基于SourceTracker分析牧场环境对乳房炎乳菌群的影响

doi:10.11843/j.issn.0366-6964.2023.09.026

畜牧兽医学报 ›› 2023, Vol. 54 ›› Issue (9): 3872-3883.doi: 10.11843/j.issn.0366-6964.2023.09.026

基于SourceTracker分析牧场环境对乳房炎乳菌群的影响

孟璐^1,2, 胡海燕^1,2, 董蕾^1,2, 郑楠^1,2, 王加启^1,2*

1. 中国农业科学院北京畜牧兽医研究所, 农业农村部奶及奶制品质量安全控制重点实验室, 北京 100193;
2. 中国农业科学院北京畜牧兽医研究所, 农业农村部奶产品质量安全风险评估实验室, 北京 100193

收稿日期:2023-02-03 发布日期:2023-09-22
通讯作者: 王加启,主要从事奶牛营养与牛奶质量安全研究,E-mail:jiaqiwang@vip.163.com
作者简介:孟璐(1986-),女,江苏徐州人,助理研究员,博士,主要从事牛奶微生物研究,E-mail:menglu@caas.cn
基金资助:
国家重点研发计划(2022YFD1301003);农产品质量安全风险评估(GJFP20220304);国家现代农业产业技术体系(CARS36);新疆重大科技专项(2020A01001-3-1);中国农业科学院科技创新工程(ASTIP-IAS12)

Influence of Dairy Farm Environment on Mastitis Milk Microbiota via SourceTracker

MENG Lu^1,2, HU Haiyan^1,2, DONG Lei^1,2, ZHENG Nan^1,2, WANG Jiaqi^1,2*

1. Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
2. Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China

Received:2023-02-03 Published:2023-09-22

摘要/Abstract

摘要： 乳房炎是奶牛常见的疾病之一,通常是由牧场环境中的病原微生物引起,因此,开展乳房炎病原微生物溯源研究对乳房炎防治具有重要意义。本研究从中国天津某牧场收集了乳房炎乳、牧场环境(空气、饮用水、饲料、粪便、垫料、新垫料及喷淋水)和挤奶厅(前药浴液、后药浴液、前药浴杯、后药浴杯、奶杯、乳头皮肤)样品共计74份,提取可培养微生物DNA和总DNA,进行16S rDNA扩增测序和SourceTracker分析。在采集的74份样品中,共检测到50个不同科水平上的细菌。Beta多样性和ANOSIM分析表明,样品间细菌群落相似性低。乳房炎乳和乳头皮肤及卧床样品的细菌群落结构相似。此外,SourceTracker结果发现,乳头皮肤是奶牛乳房炎的主要污染源,其次是空气、奶杯和粪便,这表明牧场管理会影响奶牛感染乳房炎的情况。因此,牧场应加强管理控制措施,减少或消除牧场中病原微生物的传播风险。

关键词: 奶牛乳房炎, 牧场, 挤奶厅, 16S rDNA测序, SourceTracker

Abstract: Bovine mastitis is the most economically important disease of dairy cattle, which is most commonly caused by pathogens. The pathogens that influenced dairy cows might be from the farm environment. Therefore, the flow of microbes through environments to cow mastitis should be investigated. In this study, mastitis milk, pan barn samples (air, drinking water, feces, feed, bedding material, new bedding material, spray water), and parlour samples (pre teat medicine, post teat medicine, pre medicine cup, post medicine cup, teat dip cup, teat skin) have been collected in a dairy farm in Tianjin, China. Total DNA of culture-based and nonculture-based samples were extracted and then performed 16S rDNA amplicon sequencing and SourceTracker. OTU profiles were assigned to 50 families among all the 74 samples. Beta diversity and ANOSIM analysis showed that the similarity of bacteria between the mastitis milk and environment samples was low. In general, the microbial community structure was similar between mastitis milk and teat skin and, to a lesser extent, bedding samples. Moreover, SourceTracker identified the teat skin as the most important source of pollution, followed by air, milk cups and feces, which highlighted the possible effects of farm management practices on bovine mastitis. Therefore, control measures should be introduced to reduce or eliminate the risk of transmission in the dairy farms.

