Neonatal Jaundice and the Infant Gut Microbiome: An Integrated Shotgun Metagenomics and Bidirectional Mendelian Randomization Study in Xinjiang

We conducted a case–control study in Xinjiang to characterize the neonatal gut microbiome in relation to pathologic neonatal jaundice. Fecal samples were collected non-invasively from term neonates within 48 hours after birth and stored at -80 °C. The cohort included 11 neonates with pathologic jaundice and 5 matched healthy controls. Shotgun metagenomic sequencing was performed on the Illumina NovaSeq 6000 platform using a paired-end 150 bp strategy, generating approximately 8.2–11.6 Gb of raw data per sample. Sequencing reads were quality filtered, and host-derived reads were removed by aligning clean reads to the human reference genome (GRCh38) using Bowtie2; non-host reads were retained for downstream analyses. The resulting dataset enables taxonomic and functional profiling of the early-life gut microbiome, including pathway- and enzyme-family–level comparisons between jaundiced and control neonates, and supports integrative analyses alongside genetic causal inference approaches used in the associated study.