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PreprintCC BYChemRxiv

Chemoproteomic mapping of active glycan-processing networks in a defined gut microbiome

  • Isabelle B. Pickles1,2
  • Thamy L. R. Corrêa1,2
  • Qinnan Yang3
  • Yurong Chen4
  • Zirui Li4
  • Nicole M. Koropatkin3
  • Eric C. Martens3
  • Herman S. Overkleeft4
  • Gideon J. Davies1,2
4 affiliations
  1. 1Department of Chemistry
  2. 2University of York
  3. 3University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, MI, USA, 48109-5620
  4. 4Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden, Netherlands, 2333 CC
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Abstract

Microbiome studies typically infer function from gene content or expression, but these measurements do not establish which enzymes are catalytically active or what substrates they recognise. Here we use a multiplexed panel of mechanism-based glycosidase probes to map active glycan-processing enzymes directly from caecal samples of mice colonised with a defined, 14-member, human gut microbiota. Activity-based protein profiling identifies host and microbial enzymes involved in starch, β-glucan, xyloglucan and xylan degradation and links them to defined taxa and loci. Decorated probes resolve branch and substitution preferences within active enzyme families, revealing xylanase activities poorly detected by bulk substrate assays. Several prominent activities are assigned to low-abundance Bacteroides species, while enzyme deployment differs among animals sharing a common inoculum and diet. These results establish activity-based chemoproteomics as a complementary layer to metagenomics, transcriptomics and proteomics for defining functional glycan-processing states in host-associated microbiomes.

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Cite

BibTeXRIS
BibTeX
@misc{pickles2026chemoproteomic,
  title = {{Chemoproteomic mapping of active glycan-processing networks in a defined gut microbiome}},
  author = {Isabelle B. Pickles and Thamy L. R. Corrêa and Qinnan Yang and Yurong Chen and Zirui Li and Nicole M. Koropatkin and Eric C. Martens and Herman S. Overkleeft and Gideon J. Davies},
  howpublished = {ChemRxiv},
  year = {2026},
  month = sep,
  doi = {10.26434/chemrxiv.15008529/v1},
  url = {https://chemrxiv.org/doi/full/10.26434/chemrxiv.15008529/v1},
  note = {CC BY},
}
RIS
TY  - UNPB
TI  - Chemoproteomic mapping of active glycan-processing networks in a defined gut microbiome
AU  - Isabelle B. Pickles
AU  - Thamy L. R. Corrêa
AU  - Qinnan Yang
AU  - Yurong Chen
AU  - Zirui Li
AU  - Nicole M. Koropatkin
AU  - Eric C. Martens
AU  - Herman S. Overkleeft
AU  - Gideon J. Davies
PY  - 2026
DA  - 2026/09/09
PB  - ChemRxiv
DO  - 10.26434/chemrxiv.15008529/v1
UR  - https://chemrxiv.org/doi/full/10.26434/chemrxiv.15008529/v1
AB  - Microbiome studies typically infer function from gene content or expression, but these measurements do not establish which enzymes are catalytically active or what substrates they recognise. Here we use a multiplexed panel of mechanism-based glycosidase probes to map active glycan-processing enzymes directly from caecal samples of mice colonised with a defined, 14-member, human gut microbiota. Activity-based protein profiling identifies host and microbial enzymes involved in starch, β-glucan, xyloglucan and xylan degradation and links them to defined taxa and loci. Decorated probes resolve branch and substitution preferences within active enzyme families, revealing xylanase activities poorly detected by bulk substrate assays. Several prominent activities are assigned to low-abundance Bacteroides species, while enzyme deployment differs among animals sharing a common inoculum and diet. These results establish activity-based chemoproteomics as a complementary layer to metagenomics, transcriptomics and proteomics for defining functional glycan-processing states in host-associated microbiomes.
ER  -