Microbial dispersal, skin-to-skin contact, and assembly of the neonatal gut microbiome

与人类相关的微生物群落，称为人类微生物组，为其宿主提供许多重要的有益服务。然而，尽管它们很重要，我们仍然对微生物群落形成的基本过程知之甚少。了解新生儿出生后微生物组的组装对于设计干预措施以操纵它们以改善健康和发育是必要的。一般来说，微生物组组装被认为是微生物分散和宿主选择的产物，这两者都可能在新生儿重症监护病房（NICUs）的新生儿中被破坏。新生儿重症监护病房提供了一个卫生的环境，共生微生物传播的机会相对有限，宿主选择对驻留微生物群的影响可能受到新生儿生理改变和发育不全状态的影响。描述可能增加共生体传播的因素的影响，如父母和新生儿之间的皮肤接触护理，或改变宿主选择的性质，如免疫系统的发育，将使我们对生命早期微生物组的组装有更深入的了解。我们建议研究新生儿微生物组在新生儿重症监护病房的组装，重点关注免疫系统发育，皮肤对皮肤接触护理和微生物扩散的相互作用。我们将使用高通量16S rRNA基因和霰弹枪宏基因组测序在多个时间点对新生儿NICU粪便微生物组的组成进行表征：出生后，抗生素使用前后，以及刚从NICU过渡之前，以及两者之间的定期间隔。我们还将对新生儿的免疫细胞谱进行表征，使用细胞计数法定期采集血液样本，并记录两组新生儿皮肤接触的频率和持续时间

The microbial communities associated with humans, referred to as the human microbiome, provide many important beneficial services to their hosts. Yet, despite their importance, we still know very little about the fundamental processes shaping microbial community formation. Understanding the assembly of microbiomes in newborns following birth is necessary for the design of interventions that manipulate them to improve health and development. Broadly, microbiome assembly is believed to be a product of microbial dispersal and selection by the host, both of which are likely disrupted for newborns in neonatal intensive care units (NICUs). NICUs provide a hygienic environment with relatively limited opportunities for the transmission of commensal microorganisms, and the impact of host selection on resident microbiomes is likely affected by the altered physiology and underdeveloped state of newborns in NICUs. Characterizing the effects of factors that potentially increase the dispersal of commensals, such as skin-to-skin contact care between parents and newborns, or that alter the nature of host selection, such as the development of the immune system, will provide us with a deeper understanding of microbiome assembly in early life. We propose to study the assembly of newborn microbiomes in NICUs, with a focus on the interactive effects of the development of the immune system, skin-to-skin contact care, and microbial dispersal. We will characterize the composition of newborn fecal microbiomes in the NICU using high-throughput 16S rRNA gene and shotgun metagenomic sequencing at multiple time points: just after birth, before and after antibiotic use, and just before transitioning out of the NICU, in addition to regular intervals in between. We will also characterize the immune cell profiles of newborns using mass cytometry on blood samples taken at regular intervals, as well as record the frequency and duration of skin-to-skin contact between parents and infants, and antibiotic use. Using these combined data, we will first determine the relationship between the assembly of newborn microbiomes and the development of the immune system and identify the features that most strongly determine the strength of this relationship. We will then determine the effect of skin-to-skin contact on newborn microbiomes and test the hypothesis that increases in skin-to-skin contact are correlated with increases in microbiome diversity, stability, and the rate of recovery from antibiotics. In addition, we will also test the hypothesis that skin-to-skin contact mediates the relationship between microbiome assembly and immune development. Finally, using ecological theory and dispersal-based community assembly models, we will estimate microbial migration rates and measure the contribution of microbial dispersal to microbiome assembly relative to other factors. By elucidating the ecological mechanisms driving the assembly of newborn microbiomes in NICUs, this research has the potential to inform safe and effective intervention strategies to ensure the transmission and development of healthy microbiomes in newborns.