Metagenomic profiles of the early life microbiome of Indonesian inpatient neonates and their influence on clinical characteristics

Abstract

Determining the initial normal neonatal gut microbiome is challenging. The debate regarding the sterile fetal environment is still ongoing. Therefore, studying and comparing normal and dysbiotic microbiomes requires the elucidation of both the fetal and infant microbiomes. Factors influencing the normal microbiome also include regional and genetic factors specific to different countries. Determining the normal microbiome population in our center and their association with the clinical conditions of infants is helpful as a tool for both the prevention and treatment of related diseases during neonatal care. Here, we employed metagenomic sequencing to characterize meconium and the subsequent early-life gut microbiome of preterm neonates in Jakarta, Indonesia. Microbiome diversity and complexity was higher in the meconium and on day 4 than on day 7. At the genus level, the most abundant genus overall was unidentified Enterobacteriaceae, with meconium samples dominated by Ureaplasma, day 4 fecal samples dominated by Staphylococcus, and day 7 samples dominated by Clostridiales, while at the phylum level the most abundant was Proteobacteria and Firmicutes. Perinatal factors of PROM and mother’s diet influenced the meconium microbiome, while day 4 and day 7 microbiome was associated with bacteremia and early administration of antibiotics. One of our sample sets was derived from triplets, and they had varying diversity despite being triplets. These data are valuable for understanding the formation of a healthy microbiome specific to neonates and devising a strategy to improve both the gut health and related clinical outcomes of the neonate.

Delivery mode is a larger determinant of infant gut microbiome composition at 6 weeks than exposure to peripartum antibiotics

“…Most women delivering vaginally received antibiotics for PROMs, rather than for routine surgical prophylaxis in caesarean section. A previous study found that PROMs altered the composition of the infant meconium but this disappeared 4–7 days after birth [56], so this is unlikely to be an important factor for infant gut composition at 6 weeks.…”

Investigating prenatal and perinatal factors on meconium microbiota: a systematic review and cohort study

“…In addition, we collected extensive data on maternal living environments and lifestyles during pregnancy, such as fish and meat consumption, leisure time spent in forests, the presence of older siblings or furry pets in the home, smoking in the home and maternal weight, and established that these prenatal factors had little effect on the microbial composition of meconium. It is therefore understandable that the prenatal factors considered in our systematic review, including maternal diet, 2 , 37 , 84 , 85 residential area, 37 , 44 age, 37 , 44 , 49 , 50 , 53 , 57 , 86 ethnicity, 3 , 49 weight, 3 , 38 , 44 , 49 , 53 , 56 , 57 , 75 , 86 smoking, 3 , 37 , 44 , 87 pregnancy-related health issues, 36 – 40 , 47 , 49 , 54 , 60 , 71 , 75 , 85 , 86 non-pregnancy-related health issues 3 , 37 , 38 , 44 , 45 , 49 , 70 , 76 , 88 , 89 and education, 37 , 44 , 49 together with environmental pollutants, particularly metals and microplastics 58 , 90 and the presence of furry pets 13 , 45 yielded mixed results. Another commonly studied newborn factor, which we did not analyze in our cohort study, was gestational age, 3 , 4 ...…”

Compositional Differences of Meconium Microbiomes of Preterm and Term Infants, and Infants That Developed Necrotizing Enterocolitis or Feeding Intolerance

“…Due to the small number of subjects, further analyses were difficult. However, a study on 8 preterm neonates in Indonesia reported that PROM and mother’s diet influenced the meconium microbiome [ 46 ]. Further studies including a larger cohort of preterm infants are needed to make any conclusions on the impact of early exposure to vaginal microbiomes in utero and colonization and establishment of the infants’ gut microbiome.…”