腹泻犊牛与健康犊牛粪便菌群结构组成与功能研究

doi:10.16431/j.cnki.1671-7236.2020.09.010

中国畜牧兽医 ›› 2020, Vol. 47 ›› Issue (9): 2779-2788.doi: 10.16431/j.cnki.1671-7236.2020.09.010

腹泻犊牛与健康犊牛粪便菌群结构组成与功能研究

张子敬¹, 朱肖亭¹, 吕世杰¹, 金磊¹, 徐嘉威², 黄永震², 李志明³, 王献伟³, 于翔⁴, 杨尚⁵, 李静⁶, 王二耀¹, 徐照学¹, 施巧婷¹

1. 河南省农业科学院畜牧兽医研究所, 郑州 450002;
2. 西北农林科技大学动物科技学院, 杨凌 712100;
3. 河南省畜牧总站, 郑州 450008;
4. 河南省动物卫生监督所, 郑州 450002;
5. 河南省蚕业科学研究院, 郑州 450000;
6. 泌阳县动物卫生监督所, 泌阳 463700

收稿日期:2020-03-19 出版日期:2020-09-20 发布日期:2020-09-16
通讯作者: 施巧婷 E-mail:sqtsw@126.com
作者简介:张子敬(1985-),男,河南驻马店人,博士,研究方向:动物遗传育种与繁殖,E-mail:vincezhang163@163.com
基金资助:
河南省农业科学院自主创新专项基金（2019ZC41）；河南省农业科学院优秀青年科技基金（2020YQ36）；河南省肉牛产业技术体系（S2013-08）；国家肉牛牦牛产业技术体系（CARS-37）

Study on the Structure and Function of Fecal Microbiome Between Diarrhea and Healthy Calves

ZHANG Zijing¹, ZHU Xiaoting¹, LYU Shijie¹, JIN Lei¹, XU Jiawei², HUANG Yongzhen², LI Zhiming³, WANG Xianwei³, YU Xiang⁴, YANG Shang⁵, LI Jing⁶, WANG Eryao¹, XU Zhaoxue¹, SHI Qiaoting¹

1. Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China;
2. College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China;
3. Henan Provincial Animal Husbandry General Station, Zhengzhou 450008, China;
4. Animal Health Supervision Institute of Henan Province, Zhengzhou 450002, China;
5. Henan Academy of Sericulture Science, Zhengzhou 450000, China;
6. Animal Health Supervision Institute of Biyang, Biyang 463700, China

Received:2020-03-19 Online:2020-09-20 Published:2020-09-16

摘要/Abstract

摘要： 本研究旨在探究腹泻与健康犊牛粪便微生物的结构组成与分布特征，筛选出一些可作为评价犊牛腹泻参考指标的特异性菌群。试验采集10份腹泻和10份健康夏南牛犊牛的粪便样本并提取粪便总DNA，运用16S rRNA高通量测序技术，比较腹泻组和健康组在微生物多样性方面（组成及结构）存在的差异，获得两组间具有统计学差异的Biomarker，并对差异功能基因进行注释。结果表明，腹泻犊牛粪便微生物的多样性小于健康犊牛；在门水平上，与健康组相比，腹泻组犊牛粪便中微生物相对丰度显著升高的是变形菌门和梭杆菌门，螺旋菌门显著降低（P<0.05）；在属水平上，与健康组相比，腹泻组犊牛粪便微生物中埃希氏-志贺菌属、梭杆菌属、乳杆菌属和梭状芽孢杆菌属相对丰度明显升高，不可培养拟杆菌目S24-7群、拟普雷沃菌属和普雷沃氏菌科的菌属显著降低（P<0.05）。通过对COG功能预测分析，腹泻组在翻译、核糖体结构和起源类群明显降低。通过KEGG代谢途径分析，腹泻组粪便中显著升高的代谢通路是碳水化合物代谢和外源性物质降解和代谢，显著降低的代谢通路分别是细胞增殖和死亡、复制和修复、翻译和转录（P<0.05）。本研究分析了腹泻组和健康组之间的优势菌群，筛选出可以作为犊牛腹泻参考指标的10个Biomarker，并对功能差异基因进行注释，为进一步研究犊牛腹泻的治疗及预防奠定了基础。

