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Biogeography of the human colorectum

ABSTRACT: We applied numerical ecology methods to data produced with a human intestinal tract-specific phylogenetic microarray (the Aus-HIT Chip) to examine the biogeography of mucosa-associated bacteria along the human colon. The microbial DNA associated with matched biopsy tissue samples taken from the cecum, transverse colon, sigmoid colon and rectum of 10 healthy patients was examined. Consistent with previous studies, the profiles revealed a marked inter-subject 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: with Streptococcus, Comamonadaceae, Enterococcus and Lactobacillus in greatest abundance at the cecum, with a gradual decline in their relative abundance through to the rectum. Conversely, the analyses suggest that members of the Enterobacteriaceae increase in relative abundance towards the rectum. These differences were validated by quantitative PCR. We were also able to identify significant differences in the profiles, especially for the Streptococci, on the basis of gender. The results derived by these multivariate analyses are biologically intuitive, and suggestive that the biogeography of the colonic mucosa can be monitored for changes via cross-sectional and/or inception cohort studies. 10 patients, 5 males and 5 females. Four different locations along the colorectum.

ORGANISM(S): Bacteria

SUBMITTER: Daniel Aguirre de Carcer

PROVIDER: E-GEOD-18933 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Biogeography of the human colorectum

Project description:We applied numerical ecology methods to data produced with a human intestinal tract-specific phylogenetic microarray (the Aus-HIT Chip) to examine the biogeography of mucosa-associated bacteria along the human colon. The microbial DNA associated with matched biopsy tissue samples taken from the cecum, transverse colon, sigmoid colon and rectum of 10 healthy patients was examined. Consistent with previous studies, the profiles revealed a marked inter-subject 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: with Streptococcus, Comamonadaceae, Enterococcus and Lactobacillus in greatest abundance at the cecum, with a gradual decline in their relative abundance through to the rectum. Conversely, the analyses suggest that members of the Enterobacteriaceae increase in relative abundance towards the rectum. These differences were validated by quantitative PCR. We were also able to identify significant differences in the profiles, especially for the Streptococci, on the basis of gender. The results derived by these multivariate analyses are biologically intuitive, and suggestive that the biogeography of the colonic mucosa can be monitored for changes via cross-sectional and/or inception cohort studies.

2010-03-01 | GSE18933 | GEO

The effects from DNA extraction methods on the evaluation of microbial diversity associated with human colonic tissue

Project description:Recent advances in (meta)genomic methods have provided new opportunities to examine host-microbe-environment interactions in the human gut. While opportunities exist to extract DNA from freshly sourced colonic tissue there are potentially valuable sources of DNA from historical studies that might also be examined. We examined how four different tissue DNA extraction methods employed in past clinical trials might impact the recovery of microbial DNA from a colonic tissue sample as assessed using a custom designed phylogenetic microarray for human gut bacteria and archaebacteria. While all methods of DNA extraction produced similar phylogenetic profiles some extraction specific biases were also observed. Real time PCR analysis targeting several bacterial groups substantiated this observation. These data suggest that while the efficacy of different DNA extraction methods differs somewhat all the methods tested produce an accurate representation of microbial diversity. This suggests that DNA samples archived in biobanks should be suitable for retrospective analyses. Three technical replicates per sample (extraction method) were analysed

2010-05-16 | E-GEOD-18420 | biostudies-arrayexpress

Biogeography of the human colorectum

Project description:Biogeography of the human colorectum

| PRJNA121045 | ENA

Gene expression patterns of biopsies from a colonoscopy taken in 2007 of an ulcerative colitis patient infected with Trichuris trichiura

Project description:Helminth infection may have the potential to suppress intestinal inflammation in inflammatory bowel diseases. Ulcerative colitis is more common in developed countries than in developing countries endemic for helminth infections. There are animal models, as well as clinical trials, suggesting therapeutic effects of experimental helminth infection. Here, we provide a comprehensive molecular portrait of dynamic changes in the intestinal mucosa of an individual who infected himself with Trichuris trichiura to treat his symptoms of ulcerative colitis. Genes involved in carbohydrate and lipid metabolism were upregulated in helminth-colonized tissue, while tissues with active colitis showed upregulation of proinflammatory genes such as IL-17, IL13RA2, and CHI3L1. T. trichiura colonization of the intestine may reduce symptomatic colitis by promoting goblet cell hyperplasia and mucus production through TH2 cytokines and IL-22. By better understanding the physiological effects of helminth infection, new therapies for ulcerative colitis could be identified. This is the first (out of three) series of arrays from this patient from a colonoscopy in 2007 when the patient had mild proctitis in the rectum and worms in the ascending and transverse colon. We analyzed 14 HEEBO arrays on which were hybridized RNA amplified from pinch biopsies collected from different regions of the colon. 3 samples were from the ascending colon, which was colonized by worms at the time. 2 samples were from the transverse colon, which was also colonized by worms at the time. 4 samples were from the sigmoid colon, which appeared normal at the time. 3 samples were from the rectum, which showed signs of proctitis and was inflamed at the time. 2 samples were from the terminal ileum, which was unaffected by worms or colitis.

