Early bacterial communities in the lower airways and intestines of caesarean section neonates with respiratory disease

Introduction Acute lower respiratory tract infection (ALRTI) are one of the most severe diseases affecting neonates worldwide. Many bacterial pathogens that cause respiratory infections in neonates are common residents in the respiratory tract. Therefore, the aim is to determine the early bacterial community in the lower airways and intestines of neonates. Methods Airway secretions, oral swabs, and fecal samples were collected from 19 neonates with acute respiratory tract infection and 2 control subjects. All three types of samples were amplified and sequenced using specific primer sets targeting the 16S rRNA gene. Results Bacterial composition of the feces and airway secretions in the diseased neonates significantly differed from that of the neonates in the control group. The feces microbiota in the diseased neonates had accumulated Alcaligenaceae _ge and Enterococcus . The airway secretion microbiota of control and diseased neonates was mainly Alcaligenaceae _ge and Streptococcus , and Alcaligenaceae _ge was the most abundant genus in diseased neonates. In addition, the bacterial composition of the twins’ neonates samples was more similar than that of other neonates. Discussion Insight into the source and stability of microbiota in the neonatal period might elucidate health or susceptibility for developing a respiratory disease. Microbiota analysis also promises to complement the present means of detecting respiratory pathogens.