关键词: 犊牛; 粪便微生物; 腹泻; 16S rRNA; 高通量测序

Abstract: This study was aimed to identify some specific microbiota to indicate the calf diarrhea by exploring the differences of fecal microbiota composition and function between healthy and diarrhea calves.Fecal samples were collected from 10 diarrheal and 10 healthy Xianan calves and used to extract genomic DNA.Fecal microbial diversity was investigated by 16S rRNA Illumina MiSeq high-throughput sequencing technology.Biomarkers with statistical differences were obtained,the differentially functional genes were annotated between two groups.The results showed that the fecal microbial diversity of diarrhea calves was less than healthy calves.Compared with healthy calves,the abundance of Proteobacteria and Fusobacteria was significantly increased,while Spirochaetae was decreased in calves with diarrhea at phylum level (P<0.05).At genus level,the relative abundances of Escherichia-Shigella,Fusobacterium,Lactobacillus and Clostridium_sensu_stricto_1 exhibited increased calves with diarrhea,the relative abundance of uncultured_bacterium_f_Bacteroidales_S24-7_group,Alloprevotella and Prevotellaceae_NK3B31_group exhibited decreased in calves with diarrhea (P<0.05).The differentially functional genes in diarrheal calves were significantly reduced in bacterial translation,ribosomal structure and biogenesis by COG functional profiles analyzes.The KEGG pathways was analyzed,the pathways in diarrheal calves were significantly increased in carbohydrate metabolism,xenobiotics biodegradation and metabolism,whereas they significantly decreased in cell growth,death,replication,repair,translation and transcription (P<0.05).The dominant bacteria were analyzed and ten biomarkers were identified as indicator for evaluating calf diarrhea between diarrhea and healthy groups in this study.The results provided crucial references for future research on preventing and treating calves diarrhea.

Key words: calves; fecal microbiota; diarrhea; 16S rRNA; high-throughput sequencing

中图分类号:

S814.8

张子敬, 朱肖亭, 吕世杰, 金磊, 徐嘉威, 黄永震, 李志明, 王献伟, 于翔, 杨尚, 李静, 王二耀, 徐照学, 施巧婷. 腹泻犊牛与健康犊牛粪便菌群结构组成与功能研究[J]. 中国畜牧兽医, 2020, 47(9): 2779-2788.

ZHANG Zijing, ZHU Xiaoting, LYU Shijie, JIN Lei, XU Jiawei, HUANG Yongzhen, LI Zhiming, WANG Xianwei, YU Xiang, YANG Shang, LI Jing, WANG Eryao, XU Zhaoxue, SHI Qiaoting. Study on the Structure and Function of Fecal Microbiome Between Diarrhea and Healthy Calves[J]. China Animal Husbandry and Veterinary Medicine, 2020, 47(9): 2779-2788.

