基于高通量测序分析早期新生儿肠道和咽部微生物菌群

Intestinal and pharyngeal microbiota in early neonates: an analysis based on high-throughput sequencing

摘要:

目的 初步探讨早期新生儿肠道和咽部微生物群的分布特点及相关性。方法 选取上海市浦东新区妇幼保健院2021年9月—2022年1月出生的混合喂养的足月健康新生儿为研究对象。采用16S rRNA基因测序技术分析新生儿出生当天及出生后5~7 d的粪便和咽拭子样本，分析比较早期新生儿肠道和咽部微生物群的组成及功能差异。结果 多样性分析表明，早期新生儿咽部微生物群的多样性高于肠道，但差异无统计学意义（P>0.05）。门水平上，出生当天肠道变形菌门相对丰度高于咽部（P<0.05）；出生后5~7 d肠道放线菌门和变形菌门相对丰度高于咽部、厚壁菌门相对丰度低于咽部（P<0.05）。属水平上，出生当天肠道和咽部的优势菌属组成差异无统计学意义（P>0.05）；出生后5~7 d肠道和咽部的链球菌属、葡萄球菌属、罗氏菌属、双歧杆菌属及埃希菌-志贺菌属等共生菌差异有统计学意义（P<0.05）。直系同源序列聚类数据库分析显示，咽部菌群更多地集中在染色质结构和动力学及细胞骨架上，而肠道菌群在RNA加工修饰、能量生成和转换、氨基酸转运代谢、碳水化合物转运代谢、辅酶转运和代谢等方面表现丰富（P<0.05）。京都基因和基因组百科全书分析显示，与咽部菌群相比，肠道菌群对细胞运动、细胞进程和信号转导、内分泌系统、排泄系统、免疫系统、代谢性疾病、神经系统和转录功能参数的预测程度更高（P<0.05）。结论 新生儿出生时肠道和咽部的微生物群组成及多样性无显著差异，随着出生时间的推移，两个生态位的微生物群组成开始出现分化，并逐渐显现出各自不同的功能。

Abstract:

Objective To investigate the distribution characteristics and correlation of intestinal and pharyngeal microbiota in early neonates.Methods Full-term healthy neonates who were born in Shanghai Pudong New Area Maternal and Child Health Hospital from September 2021 to January 2022 and were given mixed feeding were enrolled. The 16S rRNA sequencing technique was used to analyze the stool and pharyngeal swab samples collected on the day of birth and days 5-7 after birth, and the composition and function of intestinal and pharyngeal microbiota were analyzed and compared.Results The diversity analysis showed that the diversity of pharyngeal microbiota was higher than that of intestinal microbiota in early neonates, but the difference was not statistically significant (P>0.05). On the day of birth, the relative abundance of Proteobacteria in the intestine was significantly higher than that in the pharynx (P<0.05). On days 5-7 after birth, the relative abundance of Actinobacteria and Proteobacteria in the intestine was significantly higher than that in the pharynx (P<0.05), and the relative abundance of Firmicutes in the intestine was significantly lower than that in the pharynx (P<0.05). At the genus level, there was no significant difference in the composition of dominant bacteria between the intestine and the pharynx on the day of birth (P>0.05), while on days 5-7 after birth, there were significant differences in the symbiotic bacteria of Streptococcus, Staphylococcus, Rothia, Bifidobacterium, and Escherichia-Shigella between the intestine and the pharynx (P<0.05). The analysis based on the database of Clusters of Orthologous Groups of proteins showed that pharyngeal microbiota was more concentrated on chromatin structure and dynamics and cytoskeleton, while intestinal microbiota was more abundant in RNA processing and modification, energy production and conversion, amino acid transport and metabolism, carbohydrate transport and metabolism, coenzyme transport and metabolism, and others (P<0.05). The Kyoto Encyclopedia of Genes and Genomes analysis showed that compared with pharyngeal microbiota, intestinal microbiota was more predictive of cell motility, cellular processes and signal transduction, endocrine system, excretory system, immune system, metabolic diseases, nervous system, and transcription parameters (P<0.05).Conclusions The composition and diversity of intestinal and pharyngeal microbiota of neonates are not significantly different at birth. The microbiota of these two ecological niches begin to differentiate and gradually exhibit distinct functions over time.