Milk microbiome in dairy cattle and the challenges of low microbial biomass and exogenous contamination.
Milk microbiome in dairy cattle and the challenges of low microbial biomass and exogenous contamination.
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DOI：
10.1186/s42523-021-00144-x
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发表时间：
2021-11-18
影响因子：
4.7
通讯作者：
Hutchings MR
中科院分区：
文献类型：
--
作者：
Pollock J;Salter SJ;Nixon R;Hutchings MR
由于对抗菌素耐药性的担忧，奶牛在哺乳期结束(或“干燥”)时全面使用抗菌剂受到越来越多的审查。为了减少奶牛养殖场中抗菌剂的使用，现在鼓励农民使用“选择性干牛疗法”，即只给被视为乳房炎高风险的奶牛注射抗菌剂。重要的是要更好地了解这种做法如何影响乳房相关的微生物区系，以及对农场中流通的抗菌素耐药细菌种群的潜在连锁反应。然而，由于已知对微生物组数据集的污染影响，在研究牛奶等低生物量环境方面存在挑战。在这里，我们采集了牛在干燥时和产犊时的牛奶样本，以测量细菌负荷和微生物群组成的潜在变化，并对污染影响进行了关键评估。有几个样本没有检测到16S rRNA基因拷贝，关键是，在初始微生物组数据集中检测到了外源污染。受影响的样品被从最终的微生物组分析中删除，这影响了实验设计和统计分析。不同处理间的细菌负荷差异不显著(P >； 0.039)，但产犊时的细菌负荷低于干燥时(P = 0.05)。在细菌负荷减少、微生物组丰富度和多样性呈下降趋势的情况下，从测序和培养数据来看，大肠埃希菌数量都显著增加。牛奶样本显示了不同的微生物群，并不能反映典型的感染情况，主要由肠道和皮肤相关的分类群组成，前者在长时间密封乳头后略有下降。干燥时间对微生物区系组成和细菌负荷有重要影响，但与抗菌剂的使用无关。烘干处理方案和牛奶微生物群落动态之间的相互作用显然是复杂的，我们对这些相互作用的评估受到低生物量样品和污染影响的限制。因此，我们的分析将为未来研究的设计提供参考，以确定是否可以实施不同的选择方案，以进一步减少抗菌素的使用。网上版载有补充材料，可在10.1186/s42523-021-00144-x查阅。
The blanket usage of antimicrobials at the end of lactation (or “drying off”) in dairy cattle is under increasing scrutiny due to concerns about antimicrobial resistance. To lower antimicrobial usage in dairy farming, farmers are now encouraged to use “selective dry cow therapy” whereby only cows viewed as at high risk of mastitis are administered antimicrobial agents. It is important to gain a better understanding of how this practice affects the udder-associated microbiota and the potential knock-on effects on antimicrobial-resistant bacterial populations circulating on the farm. However, there are challenges associated with studying low biomass environments such as milk, due to known contamination effects on microbiome datasets. Here, we obtained milk samples from cattle at drying off and at calving to measure potential shifts in bacterial load and microbiota composition, with a critical assessment of contamination effects. Several samples had no detectable 16S rRNA gene copies and crucially, exogenous contamination was detected in the initial microbiome dataset. The affected samples were removed from the final microbiome analysis, which compromised the experimental design and statistical analysis. There was no significant difference in bacterial load between treatments (P > 0.05), but load was lower at calving than at drying off (P = 0.039). Escherichia coli counts by both sequence and culture data increased significantly in the presence of reduced bacterial load and a decreasing trend of microbiome richness and diversity. The milk samples revealed diverse microbiomes not reflecting a typical infection profile and were largely comprised of gut- and skin-associated taxa, with the former decreasing somewhat after prolonged sealing of the teats. The drying off period had a key influence on microbiota composition and bacterial load, which appeared to be independent of antimicrobial usage. The interactions between drying off treatment protocol and milk microbiome dynamics are clearly complex, and our evaluations of these interactions were restricted by low biomass samples and contamination effects. Therefore, our analysis will inform the design of future studies to establish whether different selection protocols could be implemented to further minimise antimicrobial usage. The online version contains supplementary material available at 10.1186/s42523-021-00144-x.