Key words: dairy cow mastitis, pan barn, parlour, 16S rDNA sequencing, SourceTracker

中图分类号:

Q938.11

孟璐, 胡海燕, 董蕾, 郑楠, 王加启. 基于SourceTracker分析牧场环境对乳房炎乳菌群的影响[J]. 畜牧兽医学报, 2023, 54(9): 3872-3883.

MENG Lu, HU Haiyan, DONG Lei, ZHENG Nan, WANG Jiaqi. Influence of Dairy Farm Environment on Mastitis Milk Microbiota via SourceTracker[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(9): 3872-3883.

参考文献

[1] BRADLEY A J. Bovine mastitis:an evolving disease[J]. Vet J, 2002, 164(2):116-128.
[2] HEIKKILÄ A M, LISKI E, PYÖRÄLÄ S, et al. Pathogen-specific production losses in bovine mastitis[J]. J Dairy Sci, 2018, 101(10):9493-9504.
[3] RUEGG P L. A 100-year review:mastitis detection, management, and prevention[J]. J Dairy Sci, 2017, 100(12):10381-10397.
[4] ANON. Veterinary investigation surveillance report[R]. London:Veterinary Laboratories Agency, 2001.
[5] GAO J, BARKEMA H W, ZHANG L M, et al. Incidence of clinical mastitis and distribution of pathogens on large Chinese dairy farms[J]. J Dairy Sci, 2017, 100(6):4797-4806.
[6] VACHEYROU M, NORMAND A C, GUYOT P, et al. Cultivable microbial communities in raw cow milk and potential transfers from stables of sixteen French farms[J]. Int J Food Microbiol, 2011, 146(3):253-262.
[7] DOYLE C J, GLEESON D, O'TOOLE P W, et al. Impacts of seasonal housing and teat preparation on raw milk microbiota:a high-throughput sequencing study[J]. Appl Environ Microbiol, 2017, 83(2):e02694-16.
[8] WU H M, NGUYEN Q D, TRAN T T M, et al. Rumen fluid, feces, milk, water, feed, airborne dust, and bedding microbiota in dairy farms managed by automatic milking systems[J]. Anim Sci J, 2019, 90(3):445-452.
[9] DU B Y, MENG L, LIU H M, et al. Impacts of milking and housing environment on milk microbiota[J]. Animals (Basel), 2020, 10(12):2339.
[10] HOGAN J S, SMITH K L, HOBLET K H, et al. Bacterial counts in bedding materials used on nine commercial dairies[J]. J Dairy Sci, 1989, 72(1):250-258.
[11] SONG X B, HUANG X P, XU H Y, et al. The prevalence of pathogens causing bovine mastitis and their associated risk factors in 15 large dairy farms in China:an observational study[J]. Vet Microbiol, 2020, 247:108757.
[12] 胡海燕, 刘慧敏, 孟璐, 等. 天津某牧场奶牛乳房炎奶样与环境中细菌的分离与鉴定[J]. 中国农业大学学报, 2021, 26(3):69-79.
HU H Y, LIU H M, MENG L, et al. Isolation and identification of mastitic milk and environment bacteria in a dairy farm in Tianjin[J]. Journal of China Agricultural University, 2021, 26(3):69-79. (in Chinese)
[13] ZHANG J J, KOBERT K, FLOURI T, et al. PEAR:a fast and accurate Illumina Paired-End reAd mergeR[J]. Bioinformatics, 2014, 30(5):614-620.
[14] EDGAR R C. UPARSE:highly accurate OTU sequences from microbial amplicon reads[J]. Nat Methods, 2013, 10(10):996-998.
[15] OKSANEN J, BLANCHET F G, KINDT R, et al. Vegan community ecology package:ordination methods, diversity analysis and other functions for community and vegetation ecologists[J]. R Package Ver, 2015:2-3.
[16] CAPORASO J G, KUCZYNSKI J, STOMBAUGH J, et al. QIIME allows analysis of high-throughput community sequencing data[J]. Nat Methods, 2010, 7(5):335-336.
[17] SCHLOSS P D, WESTCOTT S L, RYABIN T, et al. Introducing mothur:open-source, platform-independent, community-supported software for describing and comparing microbial communities[J]. Appl Environ Microbiol, 2009, 75(23):7537-7541.
[18] KNIGHTS D, KUCZYNSKI J, CHARLSON E S, et al. Bayesian community-wide culture-independent microbial source tracking[J]. Nat Methods, 2011, 8(9):761-763.
