Milk microbiome signatures of subclinical mastitis-affected cattle analysed by shotgun sequencing
Milk microbiome signatures of subclinical mastitis-affected cattle analysed by shotgun sequencing
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DOI：
10.1111/j.1365-2672.2012.05244.x
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发表时间：
2012-04-01
影响因子：
4
通讯作者：
Joshi, C. G.
中科院分区：
文献类型：
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作者：
Bhatt, V. D.;Ahir, V. B.;Joshi, C. G.
目的：采用新一代测序454 GS-FLX技术对患亚临床乳腺炎的Kankrej、Gir （Bos indicus）和杂交（Bos taurus x B. indicus）牛乳样品进行宏基因组分析，以阐明牛乳微生物群落结构。方法与结果：采用焦磷酸测序方法对Kankrej、Gir和杂交牛的牛奶样品进行宏基因组分析。元基因组分析产生的序列数据分别为6307,190,87700万碱基对（Mb），分别来自Kankrej， Gir和杂交牛的264 798,56 114和36 762个序列，平均读长分别为238,197和214个核苷酸。基于网络工具MGRAST的系统发育和代谢谱显示，乳乳中肠杆菌属的成员占主导地位，其次是假单胞菌属、芽胞杆菌属和乳杆菌属。在亚临床感染的乳汁中检测到56种不同丰度的菌种。Kankrej和Gir牛的优势菌种为大肠杆菌，其次为铜绿假单胞菌、mendocina假单胞菌、福氏志贺氏菌和蜡样芽孢杆菌。在杂交牛中检出的金黄色葡萄球菌依次为肺炎克雷伯菌、表皮葡萄球菌和大肠杆菌。代谢谱显示，微生物对氟喹诺酮类、甲氧西林类、铜类、钴锌镉类抗生素和有毒化合物具有耐药性。序列表明，潜在的生物体表现出对抗生素和有毒化合物的多药耐药性。有趣的是，存在抗葡萄球菌的噬菌体。金黄色葡萄球菌、大肠杆菌、肠杆菌和耶尔森氏菌也有检出。结论：通过对乳腺炎潜在感染菌的分析，确定了乳腺炎潜在感染菌对抗生素和化合物的耐药性，以及奶牛的天然耐药潜力。研究的意义和影响：本研究结果有助于制定奶牛乳腺炎的预防和治疗策略，从而减少因乳腺炎而造成的经济损失。
Aims: Metagenomic analysis of milk samples collected from Kankrej, Gir (Bos indicus) and crossbred (Bos taurus x B. indicus) cattle harbouring subclinical mastitis was carried out by next-generation sequencing 454 GS-FLX technology to elucidate the microbial community structure of cattle milk.Methods and Results: Milk samples from Kankrej, Gir and crossbred cattle were subjected to metagenomic profiling by pyrosequencing. The Metagenomic analysis produced 63 07, 11 09 and 7 87 million base pairs (Mb) of sequence data, assembled in 264 798, 56 114 and 36 762 sequences with an average read length of 238, 197 and 214 nucleotides in Kankrej, Gir and crossbred cattle, respectively. Phylogenetic and metabolic profiles by the web-based tool MGRAST revealed that the members of Enterobacteriales were predominant in mastitic milk followed by Pseudomonadales, Bacillales and Lactobacillales. Around 56 different species with varying abundance were detected in the subclinically infected milk. Escherichia coli was found to be the most predominant species in Kankrej and Gir cattle followed by Pseudomonas aeruginosa, Pseudomonas mendocina, Shigella flexneri and Bacillus cereus. In crossbred cattle, Staphylococcus aureus followed by Klebsiella pneumoniae, Staphylococcus epidermidis and E. coli were detected in descending order. Metabolic profiling indicated fluoroquinolones, methicillin, copper, cobalt-zinc-cadmium as the groups of antibiotics and toxic compounds to which the organisms showed resistance. Sequences indicating potential of organisms exhibiting multidrug resistance against antibiotics and resistance to toxic compounds were also present. Interestingly, presence of bacteriophages against Staph. aureus, E. coli, Enterobacter and Yersinia species was also observed.Conclusions: The analysis identified potential infectious organisms in mastitis, resistance of organisms to antibiotics and chemical compounds and the natural resistance potential of dairy cows. Significance and Impact of the Study: The findings of this study may help in formulating strategies for the prevention and treatment of mastitis in dairy animals and consequently in reducing economic losses incurred because of it.