POUCH-ANAL ANASTOMOSIS;
CORE GUT MICROBIOME;
ILEAL;
SUSCEPTIBILITY;
EXPRESSION;
DIVERSITY;
PATHOLOGY;
D O I:
10.1097/MIB.0000000000000674
中图分类号:
R57 [消化系及腹部疾病];
学科分类号:
摘要:
Inflammatory bowel disease has been associated with differential abundance of numerous organisms when compared to healthy controls (HCs); however, few studies have investigated variability in the microbiome across intestinal locations and how this variability might be related to disease location and phenotype. In this study, we have analyzed the microbiome of a large cohort of individuals recruited at Mount Sinai Hospital in Toronto, Canada. Biopsies were taken from subjects with Crohn's disease, ulcerative colitis, and HC, and also individuals having undergone ileal pouch-anal anastomosis for treatment of ulcerative colitis or familial adenomatous polyposis. Microbial 16S rRNA was sequenced using the Illumina MiSeq platform. We observed a great deal of variability in the microbiome characterizing different sampling locations. Samples from pouch and afferent limb were comparable in microbial composition. When comparing sigmoid and terminal ileum samples, more differences were observed. The greatest number of differentially abundant microbes was observed when comparing either pouch or afferent limb samples to sigmoid or terminal ileum. Despite these differences, we were able to observe modest microbial variability between inflammatory bowel disease phenotypes and HCs, even when controlling for sampling location and additional experimental factors. Most detected associations were observed between HCs and Crohn's disease, with decreases in specific genera in the families Ruminococcaceae and Lachnospiraceae characterizing tissue samples from individuals with Crohn's disease. This study highlights important considerations when analyzing the composition of the microbiome and also provides useful insight into differences in the microbiome characterizing these seemingly related phenotypes.
机构:
Univ Colorado, Cooperat Inst Res Environm Sci, Boulder, CO 80309 USA
Univ Colorado, Dept Ecol & Evolutionary Biol, Boulder, CO 80309 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Fierer, Noah
Gordon, Jeffrey I.
论文数: 0引用数: 0
h-index: 0
机构:
Washington Univ, Sch Med, Ctr Genome Sci & Syst Biol, St Louis, MO 63108 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Gordon, Jeffrey I.
Knight, Rob
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Univ Colorado, Howard Hughes Med Inst, Boulder, CO 80309 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
机构:
Univ Colorado, Dept Chem & Biochem, Boulder, CO 80309 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Caporaso, J. Gregory
Kuczynski, Justin
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado, Dept Mol Cellular & Dev Biol, Boulder, CO 80309 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Kuczynski, Justin
Stombaugh, Jesse
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado, Dept Chem & Biochem, Boulder, CO 80309 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Stombaugh, Jesse
Bittinger, Kyle
论文数: 0引用数: 0
h-index: 0
机构:
Univ Penn, Dept Microbiol, Philadelphia, PA 19104 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Bittinger, Kyle
Bushman, Frederic D.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Penn, Dept Microbiol, Philadelphia, PA 19104 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Bushman, Frederic D.
Costello, Elizabeth K.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado, Dept Chem & Biochem, Boulder, CO 80309 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Costello, Elizabeth K.
Fierer, Noah
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado, Cooperat Inst Res Environm Sci, Boulder, CO 80309 USA
Univ Colorado, Dept Ecol & Evolutionary Biol, Boulder, CO 80309 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Fierer, Noah
Pena, Antonio Gonzalez
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado, Dept Comp Sci, Boulder, CO 80309 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Pena, Antonio Gonzalez
Goodrich, Julia K.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado, Dept Comp Sci, Boulder, CO 80309 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Goodrich, Julia K.
Gordon, Jeffrey I.
论文数: 0引用数: 0
h-index: 0
机构:
Washington Univ, Sch Med, Ctr Genome Sci, St Louis, MO USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Gordon, Jeffrey I.
Huttley, Gavin A.
论文数: 0引用数: 0
h-index: 0
机构:
Australian Natl Univ, John Curtin Sch Med Res, Computat Genom Lab, Canberra, ACT 2601, AustraliaUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Huttley, Gavin A.
Kelley, Scott T.
论文数: 0引用数: 0
h-index: 0
机构:
San Diego State Univ, Dept Biol, San Diego, CA 92182 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Kelley, Scott T.
Knights, Dan
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado, Dept Comp Sci, Boulder, CO 80309 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Knights, Dan
Koenig, Jeremy E.
论文数: 0引用数: 0
h-index: 0
机构:
Cornell Univ, Dept Microbiol, Ithaca, NY USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Koenig, Jeremy E.
Ley, Ruth E.
论文数: 0引用数: 0
h-index: 0
机构:
Cornell Univ, Dept Microbiol, Ithaca, NY USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Ley, Ruth E.
Lozupone, Catherine A.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado, Dept Chem & Biochem, Boulder, CO 80309 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Lozupone, Catherine A.
McDonald, Daniel
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado, Dept Chem & Biochem, Boulder, CO 80309 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
McDonald, Daniel
Muegge, Brian D.
论文数: 0引用数: 0
h-index: 0
机构:
Washington Univ, Sch Med, Ctr Genome Sci, St Louis, MO USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Muegge, Brian D.
Pirrung, Meg
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado, Dept Chem & Biochem, Boulder, CO 80309 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Pirrung, Meg
Reeder, Jens
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado, Dept Chem & Biochem, Boulder, CO 80309 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Reeder, Jens
Sevinsky, Joel R.
论文数: 0引用数: 0
h-index: 0
机构:
Luca Technol, Golden, CO USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Sevinsky, Joel R.
Tumbaugh, Peter J.
