宏基因组技术在鸡肠道微生物中应用的研究进展

doi:10.16431/j.cnki.1671-7236.2017.03.006

Abstract

Abstract:

There are abundant microorganisms in the gastrointestinal tract of chicken, which play important roles in the metabolism and immunity of the host. The development of high-throughput sequencing technology for intestinal microbial research provides a new way of thinking. The article elaborates that metagenomics and effects of changes in intestinal microbial structure on the host and different feeding conditions, host physiological characteristics effect on intestinal microbial. This article focuses on the analysis of correlation between the intestinal microbial colony structure and characteristics of nutrient metabolism, immune function, and healthy growth of chicken on the level of metagenomics, and we hope to provide ideas for the study of intestinal microbial.

Key words: chicken; intestinal microorganisms; metagenomics; nutrient metabolism; immune fouction

CLC Number:

S831

YANG Tian-long, LIU Xu-chuan, LIAO Qi, WANG Shu-ling, ZHANG Chun-yong, GE Chang-rong, LENG Jing. Application Advances of Metagenome Technology in Intestinal Microorganisms of Chicken[J]. , 2017, 44(3): 659-666.

References

[1] Wei S, Morrison M, Yu Z. Bacterial census of poultry intestinal microbiome[J]. Poult Sci, 2013, 92(3):671-683.
[2] Salanitro J P, Fairchilds I G, Zgornicki Y D. Isolation, culture characteristics, and identification of anaerobic bacteria from the chicken cecum[J]. Applied Microbiology, 1974, 27(4):678-687.
[3] Shaufi M A M, Sieo C C, Chong C W, et al. Deciphering chicken gut microbial dynamics based on high-throughput 16S rRNA metagenomics analyses[J]. Gut Pathogens, 2015, 7(1):1-12.
[4] Verastegui Y, Cheng J, Engel K, et al. Multisubstrate isotope labeling and metagenomic analysis of active soil bacterial communities[J]. Mbio, 2014, 5(4):1114-1157.
[5] Jan C, Petersen J M, Werner J, et al. The gill chamber epibiosis of deep-sea shrimp Rimicaris exoculata:An in-depth metagenomic investigation and discovery of Zetaproteobacteria[J]. Environmental Microbiology,2014, 16(9):2723-2738.
[6] Stachler E, Bibby K. Metagenomic evaluation of the highly abundant human gut bacteriophage crAssphage for source tracking of human fecal pollution[J]. Environ Sci Technol Lett, 2014, 1(10):405-409.
[7] Rashamuse K, Ronneburg T, Sanyika W, et al. Metagenomic mining of feruloyl esterases from termite enteric flora[J]. Applied Microbiology & Biotechnology, 2014, 98(2):727-737.
[8] Rehman H U, Vahjen W, Awad W A, et al. Indigenous bacteria and bacterial metabolic products in the gastrointestinal tract of broiler chickens[J]. Arch Anim Nutr, 2007, 61(5):319-335.
[9] Fonseca B, Beletti M, Silva M, et al. Microbiota of the cecum, ileum morphometry, pH of the crop and performance of broiler chickens supplemented with probiotics[J]. Revista Brasileira De Zootecnia, 2010, 39(8):1756-1760.
[10] Zhu X Y, Zhong T, Pandya Y, et al. 16S rRNA-based analysis of microbiota from the cecum of broiler chickens[J]. Appl Environ Microbiol, 2002, 68(1):124-137.
[11] Sekelja M, Rud I, Knutsen S H, et al. Abrupt temporal fluctuations in the chicken fecal microbiota are explained by its gastrointestinal origin[J]. Appl Environ Microbiol, 2012, 78(8):2941-2948.
[12] Lu J, Idris U, Harmon B, et al. Diversity and succession of the intestinal bacterial community of the maturing broiler chicken[J]. Appl Environ Microbiol, 2003, 69(11):6816-6824.
[13] Allen H K, Donato J, Wang H H, et al. Call of the wild:Antibiotic resistance genes in natural environments[J]. Nat Rev Microbiol, 2010, 8(4):251-259.
