Gut microbiome profiling of neonates using Nanopore MinION and Illumina MiSeq sequencing

Teahyen Cha; Hoo Hugo Kim; Jihyun Keum; Min-Jin Kwak; Jae Yong Park; Jeong Kyu Hoh; Chang-Ryul Kim; Byong-Hun Jeon; Hyun-Kyung Park

doi:10.3389/fmicb.2023.1148466

Gut microbiome profiling of neonates using Nanopore MinION and Illumina MiSeq sequencing

Front Microbiol. 2023 May 15:14:1148466. doi: 10.3389/fmicb.2023.1148466. eCollection 2023.

Authors

Teahyen Cha¹, Hoo Hugo Kim², Jihyun Keum³, Min-Jin Kwak⁴, Jae Yong Park⁵, Jeong Kyu Hoh³, Chang-Ryul Kim¹, Byong-Hun Jeon², Hyun-Kyung Park¹

Affiliations

¹ Department of Pediatrics, Hanyang University College of Medicine, Seoul, Republic of Korea.
² Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul, Republic of Korea.
³ Department of Obstetrics and Gynecology, Hanyang University College of Medicine, Seoul, Republic of Korea.
⁴ Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
⁵ Division of Microbiome, Int-Gen Company, Seoul, Republic of Korea.

Abstract

This study aimed to evaluate the difference in gut microbiomes between preterm and term infants using third-generation long-read sequencing (Oxford Nanopore Technologies, ONT) compared with an established gold standard, Illumina (second-generation short-read sequencing). A total of 69 fecal samples from 51 term (T) and preterm (P) infants were collected at 7 and 28 days of life. Gut colonization profiling was performed by 16S rRNA gene sequencing using ONT. We used Illumina to validate and compare the patterns in 13 neonates. Using bioinformatic analysis, we identified features that differed between P and T. Both T1 and P1 microbiomes were dominated by Firmicutes (Staphylococcus and Enterococcus), whereas sequentially showed dominant transitions to Lactobacillus (p < 0.001) and Streptococcus in T2 (p = 0.001), and pathogenic bacteria (Klebsiella) in P2 (p = 0.001). The abundance of beneficial bacteria (Bifidobacterium and Lactobacillus) increased in T2 (p = 0.026 and p < 0.001, respectively). These assignments were correlated with the abundance at the species-level. Bacterial α-diversity increased in T (p = 0.005) but not in P (p = 0.156), and P2 showed distinct β-diversity clustering than T2 (p = 0.001). The ONT reliably identified pathogenic bacteria at the genus level, and taxonomic profiles were comparable to those identified by Illumina at the genus level. This study shows that ONT and Illumina are highly correlated. P and T had different microbiome profiles, and the α- and β-diversity varied. ONT sequencing has potential for pathogen detection in neonates in clinical settings.

Keywords: Illumina MiSeq®; Nanopore MinION; gut microbiome; neonates; preterm infants.