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Characterization of the cellulolytic bacteria communities along the gastrointestinal tract of Chinese Mongolian sheep by using PCR-DGGE and real-time PCR analysis

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Abstract

A balanced gastrointestinal microbial ecosystem is crucial for the health and growth of animals. In the gastrointestinal tract (GIT) of ruminants, cellulolytic bacteria aid in the digestion and absorption of nutrients. Rumen contents and feces in ruminants are often used to assess gastrointestinal microbial communities; however, these sites do not guarantee to represent the diversity of microbes found in the entire GIT. In this study, we investigated the microbiota along the GIT of five Chinese Mongolian sheep using PCR-denaturing gradient gel electrophoresis (DGGE) and real-time PCR analysis. Results indicated that microbiota were more abundant in the stomach and large intestine than in the small intestine. DGGE and real-time PCR revealed the predominance of Firmicutes and Bacteroidetes in the GIT. Meanwhile, Ruminococcus flavefaciens and Clostridium cluster IV showed significant difference in their abundance along the GIT (P < 0.05). Fibrobacter succinogenes was the most dominant species, followed by Ruminococcus albus and R. flavefaciens. The ileum harbored a larger number of cellulolytic bacteria, particularly—Clostridium cluster IV, than reported previously. In addition, comparisons between microbiota in the rumen and rectum indicated similar number of total bacteria, Firmicutes, Bacteroidetes, F. succinogenes, Butyrivibrio fibrisolvens, Clostridium cluster IV, and Clostridium cluster XIVa, whereas the number of R. albus and R. flavefaciens was higher in the rumen. This study investigated the composition and quantification of GIT microbial community in Chinese Mongolian sheep, and revealed for the first time the cellulolytic bacterial community in these sheep.

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References

  • Abo El-Nor S, AbuGhazaleh AA, Potu RB, Hastings D, Khattab MSA (2010) Effects of differing levels of glycerol on rumen fermentation and bacteria. Anim Feed Sci Technol 162(3):99–105

    Article  CAS  Google Scholar 

  • Bäckhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI (2005) Host-bacterial mutualism in the human intestine. Science 307(5717):1915–1920

    Article  Google Scholar 

  • Bauer E, Williams BA, Bosch MW, Voigt C, Mosenthin R, Verstegen MW (2004) Differences in microbial activity of digesta from three sections of the porcine large intestine according to in vitro fermentation of carbohydrate-rich substrates. J Sci Food Agric 84(15):2097–2104

    Article  CAS  Google Scholar 

  • Belzer C, de Vos WM (2012) Microbes inside-from diversity to function: the case of Akkermansia. ISME J 6(8):1449–1458

    Article  CAS  Google Scholar 

  • Bian G, Ma L, Su Y, Zhu W (2013) The microbial community in the feces of the white rhinoceros (Ceratotherium simum) as determined by barcoded pyrosequencing analysis. PLoS ONE 8(7):e70103

    Article  CAS  Google Scholar 

  • Burrell PC, Osullivan C, Song H, Clarke WP, Blackall LL (2004) Identification, detection, and spatial resolution of Clostridium populations responsible for cellulose degradation in a methanogenic landfill leachate bioreactor. Appl Environ Microbiol 70(4):2414–2419

    Article  CAS  Google Scholar 

  • Carberry CA, Kenny DA, Han S, McCabe MS, Waters SM (2012) Effect of phenotypic residual feed intake and dietary forage content on the rumen microbial community of beef cattle. Appl Environ Microbiol 78(14):4949–4958

    Article  CAS  Google Scholar 

  • Chanthakhoun V, Wanapat M, Kongmun P, Cherdthong A (2012) Comparison of ruminal fermentation characteristics and microbial population in swamp buffalo and cattle. Livest Sci 143(2):172–176

    Article  Google Scholar 

  • Chaudhary PP, Dagar SS, Sirohi SK (2012) Comparative quantification of major rumen microbial population in Indian Cattle and Buffalo fed on wheat straws based diet. PJMR 2(3):105–108

    Google Scholar 

  • Church DC (1988) The ruminant animal: digestive physiology and nutrition. Prentice Hall, Englewood Cliffs