[14] Ma L, Xia Y, Li B, et al. Metagenomic assembly reveals hosts of antibiotic resistance genes and the shared resistome in pig, chicken, and human feces[J]. Environ Sci Technol, 2016, 50(1):420-427.
[15] 祁丽,姜宁,张爱忠,等. 抗菌肽研发现状及其改造策略[J]. 中国畜牧兽医, 2016,43(2):450-456.
[16] Hume M E, Barbosa N A, Dowd S E, et al. Use of pyrosequencing and denaturing gradient gel electrophoresis to examine the effects of probiotics and essential oil blends on digestive microflora in broilers under mixed Eimeria infection[J]. Foodborne Pathog Dis, 2011, 8(11):1159-1167.
[17] Park S H, Lee S I, Ricke S C. Microbial populations in naked neck chicken ceca raised on pasture flock fed with commercial yeast cell wall prebiotics via an illumina MiSeq platform[J]. PLoS One, 2016, 11(3):e151944.
[18] 胥彩玉,史兆国,刘国华,等. 微生态制剂对鸡肠道微生物区系影响的研究进展[J]. 中国家禽, 2014,36(10):46-50.
[19] 齐博,武书庚,王晶,等. 枯草芽孢杆菌对肉仔鸡生长性能、肠道形态和菌群数量的影响[J]. 动物营养学报, 2016,28(6):1748-1756.
[20] 王沂蒙,郭设平,刘艳,等. 益生菌基因组DNA作为疫苗佐剂对鸡免疫效果的影响[J]. 中国家禽, 2007,29(24):19-22.
[21] 王磊,吕阳,张越,等. 抑制大肠杆菌K88的益生菌体外筛选[J]. 中国畜牧兽医, 2016,43(5):1355-1360.
[22] Ilina L A, Yildirim E A, Nikonov I N, et al. Metagenomic bacterial community profiles of chicken embryo gastrointestinal tract by using T-RFLP analysis[J]. Dokl Biochem Biophys, 2016, 466(1):47-51.
[23] Zhao L, Wang G, Siegel P, et al. Quantitative genetic background of the host influences gut microbiomes in chickens[J]. Scientific Reports, 2013, 3:1163.
[24] 崔一喆,王秋菊,李悦,等. 笼养和散养蛋鸡小肠细菌菌群区系的聚合酶链式反应-变性梯度凝胶电泳分析[J]. 动物营养学报, 2016,28(6):1677-1686.
[25] Hughes R J. Relationship between digesta transit time and apparent metabolisable energy value of wheat in chickens[J]. British Poultry Science, 2008, 49(6):716-720.
[26] Bedbury H P, Duke G E. Cecal microflora of turkeys fed low or high fiber diets:Enumeration, identification, and determination of cellulolytic activity[J]. Poultry Science, 1983, 62(4):675-682.
[27] Danzeisen J L, Kim H B, Isaacson R E, et al. Modulations of the chicken cecal microbiome and metagenome in response to anticoccidial and growth promoter treatment[J]. PLoS One, 2011, 6(11):e27949.
[28] Stanley D, Hughes R J, Moore R J. Microbiota of the chicken gastrointestinal tract:Influence on health, productivity and disease[J]. Applied Microbiology & Biotechnology, 2014, 98(10):4301-4310.
[29] Qu A, Brulc J M, Wilson M K, et al. Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome[J]. PLoS One, 2008, 3(8):e2945.
[30] Tang Y, Underwood A, Gielbert A, et al. Metaproteomics analysis reveals the adaptation process for the chicken gut microbiota[J]. Applied & Environmental Microbiology, 2014, 80(2):478-485.
[31] Sergeant M J, Constantinidou C, Cogan T A, et al. Extensive microbial and functional diversity within the chicken cecal microbiome[J]. PLoS One, 2014, 9(3):e91941.
[32] Pan D. An integrated study on chicken gut microbiome associated with diets and feed utilization using microarray and illumina sequencing[D]. Ohio State:The Ohio State University, 2014.
[33] He Z Q, Zhen Y, Liang C, et al. Vicious cycle composed of gut flora and visceral fat:A novel explanation of the initiation and progression of atherosclerosis[J]. Med Hypotheses, 2008, 70(4):808-811.
[34] Burrin D G, Stoll B. Emerging aspects of gut sulfur amino acid metabolism[J]. Curr Opin Clin Nutr Metab Care, 2007, 10(1):63-68.
[35] Rawls J F, Mahowald M A, Ley R E, et al. Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection[J]. Cell, 2006, 127(2):423-433.
