Supporting data for "Early microbial intervention reshapes phenotypes of newborn Bos taurus through metabolic regulations"

The rumen of neonatal calves has limited functionality and establishing intestinal microbiota may play a crucial role in their health and performance. We aim to explore the temporal colonization of the gut microbiome and the benefits of early microbial intervention in newborn calves. We evaluated the impact of microbiota transplantation (MT) on metabolism and later milk production performance. <br>We followed 36 newborn calves for two months and found that the composition and ecological interactions of their gut microbiomes likely reached maturity one month after birth. Temporal changes in the gut microbiome of newborn calves are widely associated with changes in their physiological statuses, such as growth and fiber digestion. Importantly, we observed that MT reshapes the gut microbiome of newborns by altering the abundance and interaction of <i>Bacteroides</i> species, as well as amino acid pathways, such as arginine biosynthesis. Two-year follow-up of those calves further showed that MT improves their later milk production. Notably, MT improves fiber digestion, antioxidant capacity of newborns while reducing diarrhea. MT also contributes to significant changes in the metabolomic landscape, and with putative causal mediation analysis, we suggest that altered gut microbial composition in newborns may influence physiological status through microbial-derived metabolites. <br>Our study provides metagenomic and metabolomic atlas of the temporal development of the gut microbiome in newborn calves. MT can alter the gut microbiome of newborns, leading to improved physiological status and later milk production. The data may help develop strategies to manipulate the gut microbiota during early life, which may be relevant to the health and production of newborn calves.

新生犊牛的瘤胃功能有限，建立肠道菌群（gut microbiota）对其健康与生产性能至关重要。本研究旨在探究新生犊牛肠道微生物组（gut microbiome）的时序定植规律，以及早期微生物干预对新生犊牛的益处。我们评估了微生物移植（microbiota transplantation, MT）对犊牛代谢及后期产奶性能的影响。
我们对36头新生犊牛开展了为期2个月的跟踪监测，结果显示其肠道微生物组的组成与生态互作关系在出生后1个月左右即趋于成熟。新生犊牛肠道微生物组的时序变化与其生长、纤维消化等生理状态的改变显著相关。值得关注的是，本研究观察到微生物移植可通过改变拟杆菌属（Bacteroides）物种的丰度及其互作模式，以及精氨酸生物合成（arginine biosynthesis）等氨基酸代谢通路，重塑新生犊牛的肠道微生物组。对这些犊牛的2年跟踪随访进一步证实，微生物移植可提升其后期产奶性能。尤为关键的是，微生物移植可改善新生犊牛的纤维消化能力与抗氧化能力，同时降低腹泻发生率。此外，微生物移植还可使代谢组（metabolomic）全景发生显著改变；通过潜在因果中介分析（putative causal mediation analysis），我们推测新生犊牛肠道微生物组成的改变可通过微生物衍生代谢物影响其生理状态。
本研究构建了新生犊牛肠道微生物组时序发育的宏基因组（metagenomic）与代谢组图谱。微生物移植可改变新生犊牛的肠道微生物组，进而改善其生理状态与后期产奶性能。本研究的数据可为开发早期肠道菌群调控策略提供参考，此类策略或与新生犊牛的健康及生产性能密切相关。