Urea supplementation-induced changes of nickel-dependent microbial community lead to the reconstruction of rumen microbiome

Urease is a kind of Ni-dependent enzyme that requires cofactor Ni for its activity. This study investigated the role of Ni in the reshaping of rumen microbiome after urea supplementation. It was found that rumen ammonia concentration and urease activity were significantly increased, while SCFAs concentrations had no significant changes after urea supplementation. Standard on the genome completeness more than 60%, 57 bacteria consisting of five kinds of Ni-dependent enzymes were detected in the metagenomic sequences. For these bacteria, the relative abundances of bacteria with urease and acetyl-CoA synthase were significantly increased, while the relative abundances of bacteria with glyoxalase I, [NiFe]-hydrogenase and lactate racemase, as well as that of the whole community, were significantly decreased after urea supplementation. Meantime, the functional modules related to the AA, glucose and lipid metabolism, as well as sulphur and nitrogen fixation, were significantly changed after urea supplementation. For the rumen microbiome, its structure and the functional modules related to the lipid and glucose metabolism were significantly changed after urea supplementation. These finding suggested that the reconstruction of rumen microbiome was induced by the compositional and functional changes of Ni-dependent microbial community after urea supplementation.

脲酶（Urease）是一类镍依赖性酶（Ni-dependent enzyme），其活性需要辅因子（cofactor）镍。本研究探讨了尿素添加（urea supplementation）后，镍在瘤胃微生物组（rumen microbiome）重塑过程中的作用。研究发现，尿素添加后瘤胃氨浓度（ammonia concentration）与脲酶活性（urease activity）显著升高，而短链脂肪酸（SCFAs）浓度无显著变化。按照基因组完整性（genome completeness）大于60%的筛选标准，在宏基因组序列（metagenomic sequences）中检测到57种携带有5类镍依赖性酶的细菌。对于这些细菌而言，携带脲酶与乙酰辅酶A合成酶（acetyl-CoA synthase）的细菌相对丰度显著升高；而携带乙二醛酶I（glyoxalase I）、镍铁氢化酶（[NiFe]-hydrogenase）与乳酸消旋酶（lactate racemase）的细菌相对丰度，以及整体菌群的相对丰度，在尿素添加后均显著降低。与此同时，与氨基酸（AA）、葡萄糖和脂质代谢，以及硫代谢和固氮作用（nitrogen fixation）相关的功能模块（functional modules），在尿素添加后均发生显著改变。就瘤胃微生物组而言，其群落结构以及与脂质和葡萄糖代谢相关的功能模块，在尿素添加后均发生显著变化。上述研究结果表明，尿素添加后，镍依赖性微生物群落的组成与功能变化可诱导瘤胃微生物组发生重构。