Microbial biofilms in the gut: visualization by electron microscopy and by acridine orange staining

Ultrastruct Pathol. 2004 Jan-Feb;28(1):23-7.


The expression of colonization factors by gut bacteria, the growth rate of gut bacteria, and the rate of plasmid exchange by gut bacteria indicate that biofilms are a normal component of bacterial growth in the large bowel. Further, in vitro experiments demonstrate that growth of normal enteric bacteria in biofilms can be facilitated by secretory IgA (SIgA) and by mucins, 2 major components of the gut milieu. However, biofilms have not been previously observed in the normal gut. In this study, bacterial colonies characteristic of biofilms were observed by electron microscopy in normal rat, baboon, and human gut by electron microscopy. Confirming these results, acridine orange staining of flash-frozen tissues revealed biofilms in the mucus lining along normal gut epithelium. Immunofluorescenct microscopy supported this finding and demonstrated an association between IgA and the biofilms. These findings provide direct evidence that biofilms are present and may play an important role in the commensal relationship between enteric bacteria and their hosts. Hematoxylin and eosin staining of formalin-fixed tissues resulted in dissociation of the luminal contents from the epithelium, suggesting that the association between biofilms and the gut epithelium is sensitive to some conditions used to preserve tissue for histologic evaluation.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Acridine Orange*
  • Animals
  • Bacteria / growth & development
  • Bacteria / immunology
  • Bacteria / ultrastructure
  • Biofilms*
  • Fluorescent Dyes
  • Humans
  • Immunoglobulin A / analysis
  • Immunohistochemistry
  • Intestine, Large / immunology
  • Intestine, Large / microbiology*
  • Intestine, Large / ultrastructure
  • Microscopy, Electron / methods*
  • Papio
  • Rats
  • Staining and Labeling / methods*


  • Fluorescent Dyes
  • Immunoglobulin A
  • Acridine Orange