• A Corrigendum to this article was published on 23 August 2017

This article has been updated


The metabolism of carbohydrate polymers drives microbial diversity in the human gut microbiota. It is unclear, however, whether bacterial consortia or single organisms are required to depolymerize highly complex glycans. Here we show that the gut bacterium Bacteroides thetaiotaomicron uses the most structurally complex glycan known: the plant pectic polysaccharide rhamnogalacturonan-II, cleaving all but 1 of its 21 distinct glycosidic linkages. The deconstruction of rhamnogalacturonan-II side chains and backbone are coordinated to overcome steric constraints, and the degradation involves previously undiscovered enzyme families and catalytic activities. The degradation system informs revision of the current structural model of rhamnogalacturonan-II and highlights how individual gut bacteria orchestrate manifold enzymes to metabolize the most challenging glycan in the human diet.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Change history

  • 05 April 2017

    The PDB code ‘5MQP’ was added to the Data Availability section; and reference citations were corrected in the final paragraph of the main text.



  1. 1.

    et al. Isotopic evidence for dietary ecology of late Neandertals in North-Western Europe. Quat. Int. 411, 327–345 (2016)

  2. 2.

    et al. Structural characterization of red wine rhamnogalacturonan II. Carbohydr. Res. 290, 183–197 (1996)

  3. 3.

    et al. Polysaccharide composition of Monastrell red wines from four different Spanish terroirs: effect of wine-making techniques. J. Agric. Food Chem. 61, 2538–2547 (2013)

  4. 4.

    et al. Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism. Nature 517, 165–169 (2015)

  5. 5.

    et al. A discrete genetic locus confers xyloglucan metabolism in select human gut Bacteroidetes. Nature 506, 498–502 (2014)

  6. 6.

    et al. Glycan complexity dictates microbial resource allocation in the large intestine. Nat. Commun. 6, 7481 (2015)

  7. 7.

    , & How glycan metabolism shapes the human gut microbiota. Nat. Rev. Microbiol. 10, 323–335 (2012)

  8. 8.

    et al. Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts. PLoS Biol. 9, e1001221 (2011)

  9. 9.

    et al. Structural insights into the catalytic mechanism of Trypanosoma cruzi trans-sialidase. Structure 12, 775–784 (2004)

  10. 10.

    , , , & The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 42, D490–D495 (2014)

  11. 11.

    et al. Tetrazoles of manno- and rhamno-pyranoses: Contrasting inhibition of mannosidases by 4.3.0 but of rhamnosidase by 3.3.0 bicyclic tetrazoles. Tetrahedron 55, 4489–4500 (1999)

  12. 12.

    , , & Dissecting conformational contributions to glycosidase catalysis and inhibition. Curr. Opin. Struct. Biol. 28, 1–13 (2014)

  13. 13.

    et al. Molecular cloning and characterization of a β-l-Arabinobiosidase in Bifidobacterium longum that belongs to a novel glycoside hydrolase family. J. Biol. Chem. 286, 5143–5150 (2011)

  14. 14.

    , , , & Isolation and characterization of 3-C-carboxy-5-deoxy-l-xylose, a naturally occurring, branched-chain, acidic monosaccharide. Carbohydr. Res. 122, 115–129 (1983)

  15. 15.

    et al. The nematode Caenorhabditis elegans synthesizes unusual O-linked glycans: identification of glucose-substituted mucin-type O-glycans and short chondroitin-like oligosaccharides. Biochem. J. 357, 167–182 (2001)

  16. 16.

    , , & Identification of 3-deoxy-lyxo-2-heptulosaric acid in the core region of lipopolysaccharides from Rhizobiaceae. FEMS Microbiol. Lett. 84, 337–343 (1991)

  17. 17.

    et al. Structural basis of the catalytic reaction mechanism of novel 1,2-α-l-fucosidase from Bifidobacterium bifidum. J. Biol. Chem. 282, 18497–18509 (2007)

  18. 18.

    et al. Crystal structure of Thermotoga maritima α-l-fucosidase. Insights into the catalytic mechanism and the molecular basis for fucosidosis. J. Biol. Chem. 279, 13119–13128 (2004)

  19. 19.

    , , & Rhamnogalacturonan II: structure and function of a borate cross-linked cell wall pectic polysaccharide. Annu. Rev. Plant Biol. 55, 109–139 (2004)

  20. 20.

    et al. Rhamnogalacturonan II structure shows variation in the side chains monosaccharide composition and methylation status within and across different plant species. Plant J. 76, 61–72 (2013)

  21. 21.

    et al. The structure and function of an arabinan-specific α-1,2-arabinofuranosidase identified from screening the activities of bacterial GH43 glycoside hydrolases. J. Biol. Chem. 286, 15483–15495 (2011)

  22. 22.

    et al. Structural basis for nutrient acquisition by dominant members of the human gut microbiota. Nature 541, 407–411 (2017)

  23. 23.

