Investigation of fiber utilization in the rumen of dairy cows based on metagenome-assembled genomes and single-cell RNA sequencing.
Investigation of fiber utilization in the rumen of dairy cows based on metagenome-assembled genomes and single-cell RNA sequencing.
复制标题
基于宏基因组组装基因组和单细胞RNA测序对奶牛瘤胃中纤维利用情况的研究
DOI：
10.1186/s40168-021-01211-w
复制
发表时间：
2022-01-20
期刊：
影响因子：
15.5
通讯作者：
Sun HZ
中科院分区：
文献类型：
--
作者：
Xue MY;Wu JJ;Xie YY;Zhu SL;Zhong YF;Liu JX;Sun HZ
奶牛利用人类不能食用的低价值植物生物质生产牛奶，这是一种营养丰富、蛋白质含量高的低成本产品。这一过程很大程度上依赖于瘤胃微生物发酵木质纤维素和纤维素产生挥发性脂肪酸（VFA）。瘤胃复层鳞状上皮对VFA的吸收和部分代谢是由不同类型的细胞介导的。在这里，我们应用宏基因组分箱方法来探索参与纤维消化的单个微生物，并对瘤胃上皮细胞进行单细胞RNA测序，以研究有助于VFA吸收和代谢的细胞亚型。本试验所用52头泌乳中期奶牛（胎次2.62 ± 0.91），产奶量33.10 ± 6.72kg。我们使用宏基因组分箱确定了186个细菌基因组的纤维消化和发酵能力，并鉴定了具有与VFA生物合成高度相关的强纤维素/木聚糖/果胶降解能力的特定细菌基因组。此外，我们基于20，728个个体上皮细胞的转录组构建了由18个瘤胃上皮细胞亚型组成的瘤胃上皮单细胞图谱。对编码VFA转运蛋白候选物的基因的表达谱的系统调查显示，IGFBP 5 + CG样棘细胞独特地高度表达SLC 16 A1和SLC 4A 9，这表明这种细胞类型可能在VFA吸收中起重要作用。还确定了微生物组和宿主细胞之间的潜在串扰及其在调节关键瘤胃上皮细胞亚型中关键基因表达中的作用。我们发现了瘤胃中分别参与纤维消化、VFA摄取和代谢的关键微生物个体基因组和上皮细胞亚型。这些数据的整合使我们能够将微生物基因组和上皮单细胞与营养系统联系起来。视频摘要在线版本包含补充材料，可在10. 1186/s40168-021-01211-w。
Dairy cows utilize human-inedible, low-value plant biomass to produce milk, a low-cost product with rich nutrients and high proteins. This process largely relies on rumen microbes that ferment lignocellulose and cellulose to produce volatile fatty acids (VFAs). The VFAs are absorbed and partly metabolized by the stratified squamous rumen epithelium, which is mediated by diverse cell types. Here, we applied a metagenomic binning approach to explore the individual microbes involved in fiber digestion and performed single-cell RNA sequencing on rumen epithelial cells to investigate the cell subtypes contributing to VFA absorption and metabolism. The 52 mid-lactating dairy cows in our study (parity = 2.62 ± 0.91) had milk yield of 33.10 ± 6.72 kg. We determined the fiber digestion and fermentation capacities of 186 bacterial genomes using metagenomic binning and identified specific bacterial genomes with strong cellulose/xylan/pectin degradation capabilities that were highly associated with the biosynthesis of VFAs. Furthermore, we constructed a rumen epithelial single-cell map consisting of 18 rumen epithelial cell subtypes based on the transcriptome of 20,728 individual epithelial cells. A systematic survey of the expression profiles of genes encoding candidates for VFA transporters revealed that IGFBP5+ cg-like spinous cells uniquely highly expressed SLC16A1 and SLC4A9, suggesting that this cell type may play important roles in VFA absorption. Potential cross-talk between the microbiome and host cells and their roles in modulating the expression of key genes in the key rumen epithelial cell subtypes were also identified. We discovered the key individual microbial genomes and epithelial cell subtypes involved in fiber digestion, VFA uptake and metabolism, respectively, in the rumen. The integration of these data enables us to link microbial genomes and epithelial single cells to the trophic system. Video abstract The online version contains supplementary material available at 10.1186/s40168-021-01211-w.
登录
查看更多内容
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
DOI：
10.1093/bioinformatics/bts565
发表时间：
2012-12-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Fu L;Niu B;Zhu Z;Wu S;Li W
通讯作者：
Li W
影响因子：
2.7
作者：
Kang DD;Froula J;Egan R;Wang Z
通讯作者：
Wang Z
影响因子：
48
作者：
Korsunsky, Ilya;Millard, Nghia;Raychaudhuri, Soumya
通讯作者：
Raychaudhuri, Soumya
DOI：
10.1038/ismej.2016.62
发表时间：
2016-12
期刊：
The ISME journal
影响因子：
--
作者：
通讯作者：
--