Spatial constraints drive amylosome-mediated resistant starch degradation by Ruminococcus bromii in the human colon
Degradation of complex dietary fiber by gut microbes is essential for colonic fermentation, short-chain fatty acid production, and microbiome function. Ruminococcus bromii is the primary resistant starch (RS) degrader in humans, which relies on the amylosome, a specialized cell-bound enzymatic complex. To unravel its architecture, function, and the interplay among its components, we applied a holistic multilayered approach: Cryo-electron tomography reveals that the amylosome comprises a constitutive extracellular layer extending toward the RS substrate. Proteomics demonstrates remodeling of its contents across different growth conditions, with Amy4 and Amy16 comprising 60% of the amylosome in response to RS. Structural and biochemical analyses reveal complementarity and synergistic RS degradation by these enzymes. We demonstrate that amylosome composition and RS degradation are regulated at two levels: structural constraints and expression-driven shifts in enzyme proportions enforce enzyme proximity, which allows R. bromii to fine-tune its adaptation to dietary fiber and shape colonic metabolism.
Authors
- Barbara Pfister (ORCID: https://orcid.org/0000-0002-4183-9625)
- Benedikt H. Wimmer (ORCID: https://orcid.org/0000-0002-6916-9360)
- Anke Trautwein‐Schult (ORCID: https://orcid.org/0000-0003-3272-5746)
- Omar E. Tovar-Herrera (ORCID: https://orcid.org/0000-0001-7627-644X)
- Meltem Tatlı (ORCID: https://orcid.org/0000-0003-3632-6208)
- Ran Zalk (ORCID: https://orcid.org/0000-0003-4251-6497)
- Sarah Moraïs (ORCID: https://orcid.org/0000-0001-9026-2386)
- Liron Levin (ORCID: https://orcid.org/0009-0003-1591-7903)
- Ohad Medalia (ORCID: https://orcid.org/0000-0003-0994-2937)
- Edward A. Bayer (ORCID: https://orcid.org/0000-0001-7749-5150)
- Dörte Becher (ORCID: https://orcid.org/0000-0002-9630-5735)
- Itzhak Mizrahi (ORCID: https://orcid.org/0000-0001-6636-8818)
- Serena Simoni
- Itai Amit
- Paloma Tödtli
- Matteo Lisibach (ORCID: https://orcid.org/0009-0003-2351-5066)
Institutions
- Ben-Gurion University of the Negev (IL)
- University of Zurich (CH)
- ETH Zurich (CH)
- Universität Greifswald (DE)
- Weizmann Institute of Science (IL)
Publication Details
- Journal
- Nature Communications
- Published
- 2025-11-26
- DOI
- https://doi.org/10.1038/s41467-025-65800-1
- Citations
- 2
- Primary Topic
- Food composition and properties
- Type
- article
- Field-Weighted Citation Impact
- 2.24
Funders
- National Science Foundation
- Novartis Foundation
- University of Aberdeen
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
- Israel Science Foundation
- Novartis Stiftung für Medizinisch-Biologische Forschung
- Universität Zürich
- Universität Greifswald