    , & Rhamnogalacturonans I and II are pectic substrates for flax-cell methyltransferases. Plant Physiol. Biochem. 35, 623–629 (1997)

  24. 24.

    et al. Primary structure of the 2-O-methyl-α-l-fucose-containing side chain of the pectic polysaccharide, rhamnogalacturonan II. Carbohydr. Res. 338, 341–352 (2003)

  25. 25.

    et al. Advancing glycomics: implementation strategies at the Consortium for Functional Glycomics. Glycobiology 16, 82R–90R (2006)

  26. 26.

    et al. Recovery and fine structure variability of RGII sub-domains in wine (Vitis vinifera Merlot). Ann. Bot. 114, 1327–1337 (2014)

  27. 27.

    , & Synthesis of an apiose-containing disaccharide fragment of rhamnogalacturonan-II and some analogues. Carbohydr. Res. 339, 21–27 (2004)

  28. 28.

    , & Synthesis of a 2,3,4-triglycosylated rhamnoside fragment of rhamnogalacturonan-II side chain A using a late stage oxidation approach. J. Org. Chem. 70, 960–966 (2005)

  29. 29.

    , , & Synthesis of apiose-containing oligosaccharide fragments of the plant cell wall: fragments of rhamnogalacturonan-II side chains A and B, and apiogalacturonan. Org. Biomol. Chem. 9, 6670–6684 (2011)

  30. 30.

    et al. The X6 “thermostabilizing” domains of xylanases are carbohydrate-binding modules: structure and biochemistry of the Clostridium thermocellum X6b domain. Biochemistry 39, 5013–5021 (2000)

  31. 31.

    et al. Subsite structure of Saccharomycopsis α-amylase secreted from Saccharomyces cerevisiae. J. Biochem. 109, 566–569 (1991)

  32. 32.

    , , & Starch catabolism by a prominent human gut symbiont is directed by the recognition of amylose helices. Structure 16, 1105–1115 (2008)

  33. 33.

    Xds. Acta Crystallogr. D 66, 125–132 (2010)

  34. 34.

    et al. Diffraction-geometry refinement in the DIALS framework. Acta Crystallogr. D 72, 558–575 (2016)

  35. 35.

    xia2: an expert system for macromolecular crystallography data reduction. J. Appl. Crystallogr. 43, 186–190 (2010)

  36. 36.

    & How good are my data and what is the resolution? Acta Crystallogr. D 69, 1204–1214 (2013)

  37. 37.

    & HKL2MAP: a graphical user interface for macromolecular phasing with SHELX programs. J. Appl. Crystallogr. 37, 843–844 (2004)

  38. 38.

    Experimental phasing with SHELXC/D/E: combining chain tracing with density modification. Acta Crystallogr. D 66, 479–485 (2010)

  39. 39.

    Fitting molecular fragments into electron density. Acta Crystallogr. D 64, 83–89 (2008)

  40. 40.

    , , & Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nat. Protocols 3, 1171–1179 (2008)

  41. 41.

    & MOLREP: an automated program for molecular replacement. J. Appl. Crystallogr. 30, 1022–1025 (1997)

  42. 42.

    et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007)

  43. 43.

    & Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004)

  44. 44.

    et al. REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use. Acta Crystallogr. D 60, 2184–2195 (2004)

  45. 45.

    et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D 66, 12–21 (2010)

  46. 46.

    , , & Automatic prediction of polysaccharide utilization loci in Bacteroidetes species. Bioinformatics 31, 647–655 (2015)

  47. 47.

    , , , & Rapid similarity search of proteins using alignments of domain arrangements. Bioinformatics 30, 274–281 (2014)

Download references


This work was supported in part by a grant to H.J.G. and B.H. from the European Research Council (grant no. 322820). B.H. was also funded by Agence Nationale de la Recherche under grant number ANR 12-BIME-0006-01. H.J.G was also supported by Biotechnology and Biological Research Council (grant numbers BB/K020358/1 and BB/K001949/1), the Wellcome Trust (grant no. WT097907MA) and, with X.Z., M.-C.R. and F.B., was funded by the European Union Seventh Framework Programme under the WallTraC project (grant agreement number 263916). M.A.O and B.R.U. were supported in part by grant DE-FG02-12ER16324 from The Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences of the US Department of Energy. I.V. was in receipt of a Marie Skłodowska-Curie Fellowship (grant no. 707922). G.J.D. is a Royal Society Ken Murray Research Professor. D.W.A. was supported by a grant from the Beef and Cattle Research Council (FDE.15.13). We thank Diamond Light Source for access to beamline I02, I04-1 and I24 (mx1960, mx7854 and mx9948) that contributed to the results presented here, and to T. Doco and S. J. Charnock who supplied the partially purified apple RG-II.

