Antonie van Leeuwenhoek

, Volume 111, Issue 11, pp 2037–2049 | Cite as

The bacterial and archaeal community structures and methanogenic potential of the cecal microbiota of goats fed with hay and high-grain diets

  • Wei Jin
  • Yin Li
  • Yanfen ChengEmail author
  • Shengyong Mao
  • Weiyun Zhu
Original Paper


The cecum plays an important role in the feed fermentation of ruminants. However, information is very limited regarding the cecal microbiota and their methane production. In the present study, the cecal content from twelve local Chinese goats, fed with either a hay diet (0% grain) or a high-grain diet (71.5% grain), were used to investigate the bacterial and archaeal community and their methanogenic potential. Microbial community analysis was determined using high-throughput sequencing of 16S rRNA genes and real-time PCR, and the methanogenesis potential was assessed by in vitro fermentation with ground corn or hay as substrates. Compared with the hay group, the high-grain diet significantly increased the length and weight of the cecum, the proportions of starch and crude protein, the concentrations of volatile fatty acids and ammonia nitrogen, but decreased the pH values (P < 0.05). The high-grain diet significantly increased the abundances of bacteria and archaea (P < 0.05) and altered their community. For the bacterial community, the genera Bifidobacterium, Prevotella, and Treponema were significantly increased in the high-grain group (P < 0.05), while Akkermansia, Oscillospira, and Coprococcus were significantly decreased (P < 0.05). For the archaeal community, Methanosphaera stadtmanae was significantly increased in the high-grain group (P < 0.05), while Methanosphaera sp. ISO3-F5 was significantly decreased (P < 0.05). In the in vitro fermentation with grain as substrate, the cecal microorganisms from the high-grain group produced a significantly higher amount of methane and volatile fatty acids (P < 0.05), and produced significantly lower amount of lactate (P < 0.05). Conclusively, high-grain diet led to more fermentable substrates flowing into the hindgut of goats, resulting in an enhancement of microbial fermentation and methane production in the cecum.


Cecal microbiota Goat High-grain diet Methanogenic potential Miseq sequencing 



This research was funded by the National Key Research and Development Program of China (2017YFD0500505), and the National Natural Science Foundation of China (31301999).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no competing interests.

Ethics approval

The animal experiment was approved by the Animal Experiment Committee of Nanjing Agricultural University, in accordance with the Regulations for the Administration of Affairs Concerning Experimental Animals (The State Science and Technology Commission of China, 1988).

Supplementary material

10482_2018_1096_MOESM1_ESM.docx (290 kb)
Supplementary material 1 (DOCX 290 kb)


