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

Abstract

Objectives: 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.

Keywords: 16S rRNA sequencing; Gut-lung axis; Intestinal microbiota; Neonate; Pharyngeal microbiota.

图1. OTU稀释性曲线图 横轴为样本中随机抽取的序列数，纵轴为该序列数下对应的OTU数目，每条曲线代表一个样本。

图2. OTU水平PCA图 横轴和纵轴表示两个选定的主成分轴，百分率表示主成分对样本组成差异的解释度值；不同颜色或形状的点代表不同组别的样本，两样本点越接近，表明两样本菌群组成越相似。

图3. 门水平各组菌群相对丰度 图中横轴代表分组名，纵轴代表菌群组成相对丰度构成比，不同颜色代表不同的菌群。

图4. 属水平各组菌群相对丰度 图中横轴代表分组名，纵轴代表菌群组成相对丰度构成比，不同颜色代表不同的菌群（总丰度大于1%的菌）。

图5. 属水平组间差异类群分析结果 图A、B中，左侧为两组样本中不同菌群分类的丰度；中间为95%置信区间内菌群分类丰度的差异；右侧为P值，P<0.05表示差异有统计学意义，用红色标识。