Numerical ecology validates a biogeographical distribution and gender-based effect on mucosa-associated bacteria along the human colon

被引:74
作者
de Carcer, Daniel Aguirre [1 ]
Cuiv, Paraic O. [1 ]
Wang, Tingting [1 ,2 ]
Kang, Seungha [1 ]
Worthley, Daniel [3 ,4 ]
Whitehall, Vicki [3 ,4 ]
Gordon, Iain
McSweeney, Chris [1 ]
Leggett, Barbara [3 ,4 ]
Morrison, Mark [1 ,5 ,6 ]
机构
[1] CSIRO Preventat Hlth Natl Res Flagship & Livestok, Queensland Biosci Precinct, Indooroopilly, Qld 4068, Australia
[2] Shanghai Jiao Tong Univ, Sch Life Sci & Biotechnol, Shanghai 200030, Peoples R China
[3] Queensland Inst Med Res, Brisbane, Qld 4006, Australia
[4] Royal Brisbane & Womens Hosp, Res Fdn, Conjoint Gastroenterol Lab, Brisbane, Qld, Australia
[5] Ohio State Univ, Dept Anim Sci, Columbus, OH 43210 USA
[6] Ohio State Univ, MAPLE Res Initat, Columbus, OH 43210 USA
关键词
biogeography; colorectum; microarray; numerical ecology; CULTURE-INDEPENDENT ANALYSIS; CROHNS-DISEASE; GASTROINTESTINAL-TRACT; ULCERATIVE-COLITIS; COLORECTAL-CANCER; MICROBIOTA; DIVERSITY; ILEAL; QUANTIFICATION; INSTABILITY;
D O I
10.1038/ismej.2010.177
中图分类号
Q14 [生态学(生物生态学)];
学科分类号
071012 ; 0713 ;
摘要
We applied constrained ordination numerical ecology methods to data produced with a human intestinal tract-specific phylogenetic microarray (the Aus-HIT Chip) to examine the microbial diversity associated with matched biopsy tissue samples taken from the caecum, transverse colon, sigmoid colon and rectum of 10 healthy patients. Consistent with previous studies, the profiles revealed a marked intersubject variability; however, the numerical ecology methods of analysis allowed the subtraction of the subject effect from the data and revealed, for the first time, evidence of a longitudinal gradient for specific microbes along the colorectum. In particular, probes targeting Streptococcus and Enterococcus spp. produced strongest signals with caecal and transverse colon samples, with a gradual decline through to the rectum. Conversely, the analyses suggest that several members of the Enterobacteriaceae increase in relative abundance towards the rectum. These collective differences were substantiated by the multivariate analysis of quantitative PCR data. We were also able to identify differences in the microarray profiles, especially for the streptococci and Faecalibacterium prausnitzii, on the basis of gender. The results derived by these multivariate analyses are biologically intuitive and suggest that the biogeography of the colonic mucosa can be monitored for changes through cross-sectional and/or inception cohort studies. The ISME Journal (2011) 5, 801-809; doi:10.1038/ismej.2010.177; published online 2 December 2010
引用
收藏
页码:801 / 809
页数:9
相关论文
共 60 条
[1]   Mucosa-associated bacterial diversity in relation to human terminal ileum and colonic biopsy samples [J].
Ahmed, Shakil ;
Macfarlane, George T. ;
Fite, Alemu ;
McBain, Andrew J. ;
Gilbert, Peter ;
Macfarlane, Sandra .
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2007, 73 (22) :7435-7442
[2]   Host-bacterial mutualism in the human intestine [J].
Bäckhed, F ;
Ley, RE ;
Sonnenburg, JL ;
Peterson, DA ;
Gordon, JI .
SCIENCE, 2005, 307 (5717) :1915-1920
[3]   Analysis with respect to instrumental variables for the exploration of microarray data structures [J].
Baty, Florent ;
Facompre, Michaeel ;
Wiegand, Jan ;
Schwager, Joseph ;
Brutsche, Martin H. .
BMC BIOINFORMATICS, 2006, 7 (1)
[4]   Stability of gene contributions and identification of outliers in multivariate analysis of microarray data [J].
Baty, Florent ;
Jaeger, Daniel ;
Preiswerk, Frank ;
Schumacher, Martin M. ;
Brutsche, Martin H. .
BMC BIOINFORMATICS, 2008, 9 (1)
[5]   Culture independent analysis of ileal mucosa reveals a selective increase in invasive Escherichia coli of novel phylogeny relative to depletion of Clostridiales in Crohn's disease involving the ileum [J].
Baumgart, Martin ;
Dogan, Belgin ;
Rishniw, Mark ;
Weitzman, Gil ;
Bosworth, Brian ;
Yantiss, Rhonda ;
Orsi, Renato H. ;
Wiedmann, Martin ;
McDonough, Patrick ;
Kim, Sung Guk ;
Berg, Douglas ;
Schukken, Ynte ;
Scherl, Ellen ;
Simpson, Kenneth W. .
ISME JOURNAL, 2007, 1 (05) :403-418
[6]   Through Ageing, and Beyond: Gut Microbiota and Inflammatory Status in Seniors and Centenarians [J].
Biagi, Elena ;
Nylund, Lotta ;
Candela, Marco ;
Ostan, Rita ;
Bucci, Laura ;
Pini, Elisa ;
Nikkila, Janne ;
Monti, Daniela ;
Satokari, Reetta ;
Franceschi, Claudio ;
Brigidi, Patrizia ;
De Vos, Willem .
PLOS ONE, 2010, 5 (05)
[7]   The bacteriology of biopsies differs between newly diagnosed, untreated, Crohn's disease and ulcerative colitis patients [J].
Bibiloni, Rodrigo ;
Mangold, Marco ;
Madsen, Karen L. ;
Fedorak, Richard N. ;
Tannock, Gerald W. .
JOURNAL OF MEDICAL MICROBIOLOGY, 2006, 55 (08) :1141-1149
[8]   A comparison of normalization methods for high density oligonucleotide array data based on variance and bias [J].
Bolstad, BM ;
Irizarry, RA ;
Åstrand, M ;
Speed, TP .
BIOINFORMATICS, 2003, 19 (02) :185-193
[9]   EFFECTS OF LACTULOSE AND OTHER LAXATIVES ON ILEAL AND COLONIC PH AS MEASURED BY A RADIOTELEMETRY DEVICE [J].
BOWN, RL ;
GIBSON, JA ;
SLADEN, GE ;
HICKS, B ;
DAWSON, AM .
GUT, 1974, 15 (12) :999-1004
[10]   Bacteria as the cause of ulcerative colitis [J].
Campieri, M ;
Gionchetti, P .
GUT, 2001, 48 (01) :132-135