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与人类肠道菌群的结构缺陷有关，因此控制其初始化和发育的原理和机制具有相当大的科学意义和临床意义。但是，我们目前对肠道微生物生长动力学的了解仍然不完整。我们使用最近引入的SameStr程序对菌株水平的微生物群进行了分析，并检测了微生物菌株的转移和转移，对1900多个新生儿，婴儿，青少年及其家庭的可用宏基因组shot弹枪样本进行了大规模，综合的荟萃分析。坚持不懈。我们发现粪便微生物群组成与年龄以及分娩方式之间存在稳固的关联，这可以测量长达两年的生命。剖腹产与非肠道菌种的相对丰度增加和从主要耐氧性向不耐性微生物群落的转换延迟有关。基于共享菌株概况的无人监督网络生成了连接婴儿，其兄弟姐妹，父母和祖父母的特定于家庭的簇，在一种情况下，建议在同一医院病房的新生儿之间进行菌株转移，但也可用于识别潜在的标签错误的元基因组样本。与剖腹产婴儿相比，经阴道分娩的新生儿与母亲分担的毒株更多，但如果母亲接受抗生素治疗，分担的分担会减少。共有的菌株在整个生命的第一年中一直存在于婴儿中，并且与成人和父母之间共享的菌株属于同一细菌种类。不论分娩类型如何，年龄较大的孩子都与母亲和父亲分担了毒株，到成年后，就可以准确地将它们与无关的样本对区分开。粪便中常见的共生细菌都是经常转移的（例如杆菌和Sutterella）和新获取的类群（例如Blautia，Faecalibacterium，和瘤胃球菌）。我们的荟萃分析比以前的研究提供了更动态，更全面的新生儿和婴儿粪便微生物群发育的图景，并提供了自然或剖腹产婴儿生命早期的分类学和功能成分差异的证据，这种差异一直持续到青春期。