固体日粮影响山羊瘤胃微生物群、上皮转录组学和蛋白质组学数据集-动脉网

Dataset of the rumen microbiota and epithelial transcriptomics and proteomics in goat affected by solid diets

Nature 等信源发布 2024-07-10 16:57

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AbstractAlthough early solid diet supplementation is a common practice to improve the growth and development in goat kids, its biological mechanism how solid diet induces rumen microbiota and epithelial development is still unknow. In this study, rumen fermentation parameters, 16S rRNA sequencing for rumen content and epithelial microbiota, transcriptomics and proteomics of epithelium were determined to classify the effects of solid diet supplementation.

摘要尽管早期固体饮食补充是改善山羊儿童生长发育的常见做法，但其固体饮食诱导瘤胃微生物群和上皮发育的生物学机制尚不清楚。在这项研究中，确定了瘤胃发酵参数，瘤胃含量和上皮微生物群的16S rRNA测序，上皮的转录组学和蛋白质组学，以分类固体饮食补充的效果。

Here, we classified the changes of goat phenotypes (i.e., growth performance, rumen fermentation and development) and linked them to the changes of rumen microbiota, transcriptome and expressed proteins. The mechanism of solid diet improving rumen development was elucidated preliminarily. Moreover, different roles between the rumen content and epithelial microbiota were identified.

在这里，我们对山羊表型的变化（即生长性能，瘤胃发酵和发育）进行了分类，并将其与瘤胃微生物群，转录组和表达蛋白的变化联系起来。。此外，确定了瘤胃内容物和上皮微生物群之间的不同作用。

Thess datasets expands our understanding of the association between the early diet intervention and rumen development, providing the useful information how nutrient strategy affects rumen function and subsequently improves the host growth. The generated data provides insights in the importance of rumen niche microbiota and microbe-host interactions, which benefits future studies..

这些数据集扩展了我们对早期饮食干预与瘤胃发育之间关系的理解，提供了营养策略如何影响瘤胃功能并随后改善宿主生长的有用信息。产生的数据提供了瘤胃生态位微生物群和微生物-宿主相互作用重要性的见解，这有利于未来的研究。。

Background & SummaryAs one of the most important livestock specie in the world, the goat (Capra hircus) provides various types of products for human consumption, such as meat, milk, pelts and fiber1,2. Now, there are over 1,000 goat breeds and total goat amount is over 1 billion globally3. The rumen, the most critical digestive organ for ruminants, can degrade the high fiber-based plant components into volatile fatty acids (VFA) and microbial protein for rumen development and body nutrient requirement via microbial fermentation process4.

背景与总结山羊（Capra hircus）是世界上最重要的牲畜品种之一，为人类提供各种类型的消费产品，如肉、牛奶、毛皮和纤维。。瘤胃是反刍动物最关键的消化器官，可以通过微生物发酵过程将高纤维植物成分降解为挥发性脂肪酸（VFA）和微生物蛋白质，用于瘤胃发育和身体营养需求4。

The ability to digest fiber is the evidence of the well-developed and functional rumen in young ruminants5. However, the rumen of goat kids develops rapidly after born. Manipulation the early development of rumen becomes the most effective way to improve life-long rumen function and animal growth6,7.

。然而，山羊宝宝出生后瘤胃发育迅速。操纵瘤胃的早期发育成为改善终身瘤胃功能和动物生长的最有效途径6,7。

Early supplementation of a concentrate diet has already been widely used in ruminant production to improve its rumen and body development because of its stimulation of microbial proliferation and VFA production that initiates epithelial development8,9,10,11. However, the biological mechanism of this practise is still unclear.Previous studies have demonstrated that early feeding starter with high grains or even alfalfa changed the rumen microbiota and improved animal growth12,13,14.

早期补充浓缩饲料已被广泛用于反刍动物生产，以改善其瘤胃和身体发育，因为它刺激微生物增殖和VFA产生，从而启动上皮发育8,9,10,11。然而，这种做法的生物学机制仍不清楚。先前的研究表明，高谷物甚至苜蓿的早期饲喂起子改变了瘤胃微生物群并改善了动物的生长[12,13,14]。

However, most studies focused on the rumen content microbiome until now, and less researches have been conducted to determine the microbiota attached on the rumen epithelium and the rumen epithelial transcriptomics and proteomics. The rumen epithelial microbiota associated with the content microbial community might be critical for nutrient absorption as it tightly attaches on the luminal side of the rumen15,16,17.

然而，到目前为止，大多数研究都集中在瘤胃内容物微生物组上，很少有研究确定附着在瘤胃上皮上的微生物群以及瘤胃上皮转录组学和蛋白质组学。与内容物微生物群落相关的瘤胃上皮微生物群可能对营养吸收至关重要，因为它紧密附着在瘤胃的腔侧15,16,17。

A previous study found differing community struct.

