基于16S rDNA测序分析生态养殖对猪粪细菌群落的影响

doi:10.16431/j.cnki.1671-7236.2023.12.008

摘要/Abstract

摘要： 【目的】现代生态猪场养殖技术与传统技术大不相同,通过对转换养殖模式的猪群粪便细菌组成进行分析,并关注物种多样性和群落结构的变化特点,从而探究现代生态猪场养殖技术对猪肠道菌群结构的影响。【方法】从传统猪场选取8头体重相近的育肥猪转移至生态猪场蓄养,每隔10 d取其粪便样本,直至达出栏月龄。对每个时期的粪便混合样本进行16S rDNA高通量测序,通过生物信息软件分析测序数据,以微生物16S rDNA基因序列分类单元(operational taxonomic units,OTUs)对其进行分类学物种注释,从而分析其物种多样性、群落结构的情况与变化规律。【结果】从传统猪场转移至生态猪场后猪粪细菌群落结构产生变化,且在培育时段内其多样性和丰富度均有所提高,以变形菌门(Proteobacteria)、拟杆菌门(Bacteroidetes)等为优势菌门;优势菌属为不可培养细菌、沉积物漠河杆菌(Moheibacter)等。在出栏前粪便中常见致病菌如伊丽莎白金菌(Elizabethkingia)、志贺氏埃希氏菌(Escherichia-Shigella)、棒状杆菌(Corynebacterium)等丰度均降至较低,但益于肠道消化的细菌如乳酸杆菌(Lactobacillus)、密螺旋体(Treponema)、梭菌(Clostridium)等丰度均有所提升。【结论】该猪群在现代生态猪场养殖技术培育下菌群结构发生较大改变,并形成与其他普通猪场不同的优势菌群。

关键词: 生态猪场; 16S rDNA测序; 粪便; 菌群结构

Abstract: 【Objective】 Modern ecological pig farming techniques differ from traditional techniques.This study was aimed to analyze the bacterial composition of feces from pigs that underwent a transition to an ecological pig farming model,focus on changes in species diversity and community structure,in order to investigate the effects of modern ecological pig farming techniques on the gut microbiota of pigs.【Method】 Eight fattening pigs with similar body weights were selected from a traditional pig farm and transferred to an ecological pig farm for breeding.Fecal samples were collected every 10 days until the pigs reached the age of slaughter.16S rDNA high-throughput sequencing was performed on mixed fecal samples from each time period,and the sequencing data was analyzed using bioinformatics software.The microbiota was annotated based on operational taxonomic units (OTUs) of microbial 16S rDNA gene sequences in order to analyze the changes in species diversity and community structure.【Result】 The bacterial community structure of pig feces changed after being transferred from a traditional pig farm to an ecological pig farm,with an increase in diversity and richness during the breeding period.Proteobacteria,Bacteroidetes,etc.were the dominant phyla,uncultured bacteria,Moheibacter,etc.were dominant genera.The abundance of common pathogenic bacteria such as Elizabethkingia,Escherichia-Shigella,and Corynebacterium decreased to lower levels in feces before slaughter,but bacteria that helped with intestinal digestion,such as Lactobacillus,Treponema and Clostridium,increased in abundance.【Conclusion】 The bacterial community structure of the pig population changed significantly under modern ecological pig farming techniques,forming a unique dominant bacterial community that differs from that of common pig farms.

Key words: ecological pig farm; 16S rDNA sequencing; feces; bacterial community

中图分类号:

S811.6

容敏靖, 万锈琳, 陈洵, 谭迪明, 刘军, 石磊, 邹忠爱. 基于16S rDNA测序分析生态养殖对猪粪细菌群落的影响[J]. 中国畜牧兽医, 2023, 50(12): 4858-4867.

RONG Minjing, WAN Xiulin, CHEN Xun, TAN Diming, LIU Jun, SHI Lei, ZOU Zhongai. Effects of Ecological Farming on Fecal Microbiota Composition in Pigs Based on 16S rDNA Sequencing Analysis[J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(12): 4858-4867.

