CRISPR-Cas-based identification of a sialylated human milk oligosaccharides utilization cluster in the infant gut commensal Bacteroides dorei
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Abstract
The infant gut microbiome is impacted by early-life feeding, as human milk oligosaccharides (HMOs) found in breastmilk cannot be digested by infants and serve as nutrients for their gut bacteria. While the vast majority of HMO-utilization research has focused on Bifidobacterium species, recent studies have suggested additional HMO-utilizers, mostly Bacteroides , yet their utilization mechanism is poorly characterized. Here, we investigate Bacteroides dorei isolates from breastfed-infants and identify that polysaccharide utilization locus (PUL) 33 enables B. dorei to utilize sialylated HMOs. We perform transcriptional profiling and identity upregulated genes when growing on sialylated HMOs. Using CRISPR-Cas12 to knock-out four PUL33 genes, combined with complementation assays, we identify GH33 as the critical gene in PUL33 for sialylated HMO-utilization. This demonstration of an HMO-utilization system by Bacteroides species isolated from infants opens the way to further characterization of additional such systems, to better understand HMO-utilization in the infant gut.
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- Authors
- Kijner, S., Ennis, D., Shmorak, S., Florentin, A., & Yassour, M.
- Affiliations
- Hebrew University of Jerusalem (IL)
- Corresponding author
- Yassour, Moran
- Venue
- Nature Communications
- Published
- 2024-01-02
- Volume
- 15
- Issue
- 1
- Pages
- 105-105
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC10761964
- OpenAlex
- W4390510313
- Cited by
- 25
- References
- 9
- Citations by year
- 2026: 9 · 2025: 10 · 2024: 6
- FWCI
- 6.68
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- Research Square (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Israel Science Foundation (2660/18)
- Azrieli Foundation
- Ministry of Health, State of Israel
- DSM Nutritional Products
- Topics
- Health Sciences › Nursing › Nutrition and Dietetics › Infant Nutrition and Health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Nursing › Nutrition and Dietetics › Microbial Metabolites in Food Biotechnology
- Keywords
- human milk oligosaccharides, Bacteroides dorei, polysaccharide utilization locus, infant gut microbiota, breast-fed infants, gene complementation, gut commensals
- MeSH terms
- Bacteroides, Humans, Infant, Milk, Human, Oligosaccharides, CRISPR-Cas Systems
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