Probiotic prescriptions for prematurebabies to reduce disease risk NatureMicrobiol
, with an AMT of 0.002 Da. Any unannotated features were removed. The remaining dataset was subject to manual feature curation in MS-DIAL, where poor quality spectral features were removed.A human intestinal organoid line was generated from preterm intestinal ileum tissue after surgical resection for NECIntestinal organoids were exposed to pooled faecal supernatants representing each PGCT and a control containing no faecal supernatant.
. Briefly, ~0.25 g of stool was pooled for each PGCT and diluted in 25% sterile phosphate-buffered saline before being vortexed for 20 min with glass beads. Faecal slurries were centrifuged for 20 min at 1,600and 4 °C, and the resulting supernatant was serially filtered . Faecal supernatant was stored at −80 °C until use.
Intestinal organoids were seeded as monolayers on 0.4 µm Transwells and, after reaching confluence , were differentiated for 4 dCo-culture of preterm intestinal organoid monolayers with sterile faecal supernatants was performed for 24 h using the organoid anaerobe co-culture model. The sterile faecal supernatants were added apically, corresponding to the intestinal lumen.
QC of raw reads was performed using fastq_quality_trimmer from the FASTX Toolkit v.0.0.14 before being mapped to the human transcriptome using Salmon v.0.13.1 (ref.
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