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Dong Q, Hua D, Wang X, Jiao Y, Liu L, Deng Q, Wu T, Zou H, Zhao C, Wang C, Reng J, Ding L, Hu S, Shi J, Wang Y, Zhang H, Sheng Y, Sun W, Shen Y, Tang L, Kong X, Chen L. Temporal colonization and metabolic regulation of the gut microbiome in neonatal oxen at single nucleotide resolution. ISME J 2024; 18:wrad022. [PMID: 38365257 PMCID: PMC10833086 DOI: 10.1093/ismejo/wrad022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/19/2023] [Accepted: 12/06/2023] [Indexed: 02/18/2024]
Abstract
The colonization of microbes in the gut is key to establishing a healthy host-microbiome symbiosis for newborns. We longitudinally profiled the gut microbiome in a model consisting of 36 neonatal oxen from birth up to 2 months postpartum and carried out microbial transplantation to reshape their gut microbiome. Genomic reconstruction of deeply sequenced fecal samples resulted in a total of 3931 metagenomic-assembled genomes from 472 representative species, of which 184 were identified as new species when compared with existing databases of oxen. Single nucleotide level metagenomic profiling shows a rapid influx of microbes after birth, followed by dynamic shifts during the first few weeks of life. Microbial transplantation was found to reshape the genetic makeup of 33 metagenomic-assembled genomes (FDR < 0.05), mainly from Prevotella and Bacteroides species. We further linked over 20 million microbial single nucleotide variations to 736 plasma metabolites, which enabled us to characterize 24 study-wide significant associations (P < 4.4 × 10-9) that identify the potential microbial genetic regulation of host immune and neuro-related metabolites, including glutathione and L-dopa. Our integration analyses further revealed that microbial genetic variations may influence the health status and growth performance by modulating metabolites via structural regulation of their encoded proteins. For instance, we found that the albumin levels and total antioxidant capacity were correlated with L-dopa, which was determined by single nucleotide variations via structural regulations of metabolic enzymes. The current results indicate that temporal colonization and transplantation-driven strain replacement are crucial for newborn gut development, offering insights for enhancing newborn health and growth.
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Affiliation(s)
- Quanbin Dong
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing 210029, China
| | - Dongxu Hua
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing 210029, China
| | - Xiuchao Wang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing 210029, China
- Changzhou Medical Center, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Nanjing Medical University, Changzhou 213164, China
| | - Yuwen Jiao
- Changzhou Medical Center, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Nanjing Medical University, Changzhou 213164, China
| | - Lu Liu
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing 210029, China
| | - Qiufeng Deng
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing 210029, China
| | - Tingting Wu
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing 210029, China
| | - Huayiyang Zou
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing 210029, China
| | - Chen Zhao
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing 210029, China
| | - Chengkun Wang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing 210029, China
| | - Jiafa Reng
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing 210029, China
| | - Luoyang Ding
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Shixian Hu
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Jing Shi
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing 210029, China
| | - Yifeng Wang
- Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, Suzhou Municipal Hospital, Suzhou 215006, China
| | - Haifeng Zhang
- Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, Suzhou Municipal Hospital, Suzhou 215006, China
| | - Yanhui Sheng
- Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, Suzhou Municipal Hospital, Suzhou 215006, China
| | - Wei Sun
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing 210029, China
| | - Yizhao Shen
- College of Animal Science and Technology, Hebei Agricultural University, Baoding 071000, China
| | - Liming Tang
- Changzhou Medical Center, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Nanjing Medical University, Changzhou 213164, China
| | - Xiangqing Kong
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing 210029, China
- Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, Suzhou Municipal Hospital, Suzhou 215006, China
| | - Lianmin Chen
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing 210029, China
- Changzhou Medical Center, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Nanjing Medical University, Changzhou 213164, China
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