参考文献

[1] 杨侗瑀,王祖力,刘小红,等.2021年世界生猪产业发展情况及2022年的趋势[J].猪业科学,2022,39(2):34-38. YANG T Y,WANG Z L,LIU X H,et al.World pig industry development in 2021 and trends in 2022[J].Swine Industry Science,2022,39(2):34-38.(in Chinese)
[2] ANDRES V M,DAVIES R H.Biosecurity measures to control Salmonella and other infectious agents in pig farms:A review[J].Comprehensive Reviews in Food Science and Food Safety,2015,14(4):317-335.
[3] 张丹琳,陈坚.猪场生态养殖及消毒技术研究[J].中国动物保健,2022,24(10):81-82. ZHANG D L,CHEN J.Study on ecological breeding and disinfection technology of pig farm[J].China Animal Health,2022,24(10):81-82.(in Chinese)
[4] 余传刚,肖石军.现代生态猪场规划设计要点[J].江西畜牧兽医杂志,2021,3:31-35. YU C G,XIAO S J.Key points of modern ecological pig farm planning and design[J].Jiangxi Journal of Animal Husbandry&Veterinary Medicine,2021,3:31-35.(in Chinese)
[5] MARCHESI J R,ADAMS D H,FAVA F,et al.The gut microbiota and host health:A new clinical frontier[J].Gut,2016,65(2):330-339.
[6] DE VOS W M,TILG H,VAN HUL M,et al.Gut microbiome and health:Mechanistic insights[J].Gut,2022,71(5):1020-1032.
[7] 金娜,邹闻书,高倩,等.枸芪多糖对育肥猪肠道菌群多样性及组成的影响[J].动物营养学报,2019,31(9):4033-4043. JIN N,ZOU W S,GAO Q,et al.Effects of Gou-Qi polysaccharides on intestinal microbial diversity and composition of growing-finishing pigs[J]. Chinese Journal of Animal Nutrition,2019,31(9):4033-4043.(in Chinese)
[8] AHMED S T,MUN H S,ISLAM M M,et al.Effects of dietary natural and fermented herb combination on growth performance,carcass traits and meat quality in grower-finisher pigs[J].Meat Science,2016,122:7-15.
[9] 李卓君,陈春香,钟小菊,等.猪肠道微生物组成、影响因素及其对重要经济性状的影响研究进展[J].中国畜牧兽医,2022,49(7):2557-2566. LI Z J,CHEN C X,ZHONG X J,et al.Research progress on porcine gut microbiota composition,influencing factors and its effects on economically important traits[J].China Animal Husbandry&Veterinary Medicine,2022,49(7):2557-2566(in Chinese)
[10] HUANG J Q,ZHANG W J,FAN R,et al.Composition and functional diversity of fecal bacterial community of wild boar,commercial pig and domestic native pig as revealed by 16S rRNA gene sequencing[J].Archives of Microbiology,2020,202(4):843-857.
[11] LEE A,LE BON M,CONNERTON I F,et al.Common colonic community indicators of the suckling pig microbiota where diversity and abundance correlate with performance[J].FEMS Microbiology Ecology,2022,98(5):fiac048.
[12] LAU S K P,TENG J L L,CHIU T H,et al.Differential microbial communities of omnivorous and herbivorous cattle in Southern China[J].Computational and Structural Biotechnology Journal,2018,16:54-60.
[13] WEI Z L,CAO S G,LIU S L,et al.Could gut microbiota serve as prognostic biomarker associated with colorectal cancer patients'survival?A pilot study on relevant mechanism[J].Oncotarget,2016,7(29):46158-46172.
[14] GUPTA R S,SETHI M.Phylogeny and molecular signatures for the phylum Fusobacteria and its distinct subclades[J].Anaerobe,2014,28:182-198.
[15] 陈鹏,丁武亿.猪肠道菌群特点和生长的关系[J].饲料博览,2017,11:1-4. CHEN P,DING W Y.Relationship between intestinal microflora characteristics and pig growth[J].Feed Review,2017,11:1-4.(in Chinese)
[16] LAZAR C S,LEHMANN R,STOLL W,et al.The endolithic bacterial diversity of shallow bedrock ecosystems[J].The Science of the Total Environment,2019,679:35-44.