论文数: 0引用数: 0
h-index: 0
机构:
Washington Univ, Sch Med, Ctr Genome Sci, St Louis, MO USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Tumbaugh, Peter J.
Walters, William A.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado, Dept Mol Cellular & Dev Biol, Boulder, CO 80309 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Walters, William A.
Widmann, Jeremy
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado, Dept Chem & Biochem, Boulder, CO 80309 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Widmann, Jeremy
Yatsunenko, Tanya
论文数: 0引用数: 0
h-index: 0
机构:
Washington Univ, Sch Med, Ctr Genome Sci, St Louis, MO USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Yatsunenko, Tanya
Zaneveld, Jesse
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado, Dept Mol Cellular & Dev Biol, Boulder, CO 80309 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Zaneveld, Jesse
Knight, Rob
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Univ Colorado, Howard Hughes Med Inst, Boulder, CO 80309 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
机构:
Univ Colorado, Cooperat Inst Res Environm Sci, Boulder, CO 80309 USA
Univ Colorado, Dept Ecol & Evolutionary Biol, Boulder, CO 80309 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Fierer, Noah
Gordon, Jeffrey I.
论文数: 0引用数: 0
h-index: 0
机构:
Washington Univ, Sch Med, Ctr Genome Sci & Syst Biol, St Louis, MO 63108 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Gordon, Jeffrey I.
Knight, Rob
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Univ Colorado, Howard Hughes Med Inst, Boulder, CO 80309 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
机构:
Univ Colorado, Dept Chem & Biochem, Boulder, CO 80309 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Caporaso, J. Gregory
Kuczynski, Justin
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado, Dept Mol Cellular & Dev Biol, Boulder, CO 80309 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Kuczynski, Justin
Stombaugh, Jesse
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado, Dept Chem & Biochem, Boulder, CO 80309 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Stombaugh, Jesse
Bittinger, Kyle
论文数: 0引用数: 0
h-index: 0
机构:
Univ Penn, Dept Microbiol, Philadelphia, PA 19104 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Bittinger, Kyle
Bushman, Frederic D.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Penn, Dept Microbiol, Philadelphia, PA 19104 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Bushman, Frederic D.
Costello, Elizabeth K.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado, Dept Chem & Biochem, Boulder, CO 80309 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Costello, Elizabeth K.
Fierer, Noah
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado, Cooperat Inst Res Environm Sci, Boulder, CO 80309 USA
Univ Colorado, Dept Ecol & Evolutionary Biol, Boulder, CO 80309 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Fierer, Noah
Pena, Antonio Gonzalez
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado, Dept Comp Sci, Boulder, CO 80309 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Pena, Antonio Gonzalez
Goodrich, Julia K.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado, Dept Comp Sci, Boulder, CO 80309 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Goodrich, Julia K.
Gordon, Jeffrey I.
论文数: 0引用数: 0
h-index: 0
机构:
Washington Univ, Sch Med, Ctr Genome Sci, St Louis, MO USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Gordon, Jeffrey I.
Huttley, Gavin A.
论文数: 0引用数: 0
h-index: 0
机构:
Australian Natl Univ, John Curtin Sch Med Res, Computat Genom Lab, Canberra, ACT 2601, AustraliaUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Huttley, Gavin A.
Kelley, Scott T.
论文数: 0引用数: 0
h-index: 0
机构:
San Diego State Univ, Dept Biol, San Diego, CA 92182 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Kelley, Scott T.
Knights, Dan
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado, Dept Comp Sci, Boulder, CO 80309 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Knights, Dan
Koenig, Jeremy E.
论文数: 0引用数: 0
h-index: 0
机构:
Cornell Univ, Dept Microbiol, Ithaca, NY USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Koenig, Jeremy E.
Ley, Ruth E.
论文数: 0引用数: 0
h-index: 0
机构:
Cornell Univ, Dept Microbiol, Ithaca, NY USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Ley, Ruth E.
Lozupone, Catherine A.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado, Dept Chem & Biochem, Boulder, CO 80309 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Lozupone, Catherine A.
McDonald, Daniel
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado, Dept Chem & Biochem, Boulder, CO 80309 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
McDonald, Daniel
Muegge, Brian D.
论文数: 0引用数: 0
h-index: 0
机构:
Washington Univ, Sch Med, Ctr Genome Sci, St Louis, MO USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Muegge, Brian D.
Pirrung, Meg
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado, Dept Chem & Biochem, Boulder, CO 80309 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Pirrung, Meg
Reeder, Jens
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado, Dept Chem & Biochem, Boulder, CO 80309 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Reeder, Jens
Sevinsky, Joel R.
论文数: 0引用数: 0
h-index: 0
机构:
Luca Technol, Golden, CO USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Sevinsky, Joel R.
Tumbaugh, Peter J.
论文数: 0引用数: 0
h-index: 0
机构:
Washington Univ, Sch Med, Ctr Genome Sci, St Louis, MO USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Tumbaugh, Peter J.
Walters, William A.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado, Dept Mol Cellular & Dev Biol, Boulder, CO 80309 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Walters, William A.
Widmann, Jeremy
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado, Dept Chem & Biochem, Boulder, CO 80309 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Widmann, Jeremy
Yatsunenko, Tanya
论文数: 0引用数: 0
h-index: 0
机构:
Washington Univ, Sch Med, Ctr Genome Sci, St Louis, MO USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Yatsunenko, Tanya
Zaneveld, Jesse
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado, Dept Mol Cellular & Dev Biol, Boulder, CO 80309 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Zaneveld, Jesse
Knight, Rob
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
Univ Colorado, Howard Hughes Med Inst, Boulder, CO 80309 USAUniv Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA