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CRISPR-Cas-based identification of a sialylated human milk oligosaccharides utilization cluster in the infant gut commensal Bacteroides dorei

Author

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  • Sivan Kijner

    (The Hebrew University of Jerusalem)

  • Dena Ennis

    (The Hebrew University of Jerusalem)

  • Shimrit Shmorak

    (The Hebrew University of Jerusalem)

  • Anat Florentin

    (The Hebrew University of Jerusalem
    Hebrew University of Jerusalem)

  • Moran Yassour

    (The Hebrew University of Jerusalem
    The Hebrew University of Jerusalem)

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.

Suggested Citation

  • Sivan Kijner & Dena Ennis & Shimrit Shmorak & Anat Florentin & Moran Yassour, 2024. "CRISPR-Cas-based identification of a sialylated human milk oligosaccharides utilization cluster in the infant gut commensal Bacteroides dorei," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-023-44437-y
    DOI: 10.1038/s41467-023-44437-y
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