参考文献

[1] 荔霞,王胜义,刘永明,等.犊牛腹泻病因及其药物防治研究进展[J].中国畜牧兽医,2010,37(10):161-165. LI X,WANG S Y,LIU Y M,et al.Progress of calf diarrhea causes and prevention of drug[J].China Animal Husbandry & Veterinary Medicine,2010,37(10):161-165.(in Chinese)
[2] 曹明泽,朱阵,王磊,等.犊牛腹泻概述[J].黑龙江畜牧兽医,2016,14:116-119. CAO M Z,ZHU Z,WANG L,et al.An overview of calf diarrhea[J].Heilongjiang Animal Science and Veterinary Medicine,2016,14:116-119.(in Chinese)
[3] KIM M K,LEE H G,PARK J A,et al.Effect of feeding direct-fed microbial as an alternative to antibiotics for the prophylaxis of calf diarrhea in Holstein calves[J].Asian Australasian Journal of Animal Sciences,2011,24(5):643-649.
[4] GUNDUZ N,ARSLAN M Ö.Determining the prevalence of Cryptosporidium infections with acid fast staining and ELISA in calves at the Kars province of Turkey[J].Turkiye Parazitolojii Dergisi,2017,41(1):5.
[5] 范晴,谢芝勋,谢志勤,等.牛病毒性腹泻病毒非结构蛋白NS3的表达及ELISA检测方法的建立[J].中国畜牧兽医,2014,41(5):85-89. FAN Q,XIE Z X,XIE Z Q,et al.Expression of nonstructural protein NS3 and establishment of ELISA method of bovine viral diarrhea virus[J].China Animal Husbandry & Veterinary Medicine,2014,41(5):85-89.(in Chinese)
[6] JIANG X T,PENG X,DENG G,et al.Illumina sequencing of 16S rRNA Tag revealed spatial variations of bacterial communities in a mangrove wetland[J].Microbial Ecology,2013,66(1):96-104.
[7] ANGEBAULT C,GHOZLANE A,VOLANT S,et al.Combined bacterial and fungal intestinal microbiota analyses:Impact of storage conditions and DNA extraction protocols[J].PLoS One,2018,13(8):e201174.
[8] BERTOLINI M,DONGARI-BAGTZOGLOU A.The relationship of Candida albicans with the oral bacterial microbiome in health and disease[J].Advances in Experimental Medicine and Biology,2019,1197:69-78.
[9] FRANK D N,AMAND A L S,FELDMAN R A,et al.Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases[J].Proceedings of the National Academy of Sciences of the United States of America,2007,104(34):13780-13785.
[10] JEFFERY I B,QUIGLEY E M M,ÖHMAN L,et al.The microbiota link to irritable bowel syndrome[J].Gut Microbes,2012,3(6):572-576.
[11] POP M,WALKER A W,PAULSON J,et al.Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition[J].Genome Biology,2014,15(6):R76.
[12] 汪群,闫鹤.腹泻仔猪与健康仔猪粪便菌群多样性的比较[J].中国畜牧杂志,2019,55(8):106-110. WANG Q,YAN H.Comparison of fecal microbial diversity between diarrheal piglets and healthy piglets[J].Chinese Journal of Animal Science,2019,55(8):106-110.(in Chinese)
[13] CHEN L,XU Y S,CHEN X Y,et al.The maturing development of gut microbiota in commercial piglets during the weaning transition[J].Frontiers in Micro-biology,2017,8:1688.
[14] GOMEZ D E,ARROYO L G,COSTA M C,et al.Characterization of the fecal bacterial microbiota of healthy and diarrheic dairy calves[J].Journal of Veterinary Internal Medicine,2017,31(3):928-939.
[15] CHO Y I,YOON K J.An overview of calf diarrhea-infectious etiology,diagnosis,and intervention[J].Journal of Veterinary Science,2014,15(1):1-17.
[16] 喻华英,杨晓华.新疆部分地区犊牛腹泻病大肠杆菌的分离、鉴定与血清型分析[J].新疆农业科学,2011,48(9):1752-1756. YU H Y,YANG X H.Isolation,identification and analysis of serotype for pathogenic Escherichia coli in calves diarrhea disease in parts of Xinjiang[J].Xinjiang Agricultural Sciences,2011,48(9):1752-1756.(in Chinese)
[17] 黄安妮.基于高通量测序技术研究病毒性腹泻仔猪肠道菌群特征[D].广州:华南理工大学,2019. HUANG A N.Gut microbiota characteristics of piglets with viral diarrhea based on high-throughput sequencing technology[D].Guangzhou:South China University of Technology,2019.(in Chinese)
[18] HERMANN-BANK M L,SKOVGAARD K,STOCKMARR A,et al.Characterization of the bacterial gut microbiota of piglets suffering from new neonatal porcine diarrhoea[J].BMC Veterinary Research,2015,11(1):139.
[19] WU X,ZHANG H,CHEN J,et al.Comparison of the fecal microbiota of dholes high-throughput Illumina sequencing of the V3-V4 region of the 16S rRNA gene[J].Applied Microbiology and Biotechnology,2016,100(8):3577-3586.
[20] ROSELLI M,FINAMORE A,BRITTI M S,et al.The novel porcine Lactobacillus sobrius strain protects intestinal cells from enterotoxigenic Escherichia coli K88 infection and prevents membrane barrier damage[J].Journal of Nutrition,2007,137(12):2709-2716.
[21] NARLA A,EBERT B L.Ribosomopathies:Human disorders of ribosome dysfunction[J].Blood,2010,115(16):3196-3205.
[22] VAREL V H,YEN J T.Microbial perspective on fiber utilization by swine[J].Journal of Animal Science,1997,75(10):2715-2722.
[23] STEFANÍA M,DMITRY R,VALÉRIE C L,et al.Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes[J].Frontiers in Genetics,2015,6:148.
[24] GONG H,VU G P,BAI Y,et al.Differential expression of Salmonella type Ⅲ secretion system factors InvJ,PrgJ,SipC,SipD,SopA and SopB in cultures and in mice[J].Microbiology,2010,156(1):116-127.
[25] FORST S,KIM D J.Genomic analysis of the histidine kinase family in bacteria and archaea[J].Microbio-logy,2001,147(5):1197-1212.
[26] 杨巧丽.腹泻仔猪粪便微生物结构和功能及SLA-DQA基因与粪便菌群的相关性[D].兰州:甘肃农业大学,2017. YANG Q L.Structure and function of the fecal microbiota in diarrheic piglets and association between SLA-DQA gene and fecal bacterial community[D].Lanzhou:Gansu Agricultural University,2017.(in Chinese)

腹泻犊牛与健康犊牛粪便菌群结构组成与功能研究

Study on the Structure and Function of Fecal Microbiome Between Diarrhea and Healthy Calves

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