Pacífico Cátia, Petri Renée Maxine, Ricci Sara, Mickdam Elsayed, Wetzels Stefanie Urimare, Neubauer Viktoria, Zebeli Qendrim
Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine, 1210 Vienna, Austria.
Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC J1M1Z7, Canada.
Microorganisms. 2021 Feb 9;9(2):342. doi: 10.3390/microorganisms9020342.
Numerous studies have used the 16S rRNA gene target in an attempt to characterize the structure and composition of the epimural microbiota in cattle. However, comparisons between studies are challenging, as the results show large variations associated with experimental protocols and bioinformatics methodologies. Here, we present a meta-analysis of the rumen epimural microbiota from 11 publicly available amplicon studies to assess key technical and biological sources of variation between experiments. Using the QIIME2 pipeline, 332 rumen epithelial microbiota samples were analyzed to investigate community structure, composition, and functional potential. Despite having a significant impact on microbial abundance, country of origin, farm, hypervariable region, primer set, animal variability, and biopsy location did not obscure the identification of a core microbiota. The bacterial genera , R-7 group, UCG-011, UCG-010, NK4A214 group, UCG-010, UCG-014, , , and spp. were found in nearly all epithelium samples (>90%). Predictive analysis (PICRUSt) was used to assess the potential functions of the epithelial microbiota. Regularized canonical correlation analysis identified several pathways associated with the biosynthesis of precursor metabolites in , , and NK4A214, highlighting key metabolic functions of these microbes within the epithelium.
许多研究使用16S rRNA基因靶点来试图描述牛的瘤胃壁微生物群的结构和组成。然而，由于结果显示与实验方案和生物信息学方法相关的巨大差异，不同研究之间的比较具有挑战性。在此，我们对11项公开的扩增子研究中的瘤胃壁微生物群进行荟萃分析，以评估实验之间关键的技术和生物学变异来源。使用QIIME2流程，对332个瘤胃上皮微生物群样本进行分析，以研究群落结构、组成和功能潜力。尽管原产国、农场、高变区、引物组、动物变异性和活检位置对微生物丰度有显著影响，但并未掩盖核心微生物群的识别。几乎在所有上皮样本中（>90%）都发现了细菌属、R-7组、UCG-011、UCG-010、NK4A214组、UCG-010、UCG-014、、和spp。使用预测分析（PICRUSt）来评估上皮微生物群的潜在功能。正则化典型相关分析确定了与、和NK4A214中前体代谢物生物合成相关的几种途径，突出了这些微生物在上皮内的关键代谢功能。
