, Giráldez F J, López S. 2012. Manipulation of rumen fermentation and methane production with plants secondary metabolites. Animal Feed Science and Technology, 176, 78–93.
Cabezas-Garicia E H, Krizsan S J, Shingfield K J, Huhtanen P. 2017. Between-cow variation in digestion and rumen fermentation variables associated with methane production. Journal of Dairy Science, 10, 4409–4424.
Carberry C A, Kenny D A, Han S, McCabe M S, Waters S M. 2012. Effect of phenotypic residual feed intake and dietary forage content on the rumen microbial community of beef cattle. Applied and Environmental Microbiology, 78, 4949–4958.
Chaney A L, Marbach E P. 1962. Modified reagents for determination of urea and ammonia. Clinical Chemistry, 8, 130–132.
Diao Q Y, Zhang R, Tu Y. 2017. Current research progresses on calf rearing and nutrition in China. Journal of Integrative Agriculture, 12, 2805–2814.
Dong L F, Ferris C P, McDowell D A, Yan T. 2015. Effects of diet forage proportion on maintenance energy requirement and the efficiency of metabolizable energy use for lactation by lactating dairy cows. Journal of Dairy Science, 98, 1–10.
Dong L F, Xu X C, Zhang N F, Tu Y, Diao Q Y. 2017a. Effects of different feeding methods and space allowance on the growth performance, individual and social behaviors of Holstein calves. Journal of Integrative Agriculture, 6, 1375–1382.
Dong L F, Zhang W B, Zhang N F, Tu Y, Diao Q Y. 2017b. Feeding different dietary protein to energy ratios to Holstein heifers: effects on growth performance, blood metabolites and rumen fermentation parameters. Journal of Animal Physiology and Animal Nutrition, 1, 30–37.
Eadie J M. 1962. Inter-relationships between certain rumen ciliate protozoa. Journal of General and Applied Microbiology, 4, 579–588.
Eckert E, Brown H E, Leslie K E, DeVries T J, Steele M A. 2015. Weaning age affects growth, feed intake, gastrointestinal development, and behavior in Holstein calves fed an elevated plane of nutrition during the preweaning stage. Journal of Dairy Science, 98, 6315–6326.
EPA (U. S. Environmental Protection Agency ). 2009. Ruminant livestock. [2012-05-01].
EPA (U.S. Environmental Protection Agency). 2018. Inventory of U.S. Greenhouse Gases Emissions and Sinks 1990–2016. [2018-04-12].
Finlay B J, Fenchel T. 1989. Hydrogenosomes in some anaerobic protozoa resemble mitochondria. FEMS Microbiology Letters, 65, 311–314.
Fricke W F, Seedorf H, Henne A, Kruer M, Liesegang H, Hedderich R, Gottschalk G, Thauer R K. 2006. The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis. Journal of Bacteriology, 188, 642–658.
Friedrich M W. 2005. Methyl-coenzyme M reductase genes: Unique functional markers for methanogenic and anaerobic methane-oxidizing archaea. Methods in Enzymology, 397, 428–442.
Geishauser T. 1993. An instrument for the collection and transfer of ruminal fluid and for the administration of water soluble drugs in adult cattle. Bovine Practice, 27, 38–42.
Greenwood R H, Morrill J L, Titgemeyer E C, Kennedy G A. 1997. A new method of measuring diet abrasion and its effect on the development of the forestomach. Journal of Dairy Science, 80, 2534–2541.
Gerber P, Vellinga T, Opio C, Steinfeld H. 2011. Productivity gains and greenhouse gas emissions intensity in dairy systems. Livestock Science, 139, 100–108.
Guzman C E, Bereza-Malcolm L T, de Groef B, Franks A E. 2015. Uptake of milk with and without solid feed during the monogastric phase: Effect on fibrolytic and methanogenic microorganisms in the gastrointestinal tract of calves. Animal Science Journal, 87, 378–388.
Hill T M, Bateman II H G, Aldrich J M, Schlotterbeck R L. 2012. Methods of reducing milk replacer to prepare dairy calves for weaning when large amounts of milk replacer have been fed. Professional Animal Science, 28, 332–337.
Hobson P N, Stewart C S. 1997. The Rumen Microbial Ecosystem. Blackie Academic and Professional, London, England.
Johnson K A, Johnson D E. 1995. Methane emissions from cattle. Journal of Animal Science, 73, 2483–2492.
Kay M, Fell B F, Boyne R. 1969. The relationship between the acidity of the rumen contents and rumenitis in calves fed barley. Research in Veterinary Science, 10, 181–187.
Khan M A, Lee H J, Lee W S, Kim H S, Kim S B, Ki K S, Ha J K, Lee H G, Choi Y J. 2007. Pre- and postweaning performance of Holstein female calves fed milk through step-down and conventional methods. Journal of Dairy Science, 90, 876–885.
Khan M A, Weary D M, von Keyerslingk M A G. 2011. Effects of milk ration on solid feed intake, weaning, and performance in dairy heifers. Journal of Dairy Science, 94, 1071–1081.
Leahy S C, Kelly W J, Li D, Li Y, Altermann E, Lambie S C, Cox F, Attwood G T. 2013. The complete genome sequence of Methanobrevibacter sp. AbM4. Standards in Genomic Science, 8, 215–227.
