UMR 1313 GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.
Animal Breeding and Genetics Program, IRTA Torre Marimon, Caldes de Montbui, Spain.
J Anim Breed Genet. 2020 Jan;137(1):49-59. doi: 10.1111/jbg.12427. Epub 2019 Aug 16.
Mitigation of greenhouse gas emissions is relevant for reducing the environmental impact of ruminant production. In this study, the rumen microbiome from Holstein cows was characterized through a combination of 16S rRNA gene and shotgun metagenomic sequencing. Methane production (CH ) and dry matter intake (DMI) were individually measured over 4-6 weeks to calculate the CH yield (CH y = CH /DMI) per cow. We implemented a combination of clustering, multivariate and mixed model analyses to identify a set of operational taxonomic unit (OTU) jointly associated with CH y and the structure of ruminal microbial communities. Three ruminotype clusters (R1, R2 and R3) were identified, and R2 was associated with higher CH y. The taxonomic composition on R2 had lower abundance of Succinivibrionaceae and Methanosphaera, and higher abundance of Ruminococcaceae, Christensenellaceae and Lachnospiraceae. Metagenomic data confirmed the lower abundance of Succinivibrionaceae and Methanosphaera in R2 and identified genera (Fibrobacter and unclassified Bacteroidales) not highlighted by metataxonomic analysis. In addition, the functional metagenomic analysis revealed that samples classified in cluster R2 were overrepresented by genes coding for KEGG modules associated with methanogenesis, including a significant relative abundance of the methyl-coenzyme M reductase enzyme. Based on the cluster assignment, we applied a sparse partial least-squares discriminant analysis at the taxonomic and functional levels. In addition, we implemented a sPLS regression model using the phenotypic variation of CH y. By combining these two approaches, we identified 86 discriminant bacterial OTUs, notably including families linked to CH emission such as Succinivibrionaceae, Ruminococcaceae, Christensenellaceae, Lachnospiraceae and Rikenellaceae. These selected OTUs explained 24% of the CH y phenotypic variance, whereas the host genome contribution was ~14%. In summary, we identified rumen microbial biomarkers associated with the methane production of dairy cows; these biomarkers could be used for targeted methane-reduction selection programmes in the dairy cattle industry provided they are heritable.
减少温室气体排放对于降低反刍动物生产的环境影响至关重要。在这项研究中，通过 16S rRNA 基因和 shotgun 宏基因组测序相结合，对荷斯坦奶牛的瘤胃微生物组进行了表征。通过 4-6 周的单独测量甲烷产量（CH ）和干物质摄入量（DMI），计算每头牛的 CH 产量（CH y = CH /DMI）。我们采用聚类、多变量和混合模型分析相结合的方法，确定了一组与 CH y 和瘤胃微生物群落结构共同相关的操作分类单元（OTU）。鉴定出 3 个反刍类型群（R1、R2 和 R3），其中 R2 与更高的 CH y 相关。R2 的分类组成中，琥珀酸菌科和产甲烷菌属的丰度较低，而瘤胃球菌科、克里斯滕森菌科和毛螺菌科的丰度较高。宏基因组数据证实了 R2 中琥珀酸菌科和产甲烷菌属的丰度较低，并确定了由分类分析未突出显示的属（纤维杆菌属和未分类拟杆菌门）。此外，功能宏基因组分析表明，归类于 R2 聚类的样本中与甲烷生成相关的 KEGG 模块编码基因的丰度较高，包括甲基辅酶 M 还原酶的相对丰度显著增加。基于聚类分配，我们在分类和功能水平上应用了稀疏偏最小二乘判别分析。此外，我们还使用 CH y 的表型变异实施了 sPLS 回归模型。通过结合这两种方法，我们鉴定了 86 个有区别的细菌 OTU，其中包括与 CH 排放相关的科，如琥珀酸菌科、瘤胃球菌科、克里斯滕森菌科、毛螺菌科和理研菌科。这些选定的 OTU 解释了 24%的 CH y 表型方差，而宿主基因组的贡献约为 14%。总之，我们确定了与奶牛甲烷生成相关的瘤胃微生物生物标志物；如果这些生物标志物具有遗传性，则可以将其用于奶牛养殖业的靶向甲烷减排选择计划。
