Department of Microbiome Research and Applied Bioinformatics, University of Hohenheim, Stuttgart, Germany.
Department of Microbiome Research and Applied Bioinformatics, University of Hohenheim, Stuttgart, Germany; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
Int J Med Microbiol. 2021 Apr;311(3):151483. doi: 10.1016/j.ijmm.2021.151483. Epub 2021 Feb 25.
As many inflammatory and metabolic disorders have been associated with structural deficits of the human gut microbiota, the principles and mechanisms that govern its initialization and development are of considerable scientific interest and clinical relevance. However, our current understanding of the developing gut microbiota dynamics remains incomplete. We carried out a large-scale, comprehensive meta-analysis of over 1900 available metagenomic shotgun samples from neonates, infants, adolescents, and their families, using our recently introduced SameStr program for strain-level microbiota profiling and the detection of microbial strain transfer and persistence. We found robust associations between fecal microbiota composition and age, as well as delivery mode, which was measurable for up to two years of life. C-section was associated with increased relative abundances of non-gut species and delayed transition from a predominantly oxygen-tolerant to intolerant microbial community. Unsupervised networks based on shared strain profiles generated family-specific clusters connecting infants, their siblings, parents and grandparents and, in one case, suggested strain transfer between neonates from the same hospital ward, but could also be used to identify potentially mislabeled metagenome samples. Vaginally delivered newborns shared more strains with their mothers than C-section infants, but strain sharing was reduced if mothers underwent antibiotic treatment. Shared strains persisted in infants throughout the first year of life and belonged to the same bacterial species as strains that were shared between adults and their parents. Irrespective of delivery type, older children shared strains with their mothers and fathers and, into adulthood, could be accurately distinguished from unrelated sample pairs. Prominent fecal commensal bacteria were both among frequently transferred (e.g. Bacteroides and Sutterella) and newly acquired taxa (e.g. Blautia, Faecalibacterium, and Ruminococcus). Our meta-analysis presents a more detailed and comprehensive picture of the highly dynamic neonatal and infant fecal microbiota development than previous studies and presents evidence for taxonomic and functional compositional differences early in life between infants born naturally or by C-section, which persist well into adolescence.
由于许多炎症和代谢性疾病都与人体肠道微生物群落的结构缺陷有关，因此，指导其初始形成和发展的原理和机制具有重要的科学意义和临床相关性。然而，我们目前对肠道微生物群动态发展的理解并不完整。我们利用最近开发的 SameStr 程序进行了一项大规模的、全面的元分析，该程序用于进行基于菌株水平的微生物群分析以及检测微生物菌株的转移和持久性，共分析了 1900 多个来自新生儿、婴儿、青少年及其家庭的宏基因组鸟枪法样本。我们发现粪便微生物群落的组成与年龄以及分娩方式之间存在很强的关联，而且这种关联在生命的两年内都可以测量到。与自然分娩相比，剖宫产会增加非肠道物种的相对丰度，并延迟从以耐氧气为主的微生物群落向不耐氧微生物群落的过渡。基于共享菌株谱的无监督网络生成了特定家庭的聚类，将婴儿、他们的兄弟姐妹、父母和祖父母联系在一起，在一个案例中，甚至表明同一医院病房的新生儿之间存在菌株转移，但也可用于识别潜在的错误标记的宏基因组样本。与剖宫产婴儿相比，经阴道分娩的新生儿与母亲共享的菌株更多，但如果母亲接受抗生素治疗，菌株共享则会减少。共享菌株在婴儿的整个第一年中都存在于婴儿体内，并与成年人与其父母之间共享的菌株属于同一细菌物种。无论分娩类型如何，较大的儿童都与他们的母亲和父亲共享菌株，而且成年后，他们可以与无亲缘关系的样本对准确区分开。常见的粪便共生细菌既存在于经常转移的细菌中（例如拟杆菌和萨特氏菌），也存在于新获得的分类群中（例如布劳特氏菌、粪杆菌和真杆菌）。我们的元分析比以前的研究更详细和全面地展示了高度动态的新生儿和婴儿粪便微生物群发展情况，并提供了证据表明，自然分娩和剖宫产出生的婴儿在生命早期就存在分类学和功能组成上的差异，这些差异在青少年时期仍然存在。