Li Z P, Wright A D G, Liu H L, Fan Z Y, Yang F H, Zhang Z G, Li G Y. 2015. Response of the rumen microbiota of Sika deer (Cervus nippon) fed different concentrations of tannin rich plants. PLoS ONE, 10, 1371.
Luton P E, Wayne J M, Sharp R J, Riley P W. 2002. The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill. Microbiology, 148, 3521–3530.
Martin C, Morgavi D P, Doreau M. 2010. Methane mitigation in ruminants: from microbe to the farm scale. Animal, 4, 351–365.
McDonald P, Edwards R A, Greenhalgh J F D, Morgan C A. 2002. Animal Nutrition. 6th ed. Longman, Harlow, United Kingdom.
Michalowski T, Belzecki G, Kwiatkowska E, Pajak J J. 2003. The effect of selected rumen fauna on fibrolytic enzyme activities, bacterial mass, fibre disappearance and fermentation pattern in sheep. Journal of Animal Feed Sciences, 1, 45–64.
Miller T L, Wolin M J. 1985. Methanosphaera stadtmaniae gen. nov., sp. nov.: A species that forms methane by reducing methanol with hydrogen. Archives of Microbiology, 141, 116–122.
Miller T L, Wolin M J, Zhao H X, Bryant M P. 1986. Characteristics of methanogens isolated from bovine rumen. Applied and Environmental Microbiology, 51, 201–202.
Mirzaei M, Dahkhah N, Baghbanzadeh-Nobari B, Agha-Tehrani A, Eshraghi M, Imani M, Shiasi-Sardoabi R, Ghaffari M H. 2018. Effects of preweaning total plane of milk intake and weaning age on intake, growth performance, and blood metabolites of dairy calves. Journal of Dairy Science, 101, 4212–4220.
Morvan B, Dore J, Rieu-Lesme F, Foucat L, Fonty G, Gouet P. 1994. Establishment of hydrogen-utilizing bacteria in the rumen of the newborn lamb. FEMS Microbiology Letters, 117, 249–256.
Moss A R, Jouany J P, Newbold J. 2000. Methane production by ruminants: Its contribution to global warming. Annales De Zootechnie, 49, 231–253.
Nemati M, Amanlou H, Khorvash M, Moshiri B, Mirzaei M, Khan M A, Ghaffari M H. 2015. Rumen fermentation, blood metabolites, and growth performance of calves during transition from liquid to solid feed: Effects of dietary level and particle size of alfalfa hay. Journal of Dairy Science, 98, 7131–7141.
Roth B A, Keil N M, Gygax L, Hillmann E. 2009. Influence of weaning method on health status and rumen development in dairy calves. Journal of Dairy Science, 92, 645–656.
Seedorf H, Kittelmann S, Janssen P H. 2015. Few highly abundant operational taxonomic units dominate within rumen methanogenic archaeal species in New Zealand sheep and cattle. Applied and Environmental Microbiology, 81, 986–995.
Terré M, Bach A, Devant M. 2006. Performance and behaviour of calves reared in groups or individually following and enhanced growth feeding program. Journal of Dairy Research, 73, 480–486.
Tomkins N W, Denman S E, Pilajun R, Wanapat M, McSweeney C S, Elliott R. 2015. Manipulating rumen fermentation and methanogenesis using an essential oil and monensin in beef cattle fed a tropical grass hay. Animal Feed Science and Technology, 200, 25–34.
Tóthová T, Piknova M, Kisidayova S, Javorsky P, Pristas P. 2008. Distinctive archaebacterial species associated with anaerobic rumen protozoan Entodinium caudatum. Folia Microbioogica, 53, 259–262.
Yáñez-Ruiz D R, Macías B, Pinloche E, Newbold C J. 2010. The persistence of bacterial and methanogenic archaeal communities residing in the rumen of young lambs. FEMS Microbiology Ecology, 72, 272–278.
Yáñez-Ruiz D R, Abecia L, Newbold C J. 2015. Manipulating rumen microbiome and fermentation through interventions during early life: A review. Frontiers in Microbiology, 6, 1133.
Yu Z T, García-González R, Schanbacher F L, Morrison M. 2008. Evaluations of different hypervariable regions of archaeal 16S rRNA genes in profiling of methanogens by archaea-specific pcr and denaturing gradient gel electrophoresis. Applied Environmental Microbiology, 74, 889–893.
Zhou M, Hernandez-Sanabria E, Guan L L. 2009. Assessment of the microbial ecology of ruminal methanogens in cattle with different feed efficiencies. Applied Environmental Microbiology, 75, 6524–6533.
Zhou M, Hernandez-Sanabria E, Guan L L. 2010. Characterization of variation in rumen methanogenic communities under different dietary and host feed efficiency conditions, as determined by PCR-denaturing gradient gel electrophoresis analysis. Applied Environmental Microbiology, 76, 3776–3786.
Zhou M, Chen Y H, Griebel P J, Guan L L. 2014. Methanogen prevalence throughout the gastrointestinal tract of pre-weaned dairy calves. Gut Microbes, 5, 628–638.
Zhou M, Hünerberg M, Beauchemin K A, McAllister T A, Okine E K, Guan L L. 2013. Individuality of ruminal methanogen/protozoa populations in beef cattle fed diets containing dried distillers’ grain with solubles. Acta Agriculture Scandinavica (Section A - Animal Science), 62, 273–288.
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