PhyloChip microarray analysis reveals altered gastrointestinal microbial communities in a rat model of colonic hypersensitivity.
BACKGROUND
Irritable bowel syndrome (IBS) is a chronic, episodic gastrointestinal disorder that is prevalent in a significant fraction of western human populations; and changes in the microbiota of the large bowel have been implicated in the pathology of the disease.


METHODS
Using a novel comprehensive, high-density DNA microarray (PhyloChip) we performed a phylogenetic analysis of the microbial community of the large bowel in a rat model in which intracolonic acetic acid in neonates was used to induce long lasting colonic hypersensitivity and decreased stool water content and frequency, representing the equivalent of human constipation-predominant IBS.


RESULTS
Our results revealed a significantly increased compositional difference in the microbial communities in rats with neonatal irritation as compared with controls. Even more striking was the dramatic change in the ratio of Firmicutes relative to Bacteroidetes, where neonatally irritated rats were enriched more with Bacteroidetes and also contained a different composition of species within this phylum. Our study also revealed differences at the level of bacterial families and species.


CONCLUSIONS
The PhyloChip is a useful and convenient method to study enteric microflora. Further, this rat model system may be a useful experimental platform to study the causes and consequences of changes in microbial community composition associated with IBS.
Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA.
T A
TA
Nelson
S
S
Holmes
A V
AV
Alekseyenko
M
M
Shenoy
T
T
Desantis
C H
CH
Wu
G L
GL
Andersen
J
J
Winston
J
J
Sonnenburg
P J
PJ
Pasricha
A
A
Spormann
D019342:Acetic Acid / Q000009:adverse effects; D000818:Animals; D001105:Archaea / Q000235:genetics / Q000302:isolation & purification; D001419:Bacteria / Q000235:genetics / Q000302:isolation & purification; D004269:DNA, Bacterial / Q000235:genetics; D041981:Gastrointestinal Tract / Q000382:microbiology*; D043183:Irritable Bowel Syndrome / Q000139:chemically induced / Q000382:microbiology*; D008297:Male; D023421:Models, Animal; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010802:Phylogeny; D051381:Rats; D017207:Rats, Sprague-Dawley
D004269:DNA, Bacterial; D019342:Acetic Acid