Microbial colonization induces dynamic temporal and spatial patterns of NF-κB activation in the zebrafish digestive tract

Gastroenterology. 2011 Jul;141(1):197-207. doi: 10.1053/j.gastro.2011.03.042. Epub 2011 Mar 24.


Background & aims: The nuclear factor κ-light-chain enhancer of activated B cells (NF-κB) transcription factor pathway is activated in response to diverse microbial stimuli to regulate expression of genes involved in immune responses and tissue homeostasis. However, the temporal and spatial activation of NF-κB in response to microbial signals have not been determined in whole living organisms, and the molecular and cellular details of these responses are not well understood. We used in vivo imaging and molecular approaches to analyze NF-κB activation in response to the commensal microbiota in transparent gnotobiotic zebrafish.

Methods: We used DNA microarrays, in situ hybridization, and quantitative reverse transcription polymerase chain reaction analyses to study the effects of the commensal microbiota on gene expression in gnotobiotic zebrafish. Zebrafish PAC2 and ZFL cells were used to study the NF-κB signaling pathway in response to bacterial stimuli. We generated transgenic zebrafish that express enhanced green fluorescent protein under transcriptional control of NF-κB, and used them to study patterns of NF-κB activation during development and microbial colonization.

Results: Bacterial stimulation induced canonical activation of the NF-κB pathway in zebrafish cells. Colonization of germ-free transgenic zebrafish with a commensal microbiota activated NF-κB and led to up-regulation of its target genes in intestinal and extraintestinal tissues of the digestive tract. Colonization with the bacterium Pseudomonas aeruginosa was sufficient to activate NF-κB, and this activation required a functional flagellar apparatus.

Conclusions: In zebrafish, transcriptional activity of NF-κB is spatially and temporally regulated by specific microbial factors. The observed patterns of NF-κB-dependent responses to microbial colonization indicate that cells in the gastrointestinal tract respond robustly to the microbial environment.

Publication types

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

MeSH terms

  • Animals
  • Animals, Genetically Modified
  • Flagella / physiology
  • Gene Expression Profiling / methods
  • Gene Expression Regulation
  • Genes, Reporter
  • Green Fluorescent Proteins / biosynthesis
  • Green Fluorescent Proteins / genetics
  • Immunity, Innate
  • In Situ Hybridization
  • Intestinal Mucosa / metabolism
  • Intestines / immunology
  • Intestines / microbiology*
  • Larva / genetics
  • Larva / metabolism
  • Myeloid Differentiation Factor 88 / genetics
  • Myeloid Differentiation Factor 88 / metabolism
  • NF-kappa B / genetics
  • NF-kappa B / metabolism*
  • Oligonucleotide Array Sequence Analysis
  • Pseudomonas aeruginosa / immunology
  • Pseudomonas aeruginosa / physiology*
  • Reverse Transcriptase Polymerase Chain Reaction
  • Signal Transduction*
  • Time Factors
  • Transcriptional Activation
  • Zebrafish / genetics
  • Zebrafish / immunology
  • Zebrafish / metabolism
  • Zebrafish / microbiology*
  • Zebrafish Proteins / genetics
  • Zebrafish Proteins / metabolism*


  • Myeloid Differentiation Factor 88
  • NF-kappa B
  • Zebrafish Proteins
  • enhanced green fluorescent protein
  • Green Fluorescent Proteins

Associated data

  • GEO/GSE16857