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。了解出生后新生儿中微生物组的组装对于设计干预措施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扩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（NICU）中被破坏。新生儿重症监护病房提供了一个卫生的环境，相对有限的机会，传播肠道微生物，宿主选择的影响，居民微生物组可能会受到影响的生理变化和新生儿在新生儿重症监护病房发育不全的状态。表征可能增加肠道菌群传播的因素的影响，例如父母和新生儿之间的皮肤接触护理，或者改变宿主选择的性质，例如免疫系统的发育，将为我们提供对早期生命中微生物组组装的更深入了解。我们建议研究新生儿微生物组在NICU的组装，重点是免疫系统的发展，皮肤与皮肤接触护理和微生物扩散的相互作用。我们将在多个时间点使用高通量16S rRNA基因和鸟枪宏基因组测序来表征NICU中新生儿粪便微生物组的组成：出生后，抗生素使用前后，以及过渡出NICU之前，以及之间的定期间隔。我们还将使用定期采集的血液样本的质量细胞仪来表征新生儿的免疫细胞谱，并记录新生儿之间皮肤接触的频率和持续时间。 父母和婴儿，以及抗生素的使用。使用这些组合数据，我们将首先确定新生儿微生物组的组装与免疫系统发育之间的关系，并确定最强烈地决定这种关系强度的特征。然后，我们将确定皮肤与皮肤接触对新生儿微生物组的影响，并测试皮肤与皮肤接触的增加与微生物组多样性，稳定性和抗生素恢复率的增加相关的假设。此外，我们还将检验皮肤接触介导微生物组组装和免疫发育之间关系的假设。最后，使用生态学理论和基于分散的群落组装模型，我们将估计微生物迁移率，并测量微生物分散相对于其他因素对微生物组组装的贡献。通过阐明驱动新生儿微生物组在NICU中组装的生态机制，这项研究有可能为安全有效的干预策略提供信息，以确保新生儿健康微生物组的传播和发展。

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.