Strain-level functional variation in the human gut microbiota based on bacterial binding to artificial food particles

Michael L. Patnode, Janaki L. Guruge, Juan J. Castillo, Garret A. Couture, Vincent Lombard, Nicolas Terrapon, Bernard Henrissat, Carlito B. Lebrilla, Jeffrey I. Gordon

Research output: Contribution to journalArticlepeer-review

Abstract

Greater understanding of the spatial relationships between members of the human gut microbiota and available nutrients is needed to gain deeper insights about community dynamics and expressed functions. Therefore, we generated a panel of artificial food particles with each type composed of microscopic paramagnetic beads coated with a fluorescent barcode and one of 60 different dietary or host glycan preparations. Analysis of 160 Bacteroides and Parabacteroides strains disclosed diverse strain-specific and glycan-specific binding phenotypes. We identified carbohydrate structures that correlated with binding by specific bacterial strains in vitro and noted strain-specific differences in the catabolism of glycans that mediate adhesion. Mixed in vitro cultures revealed that these adhesion phenotypes are maintained in more complex communities. Additionally, orally administering glycan beads to gnotobiotic mice confirmed specificity in glycan binding. This approach should facilitate analyses of how strains occupying the same physical niche interact, and it should advance the development of synbiotics, more nutritious foods, and microbiota-based diagnostics. Using fluorescently labeled, microscopic glass beads containing different bound glycans, Patnode et al. examine carbohydrate-dependent adhesion of gut bacterial strains. Strain-specific binding correlated with linkage composition of dietary glycans and adhesion was observed in mixed in vitro cultures and gnotobiotic mice. The method has basic scientific plus diagnostic and therapeutic applications.

Original languageEnglish (US)
JournalCell Host and Microbe
DOIs
StateAccepted/In press - 2021

Keywords

  • bacterial adhesion
  • glycan recognition and utilization
  • gnotobiotic mice
  • imaging microbiota spatial organization
  • multiplex bead-based phenotypic screens
  • retrievable artificial food particles

ASJC Scopus subject areas

  • Parasitology
  • Microbiology
  • Virology

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