Molecular Nutrition

Fecal Archaeal Diversity of Artificial Breeding Adult Forest Musk Deer Analyzed by High-Throughput Sequencing Technologies

  • WANG Lizhi ,
  • XU Yiying ,
  • CAI Yonghua
Expand
  • 1. Key Laboratory for Animal Disease-Resistance Nutrition of Ministry of Education, Animal Nutrition Institute of Sichuan Agricultural University, Ya'an 625014, China;
    2. Sichuan Institute of Musk Deer Breeding, Dujiangyan 611845, China

Received date: 2015-08-01

  Online published: 2016-02-19

Abstract

This experiment was conducted to invest the archaeal structure and composition in feces of artificial breeding adult forest musk deer (FMD) using high-throughput sequencing technologies, and to compare the difference between male and female FMD. Twelve healthy FMD with the age of three years were divided into male group (M) and female group (F) according to their gender (6 deer in each group). The fresh feces were collected and DNA was extracted from them. The archaeal universal primers were used to amplify V4 to V5 regions of archaeal 16S rRNA. The amplifications were high-throughput sequenced with the MiSeq 300PE sequencing platform. The QIIME and other softwares were used to analyze the data. The results showed as follows:from phylum to genus levels, the differences of the archaeal relative abundance between group M and group F were not significant (P>0.05). Genetic distance within the samples in group F and group M was 0.16±0.03 and 0.27±0.06, respectively, and that between groups was 0.24±0.07; all samples shared high similarity. The archaea in the feces of FMD can be divided into three phyla, the dominant phylum was Euryarchaeota; on the genus level they can be divided into seven existing genera, the dominant genus was Methanobrevibacter, the next one was Thermogymnomonas. In conclusion, the gender has no significant effect on the archaeal structure and composition in the feces of FMD, and Methanobrevibacter is the dominant genus.

Cite this article

WANG Lizhi , XU Yiying , CAI Yonghua . Fecal Archaeal Diversity of Artificial Breeding Adult Forest Musk Deer Analyzed by High-Throughput Sequencing Technologies[J]. Chinese Journal of Animal Nutrition, 2016 , 28(2) : 477 -484 . DOI: 10.3969/j.issn.1006-267x.2016.02.021

