Differential clustering of bowel biopsy-associated bacterial profiles of specimens collected in Mexico and Canada: what do these profiles represent?
Bowel commensals appear to be an important source of antigens that drive the chronic immune inflammation characteristic of Crohn's disease and ulcerative colitis [inflammatory bowel diseases (IBD)]. Biopsy-associated bacteria are assumed to be particularly relevant in bacteriological investigations of IBD because they are assumed to be located on the mucosal surface and hence close to immunological cells. This investigation analysed the bacterial collections associated with bowel biopsies, aspirates of residual fluid after bowel cleansing and faeces from IBD patients and non-IBD subjects in Edmonton, Canada, and Mexico City, Mexico. Temporal temperature gradient gel electrophoresis of 16S rRNA gene sequences produced profiles of the bacterial collections and their similarities were compared. Similarity analysis showed that the profiles did not cluster according to disease status, but that Canadian and Mexican profiles could be differentiated by this method. Comparison of biopsy, aspirate and faecal samples obtained from the same subject showed that, on average, the profiles were highly similar. Therefore, biopsy-associated bacteria are likely to represent, at least in part, contaminants from the fluid, which resembles a faecal solution, that pools in the bowel after cleansing prior to endoscopy.
Bibiloni
Rodrigo
R
Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada.
Tandon
Puneeta
P
Department of Medicine, Division of Gastroenterology, University of Alberta, Edmonton, Canada.
Vargas-Voracka
Florencia
F
Department of Gastroenterology, Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubrian, Mexico City, Mexico.
Barreto-Zuniga
Raphael
R
Department of Gastroenterology, Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubrian, Mexico City, Mexico.
Lupian-Sanchez
Andres
A
Department of Gastroenterology, Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubrian, Mexico City, Mexico.
Rico-Hinojosa
Miguel Angel
MA
Department of Gastroenterology, Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubrian, Mexico City, Mexico.
Guban
Jennifer
J
Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada.
Fedorak
Richard
R
Department of Medicine, Division of Gastroenterology, University of Alberta, Edmonton, Canada.
Tannock
Gerald W
GW
Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.|Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada.
D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D001706:Biopsy; D002170:Canada; D003093:Colitis, Ulcerative / Q000382:microbiology* / Q000473:pathology; D003424:Crohn Disease / Q000382:microbiology* / Q000473:pathology; D004269:DNA, Bacterial / Q000235:genetics; D006801:Humans; D007082:Ileum / Q000382:microbiology; D015212:Inflammatory Bowel Diseases / Q000382:microbiology / Q000473:pathology; D007413:Intestinal Mucosa / Q000382:microbiology* / Q000473:pathology; D008800:Mexico; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics
D004269:DNA, Bacterial; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S