Composition of Microbiota and Antibiotic Resistance Genes in Rumen, Small Intestine and Large Intestine of Wild Forest Musk Deer Analyzed by Metagenomic Sequencing

  • HE Sen ,
  • CAO Xinfang ,
  • ZHENG Xueli ,
  • WANG Dou ,
  • WANG Hongyong ,
  • JIANG Benmo ,
  • BU Shuhai
Expand
  • 1. College of Life Science, Northwest A & F University, Yangling 712100, China;
    2. College of Forestry, Northwest A & F University, Yangling 712100, China;
    3. Fengxian Fengchun Jimin Credible Science and Technology Breeding Co., Ltd., Fengxian 721000, China

Received date: 2020-06-02

  Online published: 2021-01-18

Abstract

This experiment aimed to study the microbiota composition and antibiotic resistance genes (ARGs) in the rumen, small intestine and large intestine of wild forest musk deer (Moschus berezovskii). Metagenomic sequencing was used to measure the contents of three segments of digestive tract (rumen, small intestine and large intestine) of wild forest musk deer, then general species annotation and functional annotation of ARGs were performed. The results showed that the share dominant bacterial phyla in the three segments of digestive tract were Firmicutes and Proteobacteria; and the dominant bacterial genera in the rumen were Prevotell and Selenomonas, with Streptococcus and Echerichia in the small intestine, Clostridium and Bacteroides in the large intestine. Gene general annotation showed that there were significant differences in the unsaturated fatty acid synthesis and antibiotic resistance among the microbial genes in different digestive tract segments. ARGs annotation indicated that macB, sav1866 and bcrA had the highest absolute abundance, and all of them came from large intestine's bacteria; the highest absolute abundance of ARGs in the rumen was Aminocoumarin_resistant_alaS, with adeG in the small intestine and macB in the large intestine. This paper makes a comparison of different digestive tract segments on the microbiota composition of the wild forest musk deer, it is preliminarily found that the microbiota composition and ARGs in the different segments of the digestive tract are quite different, and the bacteria in the large intestine and small intestine are more closely related to multidrug resistance of the wild forest musk deer.

Cite this article

HE Sen , CAO Xinfang , ZHENG Xueli , WANG Dou , WANG Hongyong , JIANG Benmo , BU Shuhai . Composition of Microbiota and Antibiotic Resistance Genes in Rumen, Small Intestine and Large Intestine of Wild Forest Musk Deer Analyzed by Metagenomic Sequencing[J]. Chinese Journal of Animal Nutrition, 2021 , 33(1) : 484 -493 . DOI: 10.3969/j.issn.1006-267x.2021.01.049

References

[1] 吴家炎,王伟.中国麝类[M].北京:中国林业出版社,2006:75-78. WU J Y,WANG W.The musk deer of China[M].Beijing:China Forestry Publishing House,2006:75-78.(in Chinese)
[2] 王婷.甜高粱饲草和葡萄籽对肉羊养分利用、瘤胃微生物区系及肉质性能的影响[D].硕士学位论文.兰州:兰州大学,2019:5-7. WANG T.Effects of sweet sorghum forage grass and grape seed on nutrient utilization,rumen microflora and meat quality of mutton sheep[D].Master's Thesis.Lanzhou:Lanzhou University,2019:5-7.(in Chinese)
[3] 李俊霞.提高奶山羊瘤胃发酵特性的技术研究进展[J].中国饲料,2020(6):10-13. LI J X.Advances in improving rumen fermentation characteristics of dairy goats[J].China Feed,2020(6):10-13.(in Chinese)
[4] RUSSELL J B,RYCHLIK J L.Factors that alter rumen microbial ecology[J].Science,2001,292(5519):1119-1122.(in Chinese)  
[5] 闫敏,颜其贵,杨光友.圈养麝的群发性疾病[J].经济动物学报,2016,20(2):112-117. YAN M,YAN Q G,YANG G Y.The mass diseases of captive musk deer[J].Journal of Economic Animal,2016,20(2):112-117.(in Chinese)
[6] LI Y M,HU X L,YANG S,et al.Comparative analysis of the gut microbiota composition between captive and wild forest musk deer[J].Frontiers in Microbiology,2017,8:1705,doi:10.3389/fmicb.2017.01705.
[7] LI Y M,HU X L,YANG S,et al.Comparison between the fecal bacterial microbiota of healthy and diarrheic captive musk deer[J].Frontiers in Microbiology,2018,9:300,doi:10.3389/fmicb.2018.00300.
[8] HU X L,LIU G,LI Y M,et al.High-throughput analysis reveals seasonal variation of the gut microbiota composition within forest musk deer (Moschus berezovskii)[J].Frontiers in Microbiology,2018,9:1674,doi:10.3389/fmicb.2018.01674.
[9] 叶勇,全建平,吴杰,等.家畜肠道微生物代谢组学研究进展[J].家畜生态学报,2020,41(3):1-8. YE Y,QUAN J P,WU J,et al.Advances of study on livestock intestinal microbial metabolites[J].Journal of Domestic Animal Ecology,2020,41(3):1-8.(in Chinese)
[10] 何静,海勒,斯仁达来,等.宏基因组学在哺乳动物肠道微生物中的应用[J].中国畜牧兽医,2018,45(12):3438-3446. HE J,HAI L,SIRENDALAI,et al.Application of metagenomics in mammals gut microbiom[J].China Animal Husbandry & Veterinary Medicine.2018,45(12):3438-3446.(in Chinese)
[11] 赵文静,刘书云,丁金梅,等.小鼠不同肠道段内容物和粪便中微生物的宏基因组测序和比较分析[J].上海交通大学学报(农业科学版),2016,34(3):15-21. ZHAO W J,LIU S Y,DING J M,et al.Metagenomic sequencing of gut microbiota along the intestinal tracts and feces in mice[J].Journal of Shanghai Jiaotong University (Agricultural Science),2016,34(3):15-21.(in Chinese)
[12] 单志,吴宏亮,李成磊,等.改良SDS法提取多种植物基因组DNA研究[J].广东农业科学,2011,38(8):113-115. SHAN Z,WU H L,LI C L,et al.Improved SDS method for general plant genomic DNA extraction[J].Guangdong Agricultural Sciences,2011,38(8):113-115.(in Chinese)
[13] DUNCAN S H,LOUIS P,THOMSON J M,et al.The role of pH in determining the species composition of the human colonic microbiota[J].Environmental Microbiology,2009,11(8):2112-2122.  
[14] JAMI E,ISRAEL A,KOTSER A,et al.Exploring the bovine rumen bacterial community from birth to adulthood[J].The ISME Journal,2013,7(6):1069-1079.  
[15] ISLAM K B M S,FUKIYA S,HAGIO M,et al.Bile acid is a host factor that regulates the composition of the cecal microbiota in rats[J].Gastroenterology,2011,141(5):1773-1781.  
[16] 张能荣.牛羊胆汁质量的研究[J].中草药,1983,14(7):15-17. ZHANG N R.Study on the quality of cattle and sheep bile[J].Chinese Traditional and Herbal Drugs,1983,14(7):15-17.(in Chinese)
[17] 杨事达,赵鸿梅.大肠埃希菌细菌膜外蛋白A对小肠上皮细胞增殖的影响及其作用机制[J].中国生物制品学杂志,2018,31(11):1207-1209. YANG S D,ZHAO H M.Effect of outer-membrane protein A on proliferation of intestinal epithelial cells and relevant mechanism[J].Chinese Journal of Biologicals,2018,31(11):1207-1209.(in Chinese)