References

[1] YANG Q S,MENG X X,XIA L,et al.Conservation status and causes of decline of musk deer (Moschus spp.) in China[J].Biological Conservation,2003,109(3):333-342.  
[2] WRIGHT A D G,MA X L,OBISPO N E,et al.Methanobrevibacter phylotypes are the dominant methanogens in sheep from Venezuela[J].Microbial Ecology,2008,56(2):390-394.  
[3] CHAUDHARY P P,SIROHI S K,SAXENA J,et al.Diversity analysis of methanogens in rumen of Bubalus bubalis by 16S riboprinting and sequence analysis[J].Gene,2012,493(1):13-17.  
[4] SINGH K M,TRIPATHI A K,PANDYA P R,et al.Methanogen diversity in the rumen of Indian Surti buffalo (Bubalus bubalis),assessed by 16S rDNA analysis[J].Research in Veterinary Science,2012,92(3):451-455.  
[5] WRIGHT A D G,WILLIAMS A J,WINDER B,et al.Molecular diversity of rumen methanogens from sheep in western Australia[J].Applied and Environmental Microbiology,2004,70(3):1263-1270.  
[6] EVANS P N,HINDS L A,SLY L I,et al.Community composition and density of methanogens in the foregut of the Tammar wallaby (Macropus eugenii)[J].Applied and Environmental Microbiology,2009,75(8):2598-2602.  
[7] SHIN E C,CHOI B R,LIM W J,et al.Phylogenetic analysis of archaea in three fractions of cow rumen based on the 16S rDNA sequence[J].Anaerobe,2004,10(6):313-319.  
[8] LUO Y H,WRIGHT A D G,LI Y L,et al.Diversity of methanogens in the hindgut of captive white rhinoceroses,Ceratotherium simum[J].BMC Microbiology,2013,13:207.
[9] RASTOGI G,RANADE D R,YEOLE T Y,et al.Molecular analyses of methanogen diversity associated with cattle dung[J].World Journal of Microbiology and Biotechnology,2008,24(12):2973-2979.  
[10] PEI C X,MAO S Y,CHENG Y F,et al.Diversity,abundance and novel 16S rRNA gene sequences of methanogens in rumen liquid,solid and epithelium fractions of Jinnan cattle[J].Animal,2010,4(1):20-29.  
[11] TURNBULL K L,SMITH R P,ST-PIERRE B,et al.Molecular diversity of methanogens in fecal samples from Bactrian camels (Camelusbactrianus) at two zoos[J].Research in Veterinary Science,2012,93(1):246-249.  
[12] HUANG X D,TAN H Y,LONG R J,et al.Comparison of methanogen diversity of yak (Bos grunniens) and cattle (Bos taurus) from the Qinghai-Tibetan Plateau,China[J].BMC Microbiology,2012,12:237.
[13] FRANK K L,ROGERS D R,OLINS H C,et al.Characterizing the distribution and rates of microbial sulfate reduction at middle valley hydrothermal vents[J].The ISME Journal,2013,7(7):1391-1401.  
[14] CAPORASO J G,KUCZYNSKI J,STOMBAUGH J,et al.QIIME allows analysis of high-throughput community sequencing data[J].Nature Methods,2010,7(5):335-336.  
[15] HIGHLANDER S K.High throughput sequencing methods for microbiome profiling:application to food animal systems[J].Animal Health Research Reviews,2012,13(1):40-53.  
[16] SOGIN M L,MORRISON H G,HUBER J A,et al.Microbial diversity in the deep sea and the underexplored "rare biosphere"[J].Proceedings of the National Academy of Sciences of the United States of America,2006, 103(32):12115-12120.  
[17] CAPORASO J G,LAUBER C L,WALTERS W A,et al.Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample[J].Proceedings of the National Academy of Sciences of the United States of America,2011,108(Suppl.1):4516-4522.
[18] KIM M,MORRISON M,YU Z J,et al.Status of the phylogenetic diversity census of ruminal microbiomes[J].FEMS Microbiology Ecology,2011,76(1):49-63.  
[19] 王继文,王立志,闫天海,等.山羊瘤胃与粪便微生物多样性[J].动物营养学报,2015,27(8):2259-2571.
[20] WEAVER G A,KRAUSE J A,MILLER T L,et al.Incidence of methanogenic bacteria in a sigmoidoscopy population:an association of methanogenic bacteria and diverticulosis[J].Gut,1986,27(6):698-704.  
[21] LEADBETTER J R,BREZNAK J A.Physiological ecology of Methanobrevibacter cuticularis sp.nov.and Methanobrevibacter curvatus sp.nov.,isolated from the hindgut of the termite Reticulitermes flavipes[J].Applied and Environmental Microbiology,1996,62(10):3620-3631.
[22] LEADBETTER J R,CROSBY L D,BREZNAK J A,et al.Methanobrevibacter filiformis sp.nov.,a filamentous methanogen from termite hindguts[J].Archives of Microbiology,1998,169(4):287-292.  
[23] SUNDSET M A,EDWARDS J E,CHENG Y F,et al.Rumen microbial diversity in Svalbard reindeer,with particular emphasis on methanogenic archaea[J].FEMS Microbiology Ecology,2009,70(3):553-562.  
[24] ZHOU M,HERNANDEZ-SANABRIA E,GUAN L L.Assessment of the microbial ecology of ruminal methanogens in cattle with different feed efficiencies[J]. Applied and Environmental Microbiology,2009,75(20):6524-6533.  
[25] MIN B R,SOLAIMAN S,SHANGE R,et al.Gastrointestinal bacterial and methanogenic archaea diversity dynamics associated with condensed tannin-containing pine bark diet in goats using 16S rDNA amplicon pyrosequencing[J].International Journal of Microbiology,2014,2014:141909.
Outlines

/