[36] Dai X, Tian Y, Li J, et al. Metatranscriptomic analyses of plant cell wall polysaccharide degradation by microorganisms in cow rumen[J]. Applied & Environmental Microbiology, 2014, 81(4):1375-1386.
[37] Krashevska V, Klarner B, Widyastuti R, et al. Impact of tropical lowland rainforest conversion into rubber and oil palm plantations on soil microbial communities[J]. Biology & Fertility of Soils, 2015, 51(6):697-705.
[38] Brisbin J T, Gong J, Sharif S. Interactions between commensal bacteria and the gut-associated immune system of the chicken[J]. Anim Health Res Rev, 2008, 9(1):101-110.
[39] Forder R E, Nattrass G S, Geier M S, et al. Quantitative analyses of genes associated with mucin synthesis of broiler chickens with induced necrotic enteritis[J]. Academic Emergency Medicine, 2010, 17(9):958-964.
[40] Karlsson F H, Fåk F, Nookaew I, et al. Symptomatic atherosclerosis is associated with an altered gut metagenome[J]. Nature Communications, 2012, 3(4):1245.
[41] Qin J, Li Y, Cai Z, et al. A metagenome-wide association study of gut microbiota in type 2 diabetes[J]. Nature, 2012, 490(7418):55-60.
[42] Brown C T, Davis-Richardson A G, Giongo A, et al. Gut microbiome metagenomics analysis suggests a functional model for the development of autoimmunity for type 1 diabetes[J]. PLoS One, 2011, 6(10):e25792.
[43] Ley R E, Bäckhed F, Turnbaugh P, et al. Obesity alters gut microbial ecology[J]. Proc Natl Acad Sci USA, 2005, 102(31):11070-11075.
[44] Turnbaugh P J, Hamady M, Yatsunenko T, et al. A core gut microbiome in obese and lean twins[J]. Nature, 2009, 457(7228):480-484.
[45] Jumpertz R, Le D S, Turnbaugh P J, et al. Energy-balance studies reveal associations between gut microbes, caloric load, and nutrient absorption in humans[J]. American Journal of Clinical Nutrition, 2011, 94(1):58-65.
[46] Labbé A, Ganopolsky J G, Martoni C J, et al. Bacterial bile metabolising gene abundance in Crohn's, ulcerative colitis and type 2 diabetes metagenomes[J]. PLoS One, 2014, 9(12):e115175.
[47] Derache C, Esnault E, Bonsergent C, et al. Differential modulation of β-defensin gene expression by Salmonella enteritidis in intestinal epithelial cells from resistant and susceptible chicken inbred lines[J]. Developmental & Comparative Immunology, 2009, 33(9):959-966.
[48] Newell D G, Elvers K T, Dopfer D, et al. Biosecurity-based interventions and strategies to reduce Campylobacter spp. on poultry farms[J]. Applied & Environmental Microbiology, 2011, 77(24):8605-8614.
[49] Byrne C M, Clyne M, Bourke B. Campylobacter jejuni adhere to and invade chicken intestinal epithelial cells in vitro[J]. Microbiology, 2007, 153(Pt 2):561-569.
[50] Stanley D, Geier M S, Denman S E, et al. Identification of chicken intestinal microbiota correlated with the efficiency of energy extraction from feed[J]. Vet Microbiol, 2013, 164(1-2):85-92.
[51] Chang C L T, Chung C, Kuo C, et al. Beneficial effect of bidens pilosa on body weight gain, food conversion ratio, gut bacteria and coccidiosis in chickens[J]. PLoS One, 2016, 11(1):e146141.
[52] Turnbaugh P J, Ley R E, Mahowald M A, et al. An obesity-associated gut microbiome with increased capacity for energy harvest[J]. Nature, 2006, 444(7122):1027-1031.
[53] Turnbaugh P J, Gordon J I. The core gut microbiome, energy balance and obesity[J]. The Journal of Physiology, 2009, 587(17):4153-4158.
[54] Torok V A, Hughes R J, Mikkelsen L L, et al. Identification and characterization of potential performance-related gut microbiotas in broiler chickens across various feeding trials[J]. Appl Environ Microbiol, 2011, 77(17):5868-5878.

