Rumen Microbial Community of Saanen Goats Adapted to a High-Fiber Diet in the Northeast of Iran
الموضوعات :
س.ه. ابراهیمی
1
(گروه علوم دامی، دانشکده کشاورزی، دانشگاه فردوسی مشهد)
ر. ولیزاده
2
(Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran)
و. حیدریان میری
3
(Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran)
الکلمات المفتاحية: Iran, rumen microbial community, Sannen goats,
ملخص المقالة :
Swiss Saanen goat is a widespread breed frequently found in commercial herds across the world. The present study aimed to identify the rumen microbial community of exotic Saanen goats adapted to a fibrous diet using barcoded pyrosequencing. Rumen content samples were collected from the four animals via a stomach tube after the morning graze and freeze-dried for DNA extraction. Bacterial and archaeal 16S rRNA and protozoal 18S rRNA genes were sequenced by 454 titanium pyrosequencing and analyzed using the quantitative insights into microbial ecology (QIIME) software package. Obtained results indicated that at the genus level, Prevotella (Bacteroidetes phylum) dominated the assigned sequence, with the relative abundance accounting for 29.41 ± 4.27% of the total bacteria. The second most abundant bacteria in the rumen of Saanen goats was an unclassified Bacteroidales (Bacteroidetes phylum) (11.01±0.94%). In addition, Firmicutes phylum was recorded as the second most frequent phylum and three unclassified genera, which belonged to the order Clostridiales, constituted21.42% of the total bacteria. Entodinium was the most abundant protozoal genus, comprising 46.78 ± 9.13% of the protozoal community, followed by Epidinium and Ophryoscolex (12.37±0.06 and 11.92±7.7, respectively). Almost half the archaeal community (43.71±1.57%) was composed of Methanoplasmatales- related sequences and Methanobrevibacter gottschalkii clade (35.79±4.84%) and Methanobrevibacter ruminantium clade (13.36±6.34%) were the second and third most dominant archaea, respectively. Overall, further efforts should be made to apply culture-based methods for the identification of remarkable number of unclassified bacteria in the rumen of goats.
Altschul S.F., Gish W., Miller W., Myers E.W. and Lipman D.J. (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
Asanuma N., Yokoyama S. and Hino T. (2015). Effects of nitrate addition to a diet on fermentation and microbial populations in the rumen of goats, with special reference to Selenomonas ruminantium having the ability to reduce nitrate and nitrite. Anim. Sci. J. 86, 378-384.
Borrel G., O’Toole P.W., Harris H.M.B., Peyret P., Brugère J.F. and Gribaldo S. (2013). Phylogenomic data support a seventh order of methylotrophic methanogens and provide insights into the evolution of methanogenesis. Genome Biol. Evol. 5, 1769-1780.
Caporaso J.G., Kuczynski J., Stombaugh J., Bittinger K., Bush-man F.D., Costello E.K., Fierer N., Peña A.G., Goodrich J.K., Gordon J.I., Huttley G.A., Kelley S.T., Knights D., Koenig J.E., Ley R.E., Lozupone C.A., McDonald D., Muegge B.D., Pirrung M., Reeder J., Sevinsky J.R., Turnbaugh P.J., Walters W.A., Widmann J., Yatsunenko T., Zaneveld J. and Knight R. (2010). QIIME allows analysis of high-throughput community sequencing data. Nat. Methods. 7, 335-336.
Capote J. (2016). Environments and goats around the world: importance of genetic and management factors. Pp. 1-6 in Sustainable Goat Breeding and Goat Farming in Central and Eastern European Countries. S. Kukovics, Ed. Food and Agriculture Organization of the United Nations, Rome, Italy.
Cheng Y.F., Mao S.Y., Liu J.X. and Zhu W.Y. (2009). Molecular diversity analysis of rumen methanogenic archaea from goat in eastern china by DGGE methods using different primer pairs. Lett. Appl. Microbiol. 48, 585-592.
Cunha I.S., Barreto C.C., Costa O.Y.A., Bomfim M.A., Castro A.P., Kruger R.H. and Quirino B.F. (2011). Bacteria and archaea community structure in the rumen microbiome of goats (Capra hircus) from the semiarid region of Brazil. Anaerobe. 17, 118-124.
Ebrahimi S.H., Mohini M., Singhal K.K., Heidarian Miri V. and Tyagi A.K. (2011). Evaluation of complementary effects of 9,10-anthraquinone and fumaric acid on methanogenesis and ruminal fermentation in vitro. Arch. Anim. Nutr. 65, 267-277.
Grilli D.J., Fliegerová K., Kopečný J., Lama S.P., Egea V., Sohaefer N., Pereyra C., Ruiz M.S., Sosa M.A., Arenas G.N. and Mrázek J. (2016). Analysis of the rumen bacterial diversity of goats during shift from forage to concentrate diet. Anaerobe. 42, 17-26.
Gürelli G., Canbulat S., Aldayarov N. and Dehority B.A. (2016). Rumen ciliate protozoa of domestic sheep (Ovis aries) and goat (Capra aegagrus hircus) in Kyrgyzstan. FEMS Microbiol. Lett. 363, 1-7.
Henderson G., Cox F., Ganesh S., Jonker A., Young W., Janssen P.H.. and Zunino P. (2015). Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. Sci. Rep. 5, 1-13.
Henderson G., Cox F., Kittelmann S., Miri V.H., Zethof M., Noel S.J., Waghorn G.C. and Janssen P.H. (2013). Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities. PLoS One. 8, e74787.
Huang X.D., Martinez-Fernandez G., Padmanabha J., Long R., Denman S.E. and McSweeney C.S. (2016). Methanogen diversity in indigenous and introduced ruminant species on the tibetan plateau. Archaea. 28, 1-10.