    Google Scholar 

  • Cunha IS, Barreto CC, Costa OY, Bomfim MA, Castro AP, Kruger RH, Quirino BF (2011) Bacteria and Archaea community structure in the rumen microbiome of goats (Capra hircus) from the semiarid region of Brazil. Anaerobe 17(3):118–124

    Article  Google Scholar 

  • de Oliveira MNV, Jewell KA, Freitas FS, Benjamin LA, Totola MR, Borges AC, Suen G (2013) Characterizing the microbiota across the gastrointestinal tract of a Brazilian Nelore steer. Vet Microbiol 164(3):307–314

    Article  Google Scholar 

  • Dehority BA (2003) Rumen microbiology. Nottingham University Press, Thrumpton

    Google Scholar 

  • Dong X, Reddy GB (2010) Soil bacterial communities in constructed wetlands treated with swine wastewater using PCR-DGGE technique. Bioresour Technol 101(4):1175–1182

    Article  CAS  Google Scholar 

  • Durso LM, Harhay GP, Smith TP, Bono JL, DeSantis TZ, Harhay DM, Clawson ML (2010) Animal-to-animal variation in fecal microbial diversity among beef cattle. Appl Environ Microbiol 76(14):4858–4862

    Article  CAS  Google Scholar 

  • Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Relman DA (2005) Diversity of the human intestinal microbial flora. Science 308(5728):1635–1638

    Article  Google Scholar 

  • Evans NJ, Brown JM, Murray RD, Getty B, Birtles RJ, Hart CA, Carter SD (2011) Characterization of novel bovine gastrointestinal tract Treponema isolates and comparison with bovine digital dermatitis treponemes. Appl Environ Microbiol 77(1):138–147

    Article  CAS  Google Scholar 

  • Favier CF, Vaughan EE, De Vos WM, Akkermans AD (2002) Molecular monitoring of succession of bacterial communities in human neonates. Appl Environ Microbiol 68(1):219–226

    Article  CAS  Google Scholar 

  • Fernando SC, Purvis HT, Najar FZ, Sukharnikov LO, Krehbiel CR, Nagaraja TG, DeSilva U (2010) Rumen microbial population dynamics during adaptation to a high-grain diet. Appl Environ Microbiol 76(22):7482–7490

    Article  CAS  Google Scholar 

  • Forsberg CW, Cheng KJ, White BA (1997) Polysaccharide degradation in the rumen and large intestine. In: Mackie RI, White BA (eds) Gastrointestinal microbiology. Chapman and Hall, New York, pp 319–379

    Chapter  Google Scholar 

  • Frey JC, Pell AN, Berthiaume R, Lapierre H, Lee S, Ha JK, Angert ER (2010) Comparative studies of microbial populations in the rumen, duodenum, ileum and faeces of lactating dairy cows. J Appl Microbiol 108(6):1982–1993

    CAS  Google Scholar 

  • Gao Z, Johnson ZI, Wang G (2009) Molecular characterization of the spatial diversity and novel lineages of mycoplankton in Hawaiian coastal waters. ISME J 4(1):111–120

    Article  Google Scholar 

  • Godoy-Vitorino F, Goldfarb KC, Karaoz U, Leal S, Garcia-Amado MA, Hugenholtz P, Dominguez- Bello MG (2011) Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows. ISME J 6(3):531–541

    Article  Google Scholar 

  • Gu S, Chen D, Zhang JN, Lv X, Wang K, Duan LP, Wu XL (2013) Bacterial community mapping of the mouse gastrointestinal tract. PLoS ONE 8(10):e74957

    Article  CAS  Google Scholar 

  • Guo X, Xia X, Tang R, Zhou J, Zhao H, Wang K (2008) Development of a real-time PCR method for Firmicutes and Bacteroidetes in faeces and its application to quantify intestinal population of obese and lean pigs. Lett Appl Microbiol 47(5):367–373

    Article  CAS  Google Scholar 

  • Haslberger AG, Zwielehner J, Liszt K, Handschur M, Lapin A (2009) Combined PCR-DGGE fingerprinting and quantitative-PCR indicates shifts in fecal population sizes and diversity of Bacteroides, bifidobacteria and clostridium cluster IV in institutionalized elderly. Exp Gerontol 44(6–7):440–446

