Date: 2026.04.27
Author: Yunjeong So
MILKOME is a mother-infant cohort study conducted in Copenhagen, a collaboration between the Technical University of Denmark (DTU) and Rigshospitalet. The study was led by DTU, with participants recruited by Rigshospitalet.
We sequenced the fecal samples of infants at three different time points: pre-weaning, early-weaning, and late-weaning. For the early-weaning time point, we also sequenced paired fecal samples from the mothers. Additionally, the fecal samples were enriched with diverse glycan sources, and these enriched consortia were sequenced as well.
The sequence data analysis pipeline is outlined below. The scripts used can be found under the milkome/scripts directory:
- Sequence quality check
- Sequence filtering and host read removal
- Taxonomic profiling using a Bifidobacterium longum subsp. infantis and subsp. longum resolution database
- Contig assembly
- Functional annotation — Carbohydrate Active Enzymes (CAZymes) targeting human milk oligosaccharides (HMOs), dietary fibres (arabinoxylan, pectin, and xyloglucan), and food additives (mannan and gum Arabic)
- Retrieval of metagenome-assembled genomes (MAGs)
- Annotation and charactersation of MAGs
- Downstream analyses
milkome/
├── scripts/ # Analysis scripts
├── data/ # Metadata and processed data
└── README.md # Project documentation
MILKOME workflow is released under the MIT License.
Copyright (c) 2026 Yunjeong So
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