Author information

Author notes

    • Artur Rogowski
    •  & Fanny Buffetto

    Present addresses: Megazyme, Bray, Co. Wicklow, A98 YV29, Ireland (A.R.); Institute for Wine Biotechnology, Department of Viticulture and Oenology, Stellenbosch University, Matieland 7602, South Africa (F.B.).

    • Didier Ndeh
    • , Artur Rogowski
    • , Alan Cartmell
    •  & Ana S. Luis

    These authors contributed equally to this work.


  1. Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK

    • Didier Ndeh
    • , Artur Rogowski
    • , Alan Cartmell
    • , Ana S. Luis
    • , Arnaud Baslé
    • , Joseph Gray
    • , Immacolata Venditto
    • , Jonathon Briggs
    • , Xiaoyang Zhang
    • , Aurore Labourel
    •  & Harry J. Gilbert
  2. Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Aix-Marseille University, F-13288 Marseille, France

    • Nicolas Terrapon
    •  & Bernard Henrissat
  3. INRA, UR1268 Biopolymères Interactions Assemblages, 44300 Nantes, France

    • Fanny Buffetto
    •  & Marie-Christine Ralet
  4. Department of Biological Chemistry, John Innes Centre Norwich Research Park, Norwich NR4 7UH, UK

    • Sergey Nepogodiev
    •  & Robert A. Field
  5. Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109 USA

    • Yao Xiao
    •  & Eric C. Martens
  6. Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, USA

    • Yanping Zhu
    • , Malcolm A. O’Neill
    • , Breeanna R. Urbanowicz
    •  & William S. York
  7. Department of Chemistry, University of York, York YO10 5DD, UK

    • Gideon J. Davies
  8. Lethbridge Research Centre, Lethbridge, Alberta T1J 4B1, Canada

    • D. Wade Abbott
  9. INRA, USC 1408 AFMB, F-13288 Marseille, France

    • Bernard Henrissat
  10. Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia

    • Bernard Henrissat


  1. Search for Didier Ndeh in:

  2. Search for Artur Rogowski in:

  3. Search for Alan Cartmell in:

  4. Search for Ana S. Luis in:

  5. Search for Arnaud Baslé in:

  6. Search for Joseph Gray in:

  7. Search for Immacolata Venditto in:

  8. Search for Jonathon Briggs in:

  9. Search for Xiaoyang Zhang in:

  10. Search for Aurore Labourel in:

  11. Search for Nicolas Terrapon in:

  12. Search for Fanny Buffetto in:

  13. Search for Sergey Nepogodiev in:

  14. Search for Yao Xiao in:

  15. Search for Robert A. Field in:

  16. Search for Yanping Zhu in:

  17. Search for Malcolm A. O’Neill in:

  18. Search for Breeanna R. Urbanowicz in:

  19. Search for William S. York in:

  20. Search for Gideon J. Davies in:

  21. Search for D. Wade Abbott in:

  22. Search for Marie-Christine Ralet in:

  23. Search for Eric C. Martens in:

  24. Search for Bernard Henrissat in:

  25. Search for Harry J. Gilbert in:


Enzyme characterization was by D.N., A.R., A.C., A.S.L., I.V., A.L., D.W.A., Y.Z. and X.Z. Crystallographic studies were by A.C., A.B., A.S.L., D.N. and I.V. Purification of RG-II and oligosaccharide products was by M.A.O., A.R., D.N., A.C, A.L., A.S.L., F.B. and M.-C.R. HPLC analysis was by A.R., D.N., A.C. and A.S.L., while mass spectrometry analysis was by A.R. and J.G. Chemical synthesis was by S.N. and R.A.F. Growth analysis on purified RG-II performed by D.N. and A.R. Gene deletion strains were created and characterized by D.N and I.V. Bioinformatics and genomic annotation were by N.T. and B.H. Bacterial growth and transcriptomic experiments were by J.B., Y.X. and E.C.M. Experiments were designed by D.N., A.R., A.C., A.S.L., E.C.M. and H.J.G. The manuscript was written by H.J.G. with contributions from G.J.D., B.H., M.A.O, B.R.U., E.C.M. and W.S.Y. Figures were prepared by A.R., A.L., D.N. and A.S.L.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Harry J. Gilbert.

Reviewer Information Nature thanks M. Czjzek, S. Duncan and S. Withers for their contribution to the peer review of this work.

Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    This file contains a Supplementary Discussion, additional references, Supplementary Tables 1-8 and Supplementary Figures 1-3.

About this article

Publication history






Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.