A High-Throughput Organoid Microinjection Platform to Study Gastrointestinal Microbiota and Luminal Physiology

Cell Mol Gastroenterol Hepatol. 2018 May 22;6(3):301-319. doi: 10.1016/j.jcmgh.2018.05.004. eCollection 2018.


Background & aims: The human gut microbiota is becoming increasingly recognized as a key factor in homeostasis and disease. The lack of physiologically relevant in vitro models to investigate host-microbe interactions is considered a substantial bottleneck for microbiota research. Organoids represent an attractive model system because they are derived from primary tissues and embody key properties of the native gut lumen; however, access to the organoid lumen for experimental perturbation is challenging. Here, we report the development and validation of a high-throughput organoid microinjection system for cargo delivery to the organoid lumen and high-content sampling.

Methods: A microinjection platform was engineered using off-the-shelf and 3-dimensional printed components. Microinjection needles were modified for vertical trajectories and reproducible injection volumes. Computer vision (CVis) and microfabricated CellRaft Arrays (Cell Microsystems, Research Triangle Park, NC) were used to increase throughput and enable high-content sampling of mock bacterial communities. Modeling preformed using the COMSOL Multiphysics platform predicted a hypoxic luminal environment that was functionally validated by transplantation of fecal-derived microbial communities and monocultures of a nonsporulating anaerobe.

Results: CVis identified and logged locations of organoids suitable for injection. Reproducible loads of 0.2 nL could be microinjected into the organoid lumen at approximately 90 organoids/h. CVis analyzed and confirmed retention of injected cargos in approximately 500 organoids over 18 hours and showed the requirement to normalize for organoid growth for accurate assessment of barrier function. CVis analyzed growth dynamics of a mock community of green fluorescent protein- or Discosoma sp. red fluorescent protein-expressing bacteria, which grew within the organoid lumen even in the presence of antibiotics to control media contamination. Complex microbiota communities from fecal samples survived and grew in the colonoid lumen without appreciable changes in complexity.

Conclusions: High-throughput microinjection into organoids represents a next-generation in vitro approach to investigate gastrointestinal luminal physiology and the gastrointestinal microbiota.

Keywords: 2D, 2-dimensional; 3D, 3-dimensional; Anaerobic; Barrier Function; CAG, chicken beta-actin promoter with CMV enhancer; CFU, colony-forming unit; CRA, CellRaft Array; CVis, computer vision; EGFP, enhanced green fluorescent protein; FITC, fluorescein isothiocyanate; Fecal Microbiota; GFP, green fluorescent protein; GI, gastrointestinal; HF, hydrogen fluoride; High-Content Sampling; High-Throughput; Microinjection; OUT, operational taxonomic unit; Organoid; PBS, phosphate-buffered saline; PCR, polymerase chain reaction; QIIME, Quantitative Insights Into Microbial Ecology; WT, wild-type; hiPS, Human Induced Pluripotent Stem Cell; rRNA, ribosomal RNA.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Validation Study

MeSH terms

  • Animals
  • Bifidobacterium adolescentis / genetics
  • Bifidobacterium adolescentis / growth & development
  • Bifidobacterium adolescentis / isolation & purification
  • Colon / anatomy & histology
  • Colon / cytology*
  • Escherichia coli / genetics
  • Escherichia coli / growth & development
  • Feces / microbiology
  • Gastrointestinal Microbiome / physiology*
  • Gastrointestinal Tract / physiology*
  • Humans
  • Male
  • Mice
  • Microinjections / methods*
  • Organoids / anatomy & histology
  • Organoids / cytology*
  • Single-Cell Analysis
  • Video Recording
  • Yersinia pseudotuberculosis / genetics
  • Yersinia pseudotuberculosis / growth & development