Spatial organization of intestinal microbiota in health and disease
- Alexander Swidsinski, MD
Alexander Swidsinski, MD
- Laboratory for Molecular Genetics,
- Polymicrobial Infections, and Bacterial Biofilms
- Humboldt University, Charité Hospital
- Vera Loening-Baucke, MD
Vera Loening-Baucke, MD
- Professor Emerita, Pediatrics
- The University of Iowa
The alimentary tract represents an interface between the external environment and the body. Within it exists a complex polymicrobial ecology that interacts with the internal and external environment and has an important influence on health and disease.
The properties of isolated microorganisms do not explain how the polymicrobial community functions or why its organisms can grow under conditions that should be deadly to them . An understanding of how microorganisms interact with each other, their host, and the luminal contents is expanding rapidly.
A major advance in understanding the function of the intestinal microbiota has been the development of techniques that permit a detailed assessment of the composition of the flora and its distribution throughout the alimentary tract. One of the methods to visualize single bacterial species within complex communities is called ribosomal RNA fluorescence in situ hybridization (FISH).
Each bacterium possesses tens of thousands of ribosomes, each of which includes a copy of the bacterial RNA. Some of the regions of the ribosomal RNA are strain-specific, others are universal for groups, domains, or even kingdoms. Synthetically produced oligonucleotides that are complementary to sequences of interest can be labeled with fluorescent dye and added to samples containing bacteria. These oligonucleotides, called FISH probes, hybridize with RNA of bacterial ribosomes. Bacteria can be visualized with the microscope directly without additional enhancement because of the high number of ribosomes within each bacterium [2,3].
The names of the FISH probes described in this topic review are based on abbreviations of probeBase online resource for rRNA-targeted oligonucleotide probes .
- Kuramitsu HK, He X, Lux R, et al. Interspecies interactions within oral microbial communities. Microbiol Mol Biol Rev 2007; 71:653.
- Amann RI, Ludwig W, Schleifer KH. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 1995; 59:143.
- Amann R, Fuchs BM. Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques. Nat Rev Microbiol 2008; 6:339.
- Loy A, Maixner F, Wagner M, Horn M. probeBase--an online resource for rRNA-targeted oligonucleotide probes: new features 2007. Nucleic Acids Res 2007; 35:D800.
- Swidsinski A, Göktas O, Bessler C, et al. Spatial organisation of microbiota in quiescent adenoiditis and tonsillitis. J Clin Pathol 2007; 60:253.
- Kandulski A, Selgrad M, Malfertheiner P. Helicobacter pylori infection: a clinical overview. Dig Liver Dis 2008; 40:619.
- Swidsinski A, Schlien P, Pernthaler A, et al. Bacterial biofilm within diseased pancreatic and biliary tracts. Gut 2005; 54:388.
- Scheithauer BK, Wos-Oxley ML, Ferslev B, et al. Characterization of the complex bacterial communities colonizing biliary stents reveals a host-dependent diversity. ISME J 2009; 3:797.
- Swidsinski A, Weber J, Loening-Baucke V, et al. Spatial organization and composition of the mucosal flora in patients with inflammatory bowel disease. J Clin Microbiol 2005; 43:3380.
- Franks AH, Harmsen HJ, Raangs GC, et al. Variations of bacterial populations in human feces measured by fluorescent in situ hybridization with group-specific 16S rRNA-targeted oligonucleotide probes. Appl Environ Microbiol 1998; 64:3336.
- Harmsen HJ, Raangs GC, He T, et al. Extensive set of 16S rRNA-based probes for detection of bacteria in human feces. Appl Environ Microbiol 2002; 68:2982.
- Dethlefsen L, Huse S, Sogin ML, Relman DA. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol 2008; 6:e280.
- Swidsinski A, Loening-Baucke V, Lochs H, Hale LP. Spatial organization of bacterial flora in normal and inflamed intestine: a fluorescence in situ hybridization study in mice. World J Gastroenterol 2005; 11:1131.
- Swidsinski A, Sydora BC, Doerffel Y, et al. Viscosity gradient within the mucus layer determines the mucosal barrier function and the spatial organization of the intestinal microbiota. Inflamm Bowel Dis 2007; 13:963.
- Swidsinski A, Loening-Baucke V, Verstraelen H, et al. Biostructure of fecal microbiota in healthy subjects and patients with chronic idiopathic diarrhea. Gastroenterology 2008; 135:568.
- Swidsinski A, Loening-Baucke V, Vaneechoutte M, Doerffel Y. Active Crohn's disease and ulcerative colitis can be specifically diagnosed and monitored based on the biostructure of the fecal flora. Inflamm Bowel Dis 2008; 14:147.
- Swidsinski A, Mendling W, Loening-Baucke V, et al. Adherent biofilms in bacterial vaginosis. Obstet Gynecol 2005; 106:1013.
- Okayasu I, Hatakeyama S, Yamada M, et al. A novel method in the induction of reliable experimental acute and chronic ulcerative colitis in mice. Gastroenterology 1990; 98:694.
- Swidsinski A, Ung V, Sydora BC, et al. Bacterial overgrowth and inflammation of small intestine after carboxymethylcellulose ingestion in genetically susceptible mice. Inflamm Bowel Dis 2009; 15:359.
- EVOLUTION'S ROLE IN THE DISTRIBUTION OF INTESTINAL MICROBIOTA
- BACTERIA IN THE UPPER GASTROINTESTINAL TRACT
- Stomach and duodenum
- Pancreatic tract
- Biliary tract
- - Gallstones
- Small intestine
- BACTERIA IN THE COLON
- The role of microbiota in colonic function
- Mucus barrier
- Biostructure of fecal microbiota
- DISRUPTION OF THE MUCUS BARRIER
- Unrecognized pathogens
- Substances that reduce the viscosity of the mucus barrier
- - Detergents
- - Emulsifiers
- - Other causes
- BIOSTRUCTURE OF FECAL MICROBIOTA IN HEALTH AND INFLAMMATORY BOWEL DISEASE
- Nonspecific changes of the colonic microbial biostructure
- Changes of the colonic microbial biostructure in IBD
- SUMMARY AND RECOMMENDATIONS