Huo W., Zhu W. and Mao S. (2014). Impact of subacute ruminal acidosis on the diversity of liquid and solid-associated bacteria in the rumen of goats. World J. Microbiol. Biotechnol. 30, 669-680.
Jaber L.S., Duvaux-Ponter C., Hamadeh S.K. and Giger-Reverdin S. (2016). Short water restriction episode in lactating alpine and saanen goats. Pp. 183-188 in Sustainable Goat Breeding and Goat Farming in Central and Eastern European Countries. S. Kukovics, Ed. Food and Agriculture Organization of the United Nations, Rome, Italy.
Janssen P.H. and Kirs M. (2008). Structure of the archaeal community of the rumen. Appl. Environ. Microbiol. 74, 3619-3625.
Jiao J., Huang J., Zhou C. and Tan Z. (2015). Taxonomic identification of ruminal epithelial bacterial diversity during rumen development in goats. Appl. Environ. Microbiol. 81, 3502-3509.
Kittelmann S., Seedorf H., Walters W.A., Clemente J.C., Knight R., Gordon J.I. and Janssen P.H. (2013). Simultaneous amplicon sequencing to explore co-occurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities. PLoS One. 8, e47879.
Lee H.J., Jung J.Y., Oh Y.K., Lee S.S., Madsen E.L. and Jeon C.O. (2012). Comparative survey of rumen microbial communities and metabolites across one caprine and three bovine groups, using bar-coded pyrosequencing and 1H nuclear magnetic resonance spectroscopy. Appl. Environ. Microbiol. 78, 5983-5993.
Lin B., Henderson G., Zou C., Cox F., Liang X., Janssen P.H. and Attwood G.T. (2015). Characterization of the rumen microbial community composition of buffalo breeds consuming diets typical of dairy production systems in Southern China. Anim. Feed Sci. Technol. 207, 75-84.
Lin C., Raskin L. and Stahl D.A. (1997). Microbial community structure in gastrointestinal tracts of domestic animals: Comparative analyses using rRNA targeted oligonucleotide probes. FEMS Microbiol. Ecol. 22, 281-294.
Liu J., Bian G., Zhu W. and Mao S. (2015). High-grain feeding causes strong shifts in ruminal epithelial bacterial community and expression of toll-like receptor genes in goats. Front. Microbiol. 6, 167.
Liu K., Xu Q., Wang L., Wang J., Guo W. and Zhou M. (2017). The impact of diet on the composition and relative abundance of rumen microbes in goat. Asian-Australasian J. Anim. Sci. 30, 531-537.
Mao S.Y., Huo W.J. and Zhu W.Y. (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, 525-541.
McDonald D., Price M.N., Goodrich J., Nawrocki E.P., DeSantis T.Z., Probst A., Andersen G.L., Knight R. and Hugenholtz P. (2012). An improved greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 6, 610-618.
Metzler-Zebeli B.U., Schmitz-Esser S., Klevenhusen F., Podstatzky-Lichtenstein L., Wagner M. and Zebeli Q. (2013). Grain-rich diets differently alter ruminal and colonic abundance of microbial populations and lipopolysaccharide in goats. Anaerobe. 20, 65-73.
Newbold C.J., de la Fuente G., Belanche A., Ramos-Morales E. and McEwan N.R. (2015). The role of ciliate protozoa in the rumen. Front. Microbiol. 6, 1313.
Paul K., Nonoh J.O., Mikulski L. and Brune A. (2012). Methanoplasmatales, Thermoplasmatales-related archaea in termite guts and other environments, are the seventh order of methanogens. Appl. Environ. Microbiol. 78, 8245-8253.
Poulsen M., Schwab C., Borg Jensen B., Engberg R.M., Spang A., Canibe N., Højberg O., Milinovich G., Fragner L., Schleper C., Weckwerth W., Lund P., Schramm A. and Urich T. (2013). Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen. Nat. Commun. 4, 1428-1432.
Razzaghi A., Valizadeh R., Naserian A.A., Mesgaran M.D., Carpenter A.J. and Ghaffari M.H. (2016). Effect of dietary sugar concentration and sunflower seed supplementation on lactation performance, ruminal fermentation, milk fatty acid profile, and blood metabolites of dairy cows. J. Dairy Sci. 99, 3539-3548.
Rius A.G., Kittelmann S., Macdonald K.A., Waghorn G.C., Janssen P.H. and Sikkema E. (2012). Nitrogen metabolism and rumen microbial enumeration in lactating cows with divergent residual feed intake fed high-digestibility pasture. J. Dairy Sci. 95, 5024-5034.
Shi P.J., Meng K., Zhou Z.G., Wang Y.R., Diao Q.Y. and Yao B. (2008). The host species affects the microbial community in the goat rumen. Lett. Appl. Microbiol. 46, 132-135.
Wang L., Xu Q., Kong F., Yang Y., Wu D., Mishra S. and Li Y. (2016). Exploring the goat rumen microbiome from seven days to two years. PLoS One. 11, e0154354.
Wetzels S.U., Mann E., Metzler-Zebeli B.U., Wagner M., Klevenhusen F., Zebeli Q. and Schmitz-Esser S. (2017). pyrosequencing reveals shifts in the bacterial epimural community relative to dietary concentrate amount in goats. J. Dairy Sci. 98, 5572-5587.
Williams P.P., Davis R.E., Doetsch R.N. and Gutierrez J. (1961). Physiological studies of the rumen protozoan Ophryoscolex caudatus Eberlein. Appl. Microbiol. 9, 405-409.
Zhang R., Ye H., Liu J. and Mao S. (2017). High-grain diets altered rumen fermentation and epithelial bacterial community and resulted in rumen epithelial injuries of goats. Appl. Microbiol. Biotechnol. 101(18), 1-12.