[17] 李佳萍.硫酸盐对反硝化型甲烷厌氧氧化过程影响研究[D].杭州:浙江工商大学,2020. LI J P.Effects of sulfate on nitrite/nitrate-denitrifying anaerobic methane oxidation[D].Hangzhou:Zhejiang Gongshang University,2020.(in Chinese)
[18] DING S,ZHOU D P,WEI H W,et al.Alleviating soil degradation caused by watermelon continuous cropping obstacle:Application of urban waste compost[J].Chemosphere,2021,262:128387.
[19] BINDARI Y R,MOORE R J,VAN T T H,et al.Microbial communities of poultry house dust,excreta and litter are partially representative of microbiota of chicken caecum and ileum[J].Public Library of Science,2021,16(8):e0255633.
[20] 王晨赫.中华绒螯蟹(Eriocheir sinensis)肠道微生物结构特征及与养殖环境微生物相关性研究[D].南京:南京农业大学,2019. WANG C H.Chinese mitten crab (Eriocheir sinensis) gut microbes structure characteristics and correlation research and breeding environment microorganisms[D].Nanjing:Nanjing Agricultural University,2019.(in Chinese)
[21] LIU T,AWASTHI S K,DUAN Y,et al.Effect of fine coal gasification slag on improvement of bacterial diversity community during the pig manure composting[J].Bioresource Technology,2020,304:123024.
[22] ZHU F C,LIAN C N,HE L S.Genomic characterization of a novel Tenericutes bacterium from deep-sea holothurian intestine[J].Microorganisms,2020,8(12):1874.
[23] TIAN B,HUA Y J.Carotenoid biosynthesis in extremophilic Deinococcus-Thermus bacteria[J].Trends in Microbiology,2010,18(11):512-520.
[24] 刘荷.酒鬼酒发酵车间空气源可培养细菌多样性研究[D].吉首:吉首大学,2014. LIU H.Biodiversity of culturable bacteria isolated from the air samples from a liquor fermentation workshop in Jiugui Liquor Co.Ltd.,China[D].Jishou:Jishou University,2014.(in Chinese)
[25] BERNAD-ROCHE M,BELLÉS A,GRASA L,et al.Effects of dietary supplementation with protected sodium butyrate on gut microbiota in growing-finishing pigs[J].Animals,2021,11:2137.
[26] YANG S D,XIAO J,LIANG T,et al.Response of soil biological properties and bacterial diversity to different levels of nitrogen application in sugarcane fields[J].AMB Express,2021,11(1):172.
[27] ZHANG Y P,XIAO X P,ELHAG O,et al.Hermetia illucens L.larvae-associated intestinal microbes reduce the transmission risk of zoonotic pathogens in pig manure[J].Microbial Biotechnology,2022,15(10):2631-2644.
[28] 仇潇洒.陶厄氏菌属(Thauera)富集的SBR系统脱氮性能研究[D].西安:长安大学,2020. QIU X S.Study on denitrification performance of SBR system enriched by Thauera[D].Xi'an:Chang'an University,2020.(in Chinese)
[29] RODRÍGUEZ-SORRENTO A,CASTILLEJOS L,LÓPEZ-COLOM P,et al.Effects of the administration of Bifidobacterium longum subsp.infantis CECT 7210 and Lactobacillus rhamnosus HN001 and their synbiotic combination with galacto-oligosaccharides against enterotoxigenic Escherichia coli F4 in an early weaned piglet model[J].Frontiers in Microbiology,2021,12:642549.
[30] 王蕾蕾,郭庆兰,杨帆.伊丽莎白菌属细菌生物学特征及耐药性研究进展[J].中国感染与化疗杂志,2020,20(6):711-715. WANG L L,GUO Q L,YANG F.Research progress on the biological characteristics and resistance of bacterium of Elisabethia[J].Chinese Journal of Infection and Chemotherapy, 2020,20(6):711-715.(in Chinese)
[31] ZHANG Z X,TAYLOR L,SHOMMU N,et al.A diversified dietary pattern is associated with a balanced gut microbial composition of Faecalibacterium and Escherichia/Shigella in patients with Crohn's disease in remission[J].Journal of Crohn's and Colitis,2020,14(11):1547-1557.