Clinical characteristics influence cultivable-bacteria composition in the meconium of Indonesian neonates

Jonathan, Kristien Juni Thandwi; Ong, Grasella; Prasetyaningsih, Firsty Amanah; Amandito, Radhian; Rohsiswatmo, Rinawati; Malik, Amarila

doi:10.1016/j.heliyon.2020.e05576

Cited by 3 publications

(5 citation statements)

References 43 publications

(61 reference statements)

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“…This study shows the development and diversity of the gut microbiome in 24 samples derived from the feces samples of eight preterm neonates born at CMH, Jakarta, at 3 different time points in early life. The analysis of gut microbiome development over the first week based on alpha and beta diversity in terms of relative abundance showed that for the 8 subjects providing 24 feces samples at the three time points, i.e., meconium, day 4 feces, and day 7 feces, Proteobacteria and Firmicutes were dominant at the phylum level, while at the genus level, unidentified Enterobacteriaceae were most abundant, as has been reported widely 1 , 6 , 7 , 9 , 10 , 29 – 34 . This result is similar to our previous study on cultivable bacteria from meconium from neonates born in CMH 9 .…”

Section: Discussionsupporting

confidence: 63%

“…The analysis of gut microbiome development over the first week based on alpha and beta diversity in terms of relative abundance showed that for the 8 subjects providing 24 feces samples at the three time points, i.e., meconium, day 4 feces, and day 7 feces, Proteobacteria and Firmicutes were dominant at the phylum level, while at the genus level, unidentified Enterobacteriaceae were most abundant, as has been reported widely 1 , 6 , 7 , 9 , 10 , 29 – 34 . This result is similar to our previous study on cultivable bacteria from meconium from neonates born in CMH 9 . The microbiomes of meconium, as the first feces in this study, were relatively similar, with one subject showing a high abundance of the genus Ureaplasma and the rest showing a high abundance of Enterobacter.…”

Section: Discussionsupporting

confidence: 63%

“…In this case, MIR was born the most maturely (at 34 weeks, see Table 1 ) among the subjects, with an optimum Apgar score and no risk of chorioamnionitis. This background is in accordance with having a diverse meconium microbiome, showing the importance of maintaining both a healthy mother and fetus, which will affect the immediate future of the neonate upon birth, especially regarding feeding tolerance and response to infection 4 , 9 , 30 , 35 .…”

Section: Discussionmentioning

confidence: 61%

“…Preterm infants exhibit many factors that affect colonization, including antibiotic therapy for the mother or infant, cesarean section, early separation from parents, delayed enteral feeding, invasive medical procedures, or prolonged stay in the neonatal intensive care unit (NICU) 6 – 8 . Compared with term infants, preterm infants also have a reduced number of bacterial species in their fecal microbiome, which contributes to the difficulty of detecting the bacteria when using culture-based methods 9 , 10 . Establishment of obligate anaerobes in preterm infants’ fecal microbiome is delayed, and these organisms persist for several weeks at high levels.…”

Section: Introductionmentioning

confidence: 99%

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

Amandito

Malik

Rohsiswatmo

2022

Sci Rep

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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.

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Section: Discussionsupporting

confidence: 63%

Section: Discussionsupporting

confidence: 63%

Section: Discussionmentioning

confidence: 61%

Section: Introductionmentioning

confidence: 99%

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

Amandito

Malik

Rohsiswatmo

2022

Sci Rep

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“…PCR dilakukan dengan kondisi denaturasi awal pada suhu 95 o C selama 5 menit, denaturasi pada suhu 94 o C selama 30 detik, penempelan pada suhu 63 o C selama 30 detik, pemanjangan pada suhu 68 o C selama 40 detik, dan pemanjangan akhir pada suhu 68 o C selama 6 menit. Tahap denaturasi hingga pemanjangan diulang sampai 30 siklus (13) .…”

Section: Pemilihan Kit Ekstraksiunclassified

Optimasi Perolehan DNA Mikrobioma yang Diekstraksi dari Mekonium dan Feses Neonatus Prematur untuk diaplikasikan pada Next-Gen Sequencing 16S rRNA

Rulita¹,

Malik²,

Amandito³

et al. 2021

jifi

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Komposisi mikrobioma usus pada neonatus prematur dapat diidentifikasi dari mekonium dan feses dengan teknologi Next-Generation Sequencing (NGS). Akan tetapi, perolehan DNA mikrobioma sampel mekonium dan feses memiliki tantangan karena konsistensi serta kandungan inhibitor PCR yang tinggi pada sampel tersebut. Tujuan dari penelitian ini adalah untuk mengoptimasi perolehan DNA mikrobioma dari mekonium dan feses neonatus. Proses perolehan DNA dilakukan dengan menerapkan optimasi parameter yaitu pertimbangan tahap pra-ekstraksi yaitu replikasi dan kondisi sampel, penggunaan pilihan kit ekstraksi, dan tahap elusi DNA hasil ekstraksi. DNA genomik yang diperoleh dikuantifikasi serta dikonfirmasi menggunakan Polymerase Chain Reaction. Hasil optimasi terbaik berdasarkan pengamatan visual kualitas DNA dengan agaros gel dan transiluminator UV, maupun secara kuantitas yang diukur dengan spektrofotometer nano adalah dengan replikasi jumlah sampel sebanyak 2 kali lipat, menggunakan sampel mekonium dan feses yang segar, dan terlebih dahulu disuspensikan menggunakan ddH2O untuk tahap-tahap pra-ekstraksi. Kit terbaik untuk ekstraksi DNA adalah MP Biomedical Fast DNA Spin Kit for Soil, serta penggunaan dapar elusi dengan volume yang lebih sedikit untuk menghasilkan konsentrasi serta kemurnian DNA yang lebih tinggi. Dapat disimpulkan bahwa perolehan DNA yang andal terutama dari sampel meconium berhasil teroptimasi untuk memenuhi kualitas dan kuantitas DNA untuk tahap selanjutnya dengan teknologi sekuensing mikrobioma.

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A common trajectory of gut microbiome development during the first month in healthy neonates with limited inter-individual environmental variations

Wang,

Li,

Lee

et al. 2024

Sci Rep

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The early development of the gut microbiome is governed by multiple factors and has significantly long-term effects on later-in-life health. To minimize inter-individual variations in the environment, we determined developmental trajectories of the gut microbiome in 28 healthy neonates during their stay at a postpartum center. Stool samples were collected at three time points: the first-pass meconium within 24 h of life, and at 7 and 28 days of age. Illumina sequencing of the V3–V4 region of 16S rRNA was used to investigate microbiota profiles. We found that there was a distinct microbiota structure at each time point, with a significant shift during the first week. Proteobacteria was most abundant in the first-pass meconium; Firmicutes and Actinobacteria increased with age and were substituted as the major components. Except for a short-term influence of different delivery modes on the microbiota composition, early microbiome development was not remarkably affected by gravidity, maternal intrapartum antibiotic treatment, premature rupture of membranes, or postnatal phototherapy. Hence, our data showed a similar developmental trajectory of the gut microbiome during the first month in healthy neonates when limited in environmental variations. Environmental factors external to the host were crucial in the early microbiome development.

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Clinical characteristics influence cultivable-bacteria composition in the meconium of Indonesian neonates

Cited by 3 publications

References 43 publications

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

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

Optimasi Perolehan DNA Mikrobioma yang Diekstraksi dari Mekonium dan Feses Neonatus Prematur untuk diaplikasikan pada Next-Gen Sequencing 16S rRNA

A common trajectory of gut microbiome development during the first month in healthy neonates with limited inter-individual environmental variations

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