Microbiota-host crosstalk in the newborn and adult rumen at single-cell resolution.
Microbiota-host crosstalk in the newborn and adult rumen at single-cell resolution.
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微生物群--在单细胞分辨率下，新生儿和成人瘤胃中的宿主串扰。
DOI：
10.1186/s12915-022-01490-1
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发表时间：
2022-12-14
期刊：
影响因子：
5.4
通讯作者：
Sun, Hui-Zeng
中科院分区：
文献类型：
--
作者：
Wu, Jia-Jin;Zhu, Senlin;Tang, Yi-Fan;Gu, Fengfei;Liu, Jian-Xin;Sun, Hui-Zeng
关键词：
瘤胃是反刍动物的标志性器官，在反刍动物的营养和为人类提供产品方面起着至关重要的作用。在新生哺乳反刍动物中，乳汁绕过瘤胃，而在成年反刍动物中，前胃的第一个腔室已经发展成为植物纤维微生物发酵的主要场所。随着单细胞转录组学的出现，现在可以研究瘤胃组织的基本细胞组成，并研究这与瘤胃及其上皮附着微生物之间互利共生关系的发展。我们构建了一个全面的细胞景观的瘤胃上皮，基于单细胞RNA测序的49,689高质量的单细胞从新生儿和成年瘤胃组织。我们的单细胞分析鉴定了瘤胃的6种免疫细胞亚型和17种非免疫细胞亚型。对牛瘤胃上皮细胞和人胃及皮肤上皮细胞中表达的orthostransferase基因进行跨种属分析时，我们观察到种属差异压倒了任何跨种属细胞类型相似性。成年牛和新生牛瘤胃组织中上皮细胞亚型较少，免疫细胞数量较多，以辅助性T细胞17型为主。在新生儿中，有更多的成纤维细胞和肌成纤维细胞，这是一种在成人中未见的IGFBP 3+上皮细胞亚型，而树突状细胞是最普遍的免疫细胞亚型。代谢相关功能和氧化还原过程显着上调成年瘤胃上皮细胞。利用16 SrDNA测序、荧光原位杂交和绝对定量实时PCR技术，我们发现上皮脱硫弧菌在成年牛中显著富集。整合瘤胃组织的微生物组和代谢物组分析显示，与新生牛相比，脱硫弧菌与吡哆醛在成年牛中的共现概率较高，而scRNA-seq数据表明，成年瘤胃上皮细胞亚型中的焦氧化物结合能力更强。这些结果表明，脱硫弧菌和吡哆醛可能在维持成年瘤胃氧化还原平衡中发挥重要作用。我们的综合多组学分析为瘤胃发育和功能提供了新的见解，并可能有助于未来精确改善牛的瘤胃功能和乳/肉生产。在线版本包含补充材料，可通过10.1186/s12915-022-01490-1获得。
The rumen is the hallmark organ of ruminants, playing a vital role in their nutrition and providing products for humans. In newborn suckling ruminants milk bypasses the rumen, while in adults this first chamber of the forestomach has developed to become the principal site of microbial fermentation of plant fibers. With the advent of single-cell transcriptomics, it is now possible to study the underlying cell composition of rumen tissues and investigate how this relates the development of mutualistic symbiosis between the rumen and its epithelium-attached microbes. We constructed a comprehensive cell landscape of the rumen epithelium, based on single-cell RNA sequencing of 49,689 high-quality single cells from newborn and adult rumen tissues. Our single-cell analysis identified six immune cell subtypes and seventeen non-immune cell subtypes of the rumen. On performing cross-species analysis of orthologous genes expressed in epithelial cells of cattle rumen and the human stomach and skin, we observed that the species difference overrides any cross-species cell-type similarity. Comparing adult with newborn cattle samples, we found fewer epithelial cell subtypes and more abundant immune cells, dominated by T helper type 17 cells in the rumen tissue of adult cattle. In newborns, there were more fibroblasts and myofibroblasts, an IGFBP3+ epithelial cell subtype not seen in adults, while dendritic cells were the most prevalent immune cell subtype. Metabolism-related functions and the oxidation-reduction process were significantly upregulated in adult rumen epithelial cells. Using 16S rDNA sequencing, fluorescence in situ hybridization, and absolute quantitative real-time PCR, we found that epithelial Desulfovibrio was significantly enriched in the adult cattle. Integrating the microbiome and metabolome analysis of rumen tissues revealed a high co-occurrence probability of Desulfovibrio with pyridoxal in the adult cattle compared with newborn ones while the scRNA-seq data indicated a stronger ability of pyroxidal binding in the adult rumen epithelial cell subtypes. These findings indicate that Desulfovibrio and pyridoxal likely play important roles in maintaining redox balance in the adult rumen. Our integrated multi-omics analysis provides novel insights into rumen development and function and may facilitate the future precision improvement of rumen function and milk/meat production in cattle. The online version contains supplementary material available at 10.1186/s12915-022-01490-1.
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影响因子：
44.1
作者：
Guo J;Grow EJ;Mlcochova H;Maher GJ;Lindskog C;Nie X;Guo Y;Takei Y;Yun J;Cai L;Kim R;Carrell DT;Goriely A;Hotaling JM;Cairns BR
通讯作者：
Cairns BR
影响因子：
48
作者：
Callahan BJ;McMurdie PJ;Rosen MJ;Han AW;Johnson AJ;Holmes SP
通讯作者：
Holmes SP
影响因子：
2.9
作者：
Chu J;Zhang T;He K
通讯作者：
He K
影响因子：
4.4
作者：
AMANN, RI;STROMLEY, J;STAHL, DA
通讯作者：
STAHL, DA
瘤胃上皮群落共享核心细菌菌群：16S rRNA基因Illumina Miseq测序数据集的荟萃分析。
影响因子：
5.2
作者：
Anderson CJ;Koester LR;Schmitz-Esser S
通讯作者：
Schmitz-Esser S