Differential bacterial capture and transport preferences facilitate co-growth on dietary xylan in the human gut

Abstract

Metabolism of dietary glycans is pivotal in shaping the human gut microbiota. However, the mechanisms that promote competition for glycans among gut commensals remain unclear. Roseburiaintestinalis, an abundant butyrate-producing Firmicute, is a key degrader of the major dietary fibre xylan. Despite the association of this taxon to a healthy microbiota, insight is lacking into its glycan utilization machinery. Here, we investigate the apparatus that confers R.intestinalis growth on different xylans. R.intestinalis displays a large cell-attached modular xylanase that promotes multivalent and dynamic association to xylan via four xylan-binding modules. This xylanase operates in concert with an ATP-binding cassette transporter to mediate breakdown and selective internalization of xylan fragments. The transport protein of R.intestinalis prefers oligomers of 4–5 xylosyl units, whereas the counterpart from a model xylan-degrading Bacteroides commensal targets larger ligands. Although R.intestinalis and the Bacteroides competitor co-grew in a mixed culture on xylan, R.intestinalis dominated on the preferred transport substrate xylotetraose. These findings highlight the differentiation of capture and transport preferences as a possible strategy to facilitate co-growth on abundant dietary fibres and may offer a unique route to manipulate the microbiota based on glycan transport preferences in therapeutic interventions to boost distinct taxa.

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Fig. 1: Growth of R.intestinalis and induction of extracellular activity.
Fig. 2: The core xylan utilization apparatus of R.intestinalis.
Fig. 3: A low-affinity xylan-binding module mediates extended xylan binding to the xylanase RiXyn10A.
Fig. 4: Intracellular xylo-oligosaccharide depolymerization.
Fig. 5: Model for xylan utilization by R.intestinalis and competition assay with B.ovatus.

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Acknowledgements

We thank B. Henrissat, architecture et fonction des macromolécules biologiques, CNRS, Aix-Marseille University and the curator of CAZy, for his advice and discussions on the assignment of the novel CBMx and the esterase. We also thank M. Yadav, US Department of Agriculture, Agricultural Research Service, for the kind gift of cornbran xylan, and BioCHOS AS for providing the chitooligo (CHOS) sample. M. Due, T. Holm Madsen and C. Aaarup Christensen are thanked for their technical help in cloning recombinant proteins and the performance of binding experiments. We also wish to thank A. Schultz, H. Juel Martens and M. Hansen, PLEN, University of Copenhagen, for the use of the confocal laser scanning microscopy in the initial microscopy experiments. This project was funded by a Graduate School DTU Scholarship, Lyngby, Denmark. Additional fundings were from the Danish Research Council for Independent Research, Natural Sciences (DFF, FNU) by a Research Project 2 grant (grant ID: 4002-00297B), a BIONÆR project (grant number: 244259) and the Norwegian NMR Platform, NNP (F.L.A.) from the Research Council of Norway (226244). Carlsberg Foundation is acknowledged for an ITC instrument grant (2011-01-0598).

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Growth analysis was performed by M.L.L. Transcriptomic analysis was done by M.L.L., C.W. and D.A.E. Enzyme characterization was performed by M.L.L., M.E., S.S.P., F.L.A. and B.W. qPCR was done by M.L.L. and M.I.B. Microscopy was perfromed by M.L.L. and C.S. Experiments were designed by M.L.L. and M.A.H. The manuscript written by M.L.L. and M.A.H. with contributions from T.R.L., B.W. and F.L.A. Figures were prepared by M.L.L.

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Correspondence to Maher Abou Hachem.

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Supplementary Tables 2–14, Supplementary Figures 1– 9.

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Supplementary Table 1

R. intestinalis L1–82 gene expression in response to xylose (X1) relative to glucose (Glc) obtained from RNA-seq analysis.

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Leth, M.L., Ejby, M., Workman, C. et al. Differential bacterial capture and transport preferences facilitate co-growth on dietary xylan in the human gut. Nat Microbiol 3, 570–580 (2018). https://doi.org/10.1038/s41564-018-0132-8

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