之前的一项研究发现不同的社区结构。

Code availability

代码可用性

Serum enzyme activity, antioxidant capacity, and immune parameter were statistically processed and analyzed using R version 3.6.0, default parameters or parameters recommended by the developer were used. A reproducible version of partial microbiome analysis and computer code is available at https://github.com/chaichai9521/goat-rumen-mcirobiome-analysis.git..

使用R版本3.6.0对血清酶活性，抗氧化能力和免疫参数进行统计处理和分析，使用默认参数或开发人员推荐的参数。部分微生物组分析和计算机代码的可重复版本可在https://github.com/chaichai9521/goat-rumen-mcirobiome-analysis.git..

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NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP199804 (2019).NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP236061 (2019).ProteomeXchange Consortium https://www.iprox.cn/page/project.html?id=IPX0007706000 (2023).Download referencesAcknowledgementsThis study was funded in part by grants from the National Key Research and Development Program (2022YFA1304201), the National Natural Science Foundation of China (31872385, 32222081), and the Inner Mongolia Science and Technology Key Project (2021SZD0014).Author informationAuthors and AffiliationsGuangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, 528225, ChinaJianmin Chai, Feilong Deng & Ying LiInstitute of Feed Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Beijing, 100081, ChinaJianmin Chai, Xiaokang Lv, Yimin Zhuang, Qiyu Diao, Kai Cui & Naifeng ZhangDepartment of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR, 72701, USAJianmin ChaiAnhui Province Key Laboratory of Animal Nutritional Regulation and Health, College of Animal Science, Anhui Science and Technology University, Chuzhou, ChinaXiaokang LvAuthorsJianmin ChaiView author publicationsYou can also search for this author in.

NCBI序列读取存档https://identifiers.org/ncbi/insdc.sra:SRP199804（2019年）。NCBI序列读取存档https://identifiers.org/ncbi/insdc.sra:SRP236061（2019年）。https://www.iprox.cn/page/project.html?id=IPX0007706000（2023年）。下载参考文献致谢本研究部分由国家重点研究发展计划（2022YFA1304201），国家自然科学基金（318723853222081）和内蒙古科技重点项目（2021SZD0014）资助。作者信息作者和附属机构广东省动物分子设计与精密育种重点实验室，佛山大学生命科学与工程学院，佛山，528225，中国柴建民，费隆邓和英利中国农业科学院饲料研究所，农业和农村事务部饲料生物技术重点实验室，北京，100081，中国柴建民，吕晓康，庄益民，齐玉刁，崔凯和张乃峰阿肯色大学农业系，阿肯色州费耶特维尔，72701，USAJianmin ChaiAnhui安徽省动物科学学院动物营养调控与健康重点实验室中国滁州科技大学吕晓康作者柴建民作者出版物您也可以在中搜索该作者。

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PubMed Google ScholarContributionsJ.C. X.L. and Y.Z. contributed to animal trials, and sample collection. J.C. contributed to data analysis, visualization, primary drafting, and proof. Q.D., and K.C. helped with sample collection and investigation. F.D. and Y.L. contributed to proof and revision.

PubMed谷歌学术贡献。C、 X.L.和Y.Z.为动物试验和样品采集做出了贡献。J、 C.为数据分析，可视化，初步起草和证明做出了贡献。Q、 D.和K.C.帮助进行样本收集和调查。F、 D.和Y.L.为证明和修订做出了贡献。

N.Z. contributed to the experimental design, visualization, project management, and draft proof. All authors have read and agreed to the published version of the manuscript.Corresponding authorCorrespondence to.

N、 Z.为实验设计，可视化，项目管理和草案证明做出了贡献。所有作者都阅读并同意手稿的出版版本。对应作者对应。

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Reprints and permissionsAbout this articleCite this articleChai, J., Lv, X., Zhuang, Y. et al. Dataset of the rumen microbiota and epithelial transcriptomics and proteomics in goat affected by solid diets.

转载和许可本文引用本文Chai，J.，Lv，X.，Zhuang，Y。等人受固体饮食影响的山羊瘤胃微生物群和上皮转录组学和蛋白质组学数据集。

Sci Data 11, 749 (2024). https://doi.org/10.1038/s41597-024-03584-7Download citationReceived: 10 January 2024Accepted: 28 June 2024Published: 10 July 2024DOI: https://doi.org/10.1038/s41597-024-03584-7Share this articleAnyone you share the following link with will be able to read this content:Get shareable linkSorry, a shareable link is not currently available for this article.Copy to clipboard.

Sci数据11749（2024）。https://doi.org/10.1038/s41597-024-03584-7Download引文收到日期：2024年1月10日接受日期：2024年6月28日发布日期：2024年7月10日OI：https://doi.org/10.1038/s41597-024-03584-7Share本文与您共享以下链接的任何人都可以阅读此内容：获取可共享链接对不起，本文目前没有可共享的链接。复制到剪贴板。

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细菌宿主反应蛋白质组学转录组学

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