  1. Ametaj BN, Zebeli Q, Saleem F, Psychogios N, Lewis MJ, Dunn SM, Xia J, Wishart DS (2010) Metabolomics reveals unhealthy alterations in rumen metabolism with increased proportion of cereal grain in the diet of dairy cows. Metabolomics 6(4):583–594CrossRefGoogle Scholar
  2. AOAC (2000) Official methods of analysis of AOAC International, 17th edn. AOAC International, GaithersburgGoogle Scholar
  3. Aronesty E (2011) ea-utils: command-line tools for processing biological sequencing data.
  4. Barker SB, Summerson WH (1941) The colorimetric determination of lactic acid in biological material. J Biol Chem 138:535–554Google Scholar
  5. Bartram AK, Lynch MDJ, Stearns JC, Moreno-Hagelsieb G, Neufeld JD (2011) Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end illumine reads. Appl Environ Microbiol 77:3846–3852CrossRefGoogle Scholar
  6. Belzer C, de Vos WM (2012) Microbes inside—from diversity to function: the case of Akkermansia. ISME J 6:1449–1458CrossRefGoogle Scholar
  7. Blais Lecours P, Marsolais D, Cormier Y, Berberi M, Haché C, Bourdages R, Duchaine C (2014) Increased prevalence of Methanosphaera stadtmanae in inflammatory bowel diseases. PLoS ONE 9(2):e87734CrossRefGoogle Scholar
  8. Brugère JF, Borrel G, Gaci N, Tottey W, O’Toole PW, Malpuech-Brugère C (2014) Archaebiotics: proposed therapeutic use of archaea to prevent trimethylaminuria and cardiovascular disease. Gut Microbes 5(1):5–10CrossRefGoogle Scholar
  9. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña 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 7:335–336CrossRefGoogle Scholar
  10. de Vos P, Garrity GM, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer K, Whitman WB (eds) (2009) Bergey’s manual of systematic bacteriology. Volume 3: The Firmicutes, 2nd edn. Springer, New York, pp 736–1190Google Scholar
  11. Denman SE, McSweeney CS (2006) Development of a real-time PCR assay for monitoring anaerobic fungal and cellulolytic bacterial populations within the rumen. FEMS Microbiol Ecol 58:572–582CrossRefGoogle Scholar
  12. Dennis KL, Wang Y, Blatner NR, Wang S, Saadalla A, Trudeau E, Roers A, Weaver CT, Lee JJ, Gilbert JA, Chang EB, Khazaie K (2013) Adenomatous polyps are driven by microbe-instigated focal inflammation and are controlled by IL-10—producing T cells. Cancer Res 73:5905–5913CrossRefGoogle Scholar
  13. Derrien M, Vaughan EE, Plugge CM, de Vos WM (2004) Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium. Int J Syst Evol Microbiol 54:1469–1476CrossRefGoogle Scholar
  14. Dixon RM, Nolan JV (1982) Studies of the large intestine of sheep. 1. Fermentation and absorption in sections of the large intestine. Br J Nutr 47:289–300CrossRefGoogle Scholar
  15. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27(16):2194–2200CrossRefGoogle Scholar
  16. Faichney GJ (1968) Volatile fatty acids in the caecum of the sheep. Aust J Biol Sci 21:177–180PubMedGoogle Scholar
  17. Gray FV (1947) The digestion of cellulose by sheep. The extent of cellulose digestion at successive levels of the alimentary tract. J Exp Bio 24(1–2):15Google Scholar
  18. Gressley TF, Hall MB, Armentano LE (2011) Ruminant nutrition symposium: productivity, digestion, and health responses to hindgut acidosis in ruminants. J Anim Sci 89:1120–1130CrossRefGoogle Scholar
  19. Jayaprakash G, Sathiyabarathi M, Robert MA, Tamilmani T (2016) Rumen-protected choline: a significance effect on dairy cattle nutrition. Vet World 9(8):837–841CrossRefGoogle Scholar
  20. Jiang Y, Ogunade IM, Arriola KG, Qi M, Vyas D, Staples CR, Adesogan AT (2017) Effects of the dose and viability of saccharomyces cerevisiae. 2. Ruminal fermentation, performance of lactating dairy cows, and correlations between ruminal bacteria abundance and performance measures. J Dairy Sci 100:1–17CrossRefGoogle Scholar
  21. Jin W, Meng Z, Wang J, Cheng Y, Zhu W (2017) Effect of nitrooxy compounds with different molecular structures on the rumen methanogenesis, metabolic profile, and methanogenic community. Curr Microbiol 74(8):891–898CrossRefGoogle Scholar
  22. Konikoff T, Gophna U (2016) Oscillospira: a central, enigmatic component of the human gut microbiota. Trends Microbiol 24(7):523–524CrossRefGoogle Scholar
  23. Lang K, Schuldes J, Klingl A, Poehlein A, Daniel R, Brunea A (2015) New mode of energy metabolism in the seventh order of methanogens as revealed by comparative genome analysis of “Candidatus Methanoplasma termitum”. Appl Environ Microbiol 81(4):1338–1352CrossRefGoogle Scholar