    Google Scholar 

  • Holt JG, Krieg NR, Sneath PH, Staley JT, Williams ST (1994) Bergey’s manual of determinative bacteriology, vol 75. The Williams and Wilkins Co, Baltimore, p 121

    Google Scholar 

  • Ishaq SL, Wright ADG (2012) Insight into the bacterial gut microbiome of the North American moose (Alces alces). BMC Microbiol 12(1):212

    Article  CAS  Google Scholar 

  • Jami E, Mizrahi I (2012) Composition and similarity of bovine rumen microbiota across individual animals. PLoS ONE 7(3):e33306

    Article  CAS  Google Scholar 

  • Kim JC, Hansen CF, Mullan BP, Pluske JR (2012) Nutrition and pathology of weaner pigs: nutritional strategies to support barrier function in the gastrointestinal tract. Anim Feed Sci Technol 173(1):3–16

    Article  CAS  Google Scholar 

  • 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(2):e47879

    Article  CAS  Google Scholar 

  • Koike S, Kobayashi Y (2001) Development and use of competitive PCR assays for the rumen cellulolytic bacteria: Fibrobacter succinogenes, Ruminococcus albus and Ruminococcus flavefaciens. FEMS Microbiol Lett 204(2):361–366

    Article  CAS  Google Scholar 

  • Kuritza AP, Shaughnessy P, Salyers AA (1986) Enumeration of polysaccharide-degrading Bacteroides species in human feces by using species-specific DNA probes. Appl Environ Microbiol 51(2):385–390

    CAS  Google Scholar 

  • Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI (2008) Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol 6(10):776–788

    Article  CAS  Google Scholar 

  • Li RW, Connor EE, Li C, Baldwin VI, Ransom L, Sparks ME (2012) Characterization of the rumen microbiota of pre-ruminant calves using metagenomic tools. Environ Microbiol 14(1):129–139

    Article  Google Scholar 

  • Lin B, Lu Y, Salem AZM, Wang JH, Liang Q, Liu JX (2013) Effects of essential oil combinations on sheep ruminal fermentation and digestibility of a diet with fumarate included. Anim Feed Sci Technol 184(1):24–32

    Article  CAS  Google Scholar 

  • Matsuki T, Watanabe K, Fujimoto J, Miyamoto Y, Takada T, Matsumoto K, Tanaka R (2002) Development of 16S rRNA-gene-targeted group-specific primers for the detection and identification of predominant bacteria in human feces. Appl Environ Microbiol 68(11):5445–5451

    Article  CAS  Google Scholar 

  • Matsuki T, Watanabe K, Fujimoto J, Takada T, Tanaka R (2004) Use of 16S rRNA gene-targeted group-specific primers for real-time PCR analysis of predominant bacteria in human feces. Appl Environ Microbiol 70(12):7220–7228

    Article  CAS  Google Scholar 

  • McDonald P (2002) Animal nutrition. Pearson Education, London

    Google Scholar 

  • Mosoni P, Martin C, Forano E, Morgavi DP (2011) Long-term defaunation increases the abundance of cellulolytic ruminococci and methanogens but does not affect the bacterial and methanogen diversity in the rumen of sheep. J Anim Sci 89(3):783–791

    Article  CAS  Google Scholar 

  • Mrazek J, Tepsic K, Avgustin G, Kopecny J (2006) Diet-dependent shifts in ruminal butyrate-producing bacteria. Folia Microbiol 51(4):294–298

    Article  CAS  Google Scholar 

  • Nagaraja TG, Titgemeyer EC (2007) Ruminal acidosis in beef cattle: the current microbiological and nutritional outlookand. J Dairy Sci 90:E17–E38

    Article  Google Scholar 

  • O’Hara AM, Shanahan F (2007) Gut microbiota: mining for therapeutic potential. Clin Gastroenterol Hepatol 5(3):274–284

    Article  Google Scholar 

  • Ransom-Jones E, Jones DL, McCarthy AJ, McDonald JE (2012) The fibrobacteres: an important phylum of cellulose-degrading bacteria. Microbial Ecol 63(2):267–281

    Article  CAS  Google Scholar 

  • Russell JB, Rychlik JL (2001) Factors that alter rumen microbial ecology. Science 292(5519):1119–1122