Application Advances of Metagenome Technology in Intestinal Microorganisms of Chicken

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	DU Yuanjun, DUAN Guochao, LIU Wei, LI Dapeng, HAN Haixia, LEI Qiuxia, ZHOU Yan, LIU Jie, WANG Jie, CAO Dingguo, LI Fuwei, CHEN Fu. Effect of Translucent on Egg Quality and Its Relationship with Intestinal Function of Laying Hen [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(6): 2305-2311.
[2]	WANG Haorui, YU Baojun, YANG Jiayi, WEI Rong, FU Xi, WANG Chuanchuan, ZHANG Di, LI Desheng, CAI Zhengyun, GU Yaling, ZHANG Juan. Bioinformatics Analysis and Tissue Expression of DERA Gene in Jingyuan Chickens [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(5): 1764-1773.
[3]	LIU Jialong, ZHANG Yiwen, ZHANG Yueran, SUN Qijuan, CHEN Jian, HE Lei, JIA Yanyan, DING Ke, YU Zuhua. Cloning,Prokaryotic Expression and Bioinformatics Analysis of ELAVL1 Gene in Chicken [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(5): 1807-1817.
[4]	WU Jingxuan, SUN Zheng, MA Xuelian, ZHANG Liyang, LIAO Xiudong, LUO Xugang, LI Sufen, LYU Lin. A Survey on Magnesium Contents in Feed Resources for Livestock and Poultry in China [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(5): 1888-1898.
[5]	JIANG Shanyi, ZHOU Bijun, WEN Ming, WANG Kaigong. Prevention of Traditional Chinese Medicine with Probiotics on Eimeria tenella [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(5): 2092-2102.
[6]	LIU Xin, CHEN Qun, QIU Yulang, LI Lin, HOU Guoxi, YAN Xiaogang, LI Zhonghe, CHEN Long, GAO Xingai, LIU Dongmei, ZHAI Di, YAN Qiuliang. Research Progress on the Production Mechanism and Control Technology of Chicken Manure Composting Nitrogen-containing and Sulfur-containing Waste Gases [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(5): 2166-2174.
[7]	WU Zhi, ZHANG Cong, YUAN Huisha, DONG Hongyan, DAI Lixia, JIA Luqi, WU Shuang, ZHU Shanyuan. Isolation,Identification,Virulence and Drug Resistance of Salmonella from Yellow Chicken [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(4): 1695-1706.
[8]	HUANG Xiaoqian, YUAN Junzhao, LIU Jinhe, ZOU Hui, GU Jianhong, YUAN Yan, LIU Xuezhong, LIU Zongping, BIAN Jianchun. Protective Effect of Honokiol on Cadmium-induced Renal Injury in Chickens [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(3): 1007-1015.
[9]	LI Xinran, ZHANG Qingyan, ZHA Weiwei, ZHU Miao. Bioinformatics Analysis and Expression of Wnt Gene Family in Chickens [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(1): 15-25.
[10]	XIE Jingjing, REN Mengting, FAN Jiahui, JIAO Yaru, HAN Zongxi, MA Deying. Study on Immune Response of Infectious Bronchitis Virus to Chickens and Antiviral Effect of Recombinant Avian Beta-defensins 11 and 12 [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(1): 246-259.
[11]	ZHANG Hao, LIU Yixuan, ZHU Huiyuan, ZHANG Pengwei, LEI Yanru, GAO Chaoqun, LI Donghua, KANG Xiangtao. Bioinformatics Analysis of Differential Genes of Skin Feather Follicles in Chickens [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(9): 3273-3282.
[12]	GAO Xiaomin, ZHOU Shujian, CHEN Chen, JIN Jing, HU Cai, ZHANG Chen, ZUO Qisheng, ZHANG Yani, CHEN Guohong, LI Bichun. Regulation of STAT1 and Histone Acetylation Modification on lncRNA-BMP4 Transcription in Chickens [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(9): 3321-3332.
[13]	GAO Yefan, SONG Hanan, WANG Yunan, WU Yue, NIU Ruili, ZONG Xianchun, GUAN Weijun. Study on the Isolation, Culture and Differentiation Potential of Limbal Stem Cells from Beijing You Chickens [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(9): 3372-3381.
[14]	WANG Xuefang, GUI Rong, CHEN Gongyi, WANG Wei, ZHANG Hongying, WANG Xuebing, LI Xiao. Clinical Study of Lianhuachaiqin Soluble Powder on Chicken Syndrome of Wind-heat Invading Lung [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(9): 3610-3621.
[15]	DING Mengqin, HEIDAXI·Bahati, PENG Fengqiang, HU Yali, SHAERSHANBIEKE·Abudilida. Analysis of Polymorphisms of FSHR Gene and Its Association with Production Performance of Baicheng You Chickens [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(8): 3044-3053.