  24. Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R, Beiko RG, Huttenhower C (2013) Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol 31:814–821CrossRefGoogle Scholar
  25. Leiva T, Cooke RF, Brandão AP, Marques RS, Vasconcelos JL (2015) Effects of rumen-protected choline supplementation on metabolic and performance responses of transition dairy cows. J Anim Sci 93(4):1896–1904CrossRefGoogle Scholar
  26. Li S, Khafipour E, Krause DO, Kroeker A, Rodriguez-Lecompte JC, Gozho GN, Plaizier JC (2012) Effects of subacute ruminal acidosis challenges on fermentation and endotoxins in the rumen and hindgut of dairy cows. J Dairy Sci 95(1):294–303CrossRefGoogle Scholar
  27. Li M, Jin W, Li Y, Zhao L, Cheng Y, Zhu W (2016) Spatial dynamics of the bacterial community structure in the gastrointestinal tract of red kangaroo (Macropus rufus). World J Microbiol Biotechnol 32(6):98CrossRefGoogle Scholar
  28. Liu J, Xu T, Zhu W, Mao S (2014) High-grain feeding alters caecal bacterial microbiota composition and fermentation and results in caecal mucosal injury in goats. Br J Nutr 112(3):416–427CrossRefGoogle Scholar
  29. Liu J, Pu YY, Xie Q, Wang JK, Liu JX (2015) Pectin induces an in vitro rumen microbial population shift attributed to the pectinolytic treponema group. Curr Microbiol 70(1):67–74. CrossRefPubMedGoogle Scholar
  30. Mackie RI, Aminov RI, Hu W, Klieve AV, Ouwerkerk D, Sundset MA, Kamagata Y (2003) Ecology of uncultivated oscillospira species in the rumen of cattle, sheep, and reindeer as assessed by microscopy and molecular approaches. Appl Environ Microbiol 69(11):6808–6815CrossRefGoogle Scholar
  31. Makkar HPS, Sharma OP, Dawra RK, Negi SS (1982) Simple determination of microbial protein in rumen liquor. J Dairy Sci 65:2170–2173CrossRefGoogle Scholar
  32. Mao S, Zhang M, Liu J, Zhu W (2015) Characterising the bacterial microbiota across the gastrointestinal tracts of dairy cattle: membership and potential function. Sci Rep 5:16116CrossRefGoogle Scholar
  33. Mao SY, Huo WJ, Zhu WY (2016) Microbiome–metabolome analysis reveals unhealthy alterations in the composition and metabolism of ruminal microbiota with increasing dietary grain in a goat model. Environ Microbiol 18(2):525–541CrossRefGoogle Scholar
  34. Martin C, Philippeau C, Michalet-Doreau B (1999) Effect of wheat and corn variety on fiber digestion in beef steers fed high-grain diets. J Anim Sci 77:2269–2278CrossRefGoogle Scholar
  35. McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, Andersen GL, Knight R, Hugenholtz P (2012) An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6:610–618CrossRefGoogle Scholar
  36. Menke KH, Rabb L, Salewski A, Steingass H, Fritz D, Schneider W (1979) The estimation of the digestibility and metabolisable energy content of ruminant feedstuffs from the gas production when they are incubated with rumen liquor in vitro. J Agric Sci 93:217–222CrossRefGoogle Scholar
  37. Oren A, Garrity GM (2015) The correct name of the type species of the genus Methanocorpusculum. Request for an opinion. Int J Syst Evol Microbiol 65:2013–2014CrossRefGoogle Scholar
  38. Paster BJ, Canale-Parola E (1985) Treponema saccharophilum sp. nov., a large pectinolytic spirochete from the bovine rumen. Appl Environ Microbiol 50:212–219PubMedPubMedCentralGoogle Scholar
  39. Patel TR, Jure KG, Jones GA (1981) Catabolism of phloroglucinol by the rumen anaerobe coprococcus. Appl Environ Microbiol 42(6):1010–1017PubMedPubMedCentralGoogle Scholar
  40. Plaizier JC, Li S, Tun HM, Khafipour E (2017) Nutritional models of experimentally-induced subacute ruminal acidosis (SARA) differ in their impact on rumen and hindgut bacterial communities in dairy cows. Front Microbiol 7:2128CrossRefGoogle Scholar
  41. Popova M, Morgavi DP, Martin C (2013) Methanogens and methanogenesis in the rumens and ceca of lambs fed two different high-grain-content diets. Appl Environ Microbiol 79(6):1777–1786CrossRefGoogle Scholar
  42. Prasad J, Gill H, Smart J, Gopal PK (1998) Selection and characterisation of Lactobacillus and Bifidobacterium strains for use as probiotics. Int Dairy J 8:993–1002CrossRefGoogle Scholar
  43. Sakamoto M, Ohkuma M (2012) Reclassification of Xylanibacter oryzae as Prevotella oryzae comb. nov., with an emended description of the genus Prevotella. Int J Syst Evol Microbiol 62:2637–2642CrossRefGoogle Scholar
  44. Seedorf H, Kittelmann S, Henderson G, Janssen PH (2014) RIM-DB: a taxonomic framework for community structure analysis of methanogenic archaea from the rumen and other intestinal environments. Peer J 2:e494CrossRefGoogle Scholar
  45. Seedorf H, Kittelmann S, Janssen PH (2015) Few highly abundant operational taxonomic units dominate within rumen methanogenic archaeal species in New Zealand sheep and cattle. Appl Environ Microbiol 81(3):986–995CrossRefGoogle Scholar
  46. Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C (2011) Metagenomic biomarker discovery and explanation. Genome Biol 12:R60CrossRefGoogle Scholar
  47. Shah HN, Collins DM (1990) Prevotella, a new genus to include Bacteroides melaninogenicus and related species formerly classified in genus Bacteroides. Int J Syst Bacteriol 40(2):205–208CrossRefGoogle Scholar
  48. Söllinger A, Schwab C, Weinmaier T, Loy A, Tveit AT, Schleper C, Urich T (2016) Phylogenetic and genomic analysis of Methanomassiliicoccales in wetlands and animal intestinal tracts reveals clade-specific habitat preferences. FEMS Microbiol Ecol. CrossRefPubMedGoogle Scholar
  49. Su Y, Bian G, Zhu Z, Smidt H, Zhu W (2014) Early methanogenic colonisation in the faeces of meishan and yorkshire piglets as determined by pyrosequencing analysis. Archaea 2014:547908CrossRefGoogle Scholar
  50. Theodorou MK, Williams BA, Dhanoa MS, MacAllan AB, France J (1994) A simple gas production method using a pressure transducer to determine the fermentation kinetics of ruminant feeds. Anim Feed Sci Technol 48:185–197CrossRefGoogle Scholar
  51. Tsai CG, Gates DM, Ingledew WM, Jones GA (1976) Products of anaerobic phloroglucinol degradation by Coprococcus sp. pe15. Can J Microbiol 22(2):159–164CrossRefGoogle Scholar
  52. Van de Merwe JP, Stegeman JH (1985) Binding of Coprococcus comes to the fc portion of igg. A possible role in the pathogenesis of Crohn’s disease? Eur J Immunol 15(8):860–863CrossRefGoogle Scholar
  53. Van Soest PJ, Robertson JB, Lewis BA (1991) Methods for dietary fibre, neutral detergent fibre, and non-starch polysaccharides in relation to animal nutrition. J Dairy Sci 74:3583–3597CrossRefGoogle Scholar
  54. Weatherburn MW (1967) Phenol-hypochlorite reaction for determination of ammonia. Anal Chem 39:971–974CrossRefGoogle Scholar
  55. Whitman WB, Bowen KN, Fonty G (2006) The methanogenic bacteria. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K, Stackebrandt E (eds) Prokaryotes, 3rd edn. Springer, New York, pp 165–207CrossRefGoogle Scholar
  56. Wolin MJ, Miller TL, Stewart CS (1997) Microbe–microbe interactions. In: Hobson PN, Stewart CS (eds) Rumen microbial ecosystem, 2nd edn. Chapman & Hall, London, pp 467–491CrossRefGoogle Scholar
  57. Wright ADG, Dehority BA, Lynn DH (1997) Phylogeny of the rumen ciliates Entodinium, Epidinium and Polyplastron (Litostomatea: Entodiniomorphida) inferred from small subunit ribosomal RNA sequences. J Euk Microbiol 44:61–67CrossRefGoogle Scholar
  58. Yanagita K, Manome A, Meng XY, Hanada S, Kanagawa T, Tsuchida T, Mackie RI, Kamagata Y (2003) Flow cytometric sorting, phylogenetic analysis and in situ detection of Oscillospira guillermondii, a large, morphologically conspicuous but uncultured ruminal bacterium. Int J Syst Evol Microbiol 53(Pt 5):1609–1614CrossRefGoogle Scholar
  59. Ye H, Liu J, Feng P, Zhu W, Mao S (2016) Grain-rich diets altered the colonic fermentation and mucosa-associated bacterial communities and induced mucosal injuries in goats. Sci Rep 6:20329CrossRefGoogle Scholar
  60. Zellner G, Stackebrandt E, Messner P, Tindall BJ, Conway de Macario E, Kneifel H, Sleytr UB, Winter J (1989) Methanocorpusculaceae, fam. nov. represented by Methanocorpusculum parvum, Methanocorpusculum sinense, spec. nov. and Methanocorpusculum bavaricum, spec. nov. Arch Microbiol 151(5):381–390CrossRefGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Wei Jin
    • 1
    • 2
  • Yin Li
    • 1
    • 2
  • Yanfen Cheng
    • 1
    • 2
    Email author
  • Shengyong Mao
    • 1
    • 2
  • Weiyun Zhu
    • 1
    • 2
  1. 1.Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and TechnologyNanjing Agricultural UniversityNanjingChina
  2. 2.National Center for International Research on Animal Gut NutritionNanjing Agricultural UniversityNanjingChina

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