    Article  CAS  Google Scholar 

  • Saro C, Ranilla MJ, Carro MD (2012) Postprandial changes of fiber-degrading microbes in the rumen of sheep fed diets varying in type of forage as monitored by real-time PCR and automated ribosomal intergenic spacer analysis. J Anim Sci 90(12):4487–4494

    Article  CAS  Google Scholar 

  • Singh KM, Tripathi AK, Pandya PR, Parnerkar S, Kothari RK, Joshi CG (2013) Molecular genetic diversity and quantitation of methanogen in ruminal fluid of buffalo (Bubalus bubalis) fed ration (wheat straw and concentrate mixture diet). Genet Res Int 2013:1–7

  • Spence C, Wells WG, Smith CJ (2006) Characterization of the primary starch utilization operon in the obligate anaerobe Bacteroides fragilis: regulation by carbon source and oxygen. J Bacteriol 188(13):4663–4672

    Article  CAS  Google Scholar 

  • Stephen AM, Cummings JH (1980) The microbial contribution to human faecal mass. J Med Microbiol 13(1):45–56

    Article  CAS  Google Scholar 

  • St-Pierre B, Wright ADG (2012) Molecular analysis of methanogenic archaea in the forestomach of the alpaca (Vicugna pacos). BMC Microbiol 12:1

    Article  CAS  Google Scholar 

  • Sung HG, Kobayashi Y, Chang J, Ha A, Hwang IH, Ha JK (2007) Low ruminal pH reduces dietary fiber digestion via reduced microbial attachment. Asian Austral J Anim 20(2):200

    Article  CAS  Google Scholar 

  • Thompson JR, Marcelino LA, Polz MF (2002) Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by ‘reconditioning PCR’. Nucl Acids Res 30(9):2083–2088

    Article  CAS  Google Scholar 

  • Walter J, Hertel C, Tannock GW, Lis CM, Munro K, Hammes WP (2001) Detection of Lactobacillus, Pediococcus, Leuconostoc, and Weissella species in human feces by using group-specific PCR primers and denaturing gradient gel electrophoresis. Appl Environ Microbiol 67(6):2578–2585

    Article  CAS  Google Scholar 

  • Wang HF, Zhu WY, Yao W, Liu JX (2007) DGGE and 16S rDNA sequencing analysis of bacterial communities in colon content and feces of pigs fed whole crop rice. Anaerobe 13(3):127–133

    Article  Google Scholar 

  • Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci USA 95(12):6578–6583

    Article  CAS  Google Scholar 

  • Williams AG, Coleman GS (1992) The rumen protozoa. Springer, New York

    Book  Google Scholar 

  • Woodmansey EJ (2007) Intestinal bacteria and ageing. J Appl Microbiol 102(5):1178–1186

    Article  CAS  Google Scholar 

  • Zhang XL, He XL, Wu RTY, Sa RL (2008) The origin, domestication, differentiation, and preservation of Mongolian sheep. Anim Husb Feed Sci 3:36–38

    Google Scholar 

Download references

Acknowledgments

The present study was supported by the Scientific Research Foundation for Returned Overseas Chinese Scholars, State Education Ministry, Program for Changjiang Scholars and Innovative Research Team of the University of China (ITT0848), and International Cooperative Project of Science and Technology Bureau of Sichuan Province (2013HH0055).

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Authors and Affiliations

  1. Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Ya’an, 625014, China

    Yan Zeng, Dong Zeng, Yan Zhang, Xueqin Ni, Yurui Tang, Hui Zhu, Hesong Wang, Kangcheng Pan & Bo Jing

  2. Key Laboratory of Animal Disease and Human Health of Sichuan Province, Ya’an, 625014, China

    Yan Zeng, Dong Zeng, Yan Zhang, Xueqin Ni, Yurui Tang, Hui Zhu, Hesong Wang, Zhongqiong Yin, Kangcheng Pan & Bo Jing

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  1. Yan Zeng
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  2. Dong Zeng
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Correspondence to Xueqin Ni.

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Dong Zeng: Joint first author.

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Zeng, Y., Zeng, D., Zhang, Y. et al. Characterization of the cellulolytic bacteria communities along the gastrointestinal tract of Chinese Mongolian sheep by using PCR-DGGE and real-time PCR analysis. World J Microbiol Biotechnol 31, 1103–1113 (2015). https://doi.org/10.1007/s11274-015-1860-z

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