[19] FURSOVA K K, SOKOLOV S L, SHCHANNIKOVA M P, et al. Changes in the microbiome of milk in cows with mastitis[J]. Dokl Biochem Biophys, 2021, 497(1):75-80.
[20] GANDA E K, BISINOTTO R S, LIMA S F, et al. Longitudinal metagenomic profiling of bovine milk to assess the impact of intramammary treatment using a third-generation cephalosporin[J]. Sci Rep, 2016, 6:37565.
[21] KORSAK N, TAMINIAU B, HUPPERTS C, et al. Assessment of bacterial superficial contamination in classical or ritually slaughtered cattle using metagenetics and microbiological analysis[J]. Int J Food Microbiol, 2017, 247:79-86.
[22] NGUYEN T T, WU H M, NISHINO N. An investigation of seasonal variations in the microbiota of milk, feces, bedding, and airborne dust[J]. Asian-Australas J Anim Sci, 2020, 33(11):1858-1865.
[23] BI Y L, WANG Y J, QIN Y, et al. Prevalence of bovine mastitis pathogens in bulk tank milk in China[J]. PLoS One, 2016, 11(5):e0155621.
[24] PATEL S H, VAIDYA Y H, PATEL R J, et al. Culture independent assessment of human milk microbial community in lactational mastitis[J]. Sci Rep, 2017, 7(1):7804.
[25] GÁMEZ-VALDEZ J S, GARCÍA-MAZCORRO J F, RINCÓN A H M, et al. Compositional analysis of the bacterial community in colostrum samples from women with gestational diabetes mellitus and obesity[J]. Res Square, 2020.
[26] MARIN-GÓMEZ W, GRANDE M J, PÉREZ-PULIDO R, et al. Changes in the bacterial diversity of human milk during late lactation period (weeks 21 to 48)[J]. Foods, 2020, 9(9):1184.
[27] MA C, SUN Z, ZENG B H, et al. Cow-to-mouse fecal transplantations suggest intestinal microbiome as one cause of mastitis[J]. Microbiome, 2018, 6(1):200.
[28] LIU H Y, LI C X, LIANG Z Y, et al. Moraxellaceae and Moraxella interact with the altered airway mycobiome in asthma[J]. bioRxiv, 2019:525113.
[29] WU H M, WANG Y, DONG L, et al. Microbial characteristics and safety of dairy manure ComPosting for reuse as dairy bedding[J]. Biology (Basel), 2020, 10(1):13.
[30] MOON K, KANG I, KIM S, et al. Genomic and ecological study of two distinctive freshwater bacteriophages infecting a Comamonadaceae bacterium[J]. Sci Rep, 2018, 8(1):7989.
[31] RAULT L, LÉVÊQUE P A, BARBEY S, et al. Bovine teat cistern microbiota composition and richness are associated with the immune and microbial responses during transition to once-daily milking[J]. Front Microbiol, 2020, 11:602404.
[32] NGUYEN Q D, TSURUTA T, NISHINO N. Examination of milk microbiota, fecal microbiota, and blood metabolites of Jersey cows in cool and hot seasons[J]. Anim Sci J, 2020, 91(1):e13441.
[33] ANDREWS T, NEHER D A, WEICHT T R, et al. Mammary microbiome of lactating organic dairy cows varies by time, tissue site, and infection status[J]. PLoS One, 2019, 14(11):e0225001.
[34] VERDIER-METZ I, GAGNE G, BORNES S, et al. Cow teat skin, a potential source of diverse microbial populations for cheese production[J]. Appl Environ Microbiol, 2012, 78(2):326-333.
[35] DOYLE C J, O'TOOLE P W, COTTER P D. Metagenome-based surveillance and diagnostic approaches to studying the microbial ecology of food production and processing environments[J]. Environ Microbiol, 2017, 19(11):4382-4391.

基于SourceTracker分析牧场环境对乳房炎乳菌群的影响

Influence of Dairy Farm Environment on Mastitis Milk Microbiota via SourceTracker

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