[18] 张明昱,杜肖彦,赵鹏伟.大肠埃希菌诱导小肠上皮细胞产生β防御素-3的机制[J].中国生物制品学杂志,2018,31(11):1219-1221. ZHANG M Y,DU X Y,ZHAO P W.Mechanism of induction of β-defensin-3 production in intestinal epithelial cells by E.coli[J].Chinese Journal of Biologicals,2018,31(11):1219-1221.(in Chinese)
[19] CHUNG L K,RAFFATELLU M.G.I.pros:antimicrobial defense in the gastrointestinal tract[J].Seminars in Cell & Developmental Biology,2019,88:129-137.
[20] HAN X F,YANG Y X,YAN H L,et al.Rumen bacterial diversity of 80 to 110-day-old goats using 16S rRNA sequencing[J].PLoS One,2015,10(2):e0117811,doi:10.1371/journal.pone.0117811.
[21] MATSUI H,OGATA K,TAJIMA K,et al.Phenotypic characterization of polysaccharidases produced by Four Prevotella type strains[J].Current Microbiology,2000,41(1):45-49.  
[22] MOAYYEDI P.The epidemiology of obesity and gastrointestinal and other diseases:an overview[J].Digestive Diseases and Sciences,2008,53(9):2293-2299.  
[23] 冯泽猛,包显颖,印遇龙.胃肠道黏液层中Akkermansia muciniphila的定殖研究及其与宿主的相互作用[J].中国农业科学,2016,49(8):1577-1584. FENG Z M,BAO X Y,YIN Y L.The Interaction of colonization of Akkermansia muciniphila in gastrointestinal tract and its host[J].Scientia Agricultura Sinica,2016,49(8):1577-1584.(in Chinese)
[24] GANESH B P,KLOPFLEISCH R,LOH G,et al.Commensal Akkermansia muciniphila exacerbates gut inflammation in Salmonella typhimurium-infected gnotobiotic mice[J].PLoS One,2013,8(9):e74963,doi:10.1371/journal.pone.0074963.
[25] THAREJA A,PUNIYA A K,GOEL G,et al.In vitro degradation of wheat straw by anaerobic fungi from small ruminants[J].Archives of Animal Nutrition,2006,60(5):412-417.  
[26] GRIFFITH G W,OZKOSE E,THEODOROU M K,et al.Diversity of anaerobic fungal populations in cattle revealed by selective enrichment culture using different carbon sources[J].Fungal Ecology,2009,2(2):87-97.  
[27] BIDELLAOUI B,SEGARRA G,HAKKOU A,et al.Beneficial effects of Rhizophagus irregularis and Trichoderma asperellum strain T34 on growth and fusarium wilt in tomato plants[J].Journal of Plant Pathology,2018,101(1):121-127.
[28] 安雅静,文勇立,赵佳琦,等.宏基因组学揭示AFB1对牦牛瘤胃微生物多样性及CAZy谱影响[J].家畜生态学报,2019,40(2):13-20. AN Y J,WEN Y L,ZHAO J Q,et al.Metagenomics reveals the effect of AFB1 on rumen microbial diversity and CAZy of yak[J].Journal of Domestic Animal Ecology,2019(2):13-20.(in Chinese)
[29] 王立志,徐谊英,蔡永华.高通量测序分析人工养殖成年林麝粪便古菌菌群多样性[J].动物营养学报,2016,28(2):477-484. WANG L Z,XU Y Y,CAI Y H.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.(in Chinese)
[30] 田彦.基于高通量测序的中国荷斯坦奶牛瘤胃宏转录组研究[D].博士学位论文.北京:中国科学院北京基因组研究所,2015:21-23. TIAN Y.Metatranscriptomic study of Chinese Holstein dairy cow rumen based on high-throughput sequencing[D].Ph.D.Thesis.Beijing:Beijing Institute of Genomics Chinese Academy of Sciences,2015:21-23.(in Chinese)
[31] VILA A R,BRICEÑO C,MCALOOSE D,et al.Putative parapoxvirus-associated foot disease in the endangered huemul deer (Hippocamelus bisulcus) in Bernardo O'Higgins National Park,Chile[J].PLoS One,2019,14(4):e0213667,doi:10.1371/journal.pone.0213667.
[32] GÓRSKI A,WA?NA E,DABROWSKA B K,et al.Bacteriophage translocation[J].FEMS Immunology & Medical Microbiology,2006,46(3):313-319.  
[33] LUO X,WANG P,CHENG J G,et al.Characterization of virulence genes and antimicrobial resistance of lung pathogenic Escherichia coli isolates in forest musk deer (Moschus berezovskii)[J].Journal of Zoo and Wildlife Medicine,2016,47(2):540-550.  
[34] 周黎明,王正荣,王浴生.大肠杆菌主动外排泵与抗生素多重耐药性研究进展[J].四川生理科学杂志,2003,25(4):163-164. ZHOU L M,WANG Z R,WANG Y S.Research progress on active efflux pump of Escherichia coli and antibiotic multi-resistance[J].Sichuan Journal of Physiological Sciences,2003,25(4):163-164.(in Chinese)
Outlines

/