2010-11-20 | E-GEOD-25275 | biostudies-arrayexpress

Microorganisms with Novel Dissimilatory (Bi)Sulfite Reductase Genes are Widespread and Core Microbiota in Low-Sulfate Peatlands

Project description:Peatlands of the Lehstenbach catchment (Germany) house so far unidentified microorganisms with phylogenetically novel variants of the dissimilatory (bi)sulfite reductase genes dsrAB. These genes are characteristic for microorganisms that reduce sulfate, sulfite, or some organosulfonates for energy conservation, but can also be present in anaerobic syntrophs. However, nothing is currently known regarding the abundance, community dynamics, and biogeography of these dsrAB-carrying microorganisms in peatlands. To tackle these issues, soils from a Lehstenbach catchment site (Schlöppnerbrunnen II fen) from different depths were sampled at three time points over a six-year period to analyze the diversity and distribution of dsrAB-containing microorganisms by a newly developed functional gene microarray and quantitative PCR assays. Members of novel, uncultivated dsrAB lineages (approximately representing species-level groups) (i) dominated a temporally stable but spatially structured dsrAB community and (ii) represented ‘core’ members (up to 1-1.7% relative abundance) of the autochthonous microbial community in this fen. In addition, denaturing gradient gel electrophoresis (DGGE)- and clone library-based comparison of the dsrAB diversity in soils from a wet meadow, three bogs, and five fens of various geographic locations (distance ~1-400 km), identified one Syntrophobacter-related and nine novel dsrAB lineages to be widespread in low-sulfate peatlands. Signatures of biogeography in dsrB-DGGE data were not correlated with geographic distance but could largely be explained by soil pH and wetland type, implying that distribution of dsrAB-carrying microorganisms in wetlands on the scale of a few hundred kilometers is not limited by dispersal but determined by contemporary environmental conditions. 36 dsrAB clones for chip evaluation, 33 hybridizations of labeled dsrAB RNA from environmental peatsoil samples

2010-11-26 | E-GEOD-24582 | biostudies-arrayexpress

Effect of ribosomal protein intron deletion on gene expression

Project description:Ribosomal proteins are essential to life. While the functions of ribosomal protein-encoding genes (RPGs) are highly conserved, the evolution of their regulatory mechanisms is remarkably dynamic. In Saccharomyces cerevisiae, RPGs are unusual in that they are commonly present as two highly similar gene copies and that they are over-represented among intron-containing genes. To investigate the role of introns in the regulation of RPG expression, we constructed 16 S. cerevisiae strains with precise deletions of RPG introns. We found that several yeast introns function to repress rather than to increase steady-state mRNA levels. Among these, the RPS9A and RPS9B introns were required for cross-regulation of the two paralogous gene copies, which is consistent with the duplication of an autoregulatory circuit. Splicing specific microarrays were used to assess the genome-wide defects in gene expression and pre-mRNA splicing that result from a deletion of a single ribosomal protein gene intron.

2012-03-01 | E-GEOD-35541 | biostudies-arrayexpress

Transcription profiling of primary rat hepatocyte model toxicology system dosed with carbon tetrachloride using three starting qualities of RNA to evaluate impact on the quality of hybridization signals on Agilent Platform

Project description:Array data from a primary rat hepatocyte model toxicology system dosed with carbon tetrachloride has been produced on Agilent and Codelink microarray platforms using three starting qualities of RNA (high (RIN: 9.0), medium (RIN: 5.0) and low (RIN: 2.5) quality, assessed by RIN number).

2007-11-01 | E-LGCL-7 | biostudies-arrayexpress

Structural evidence for consecutive Hel308-like modules in the spliceosomal ATPase Brr2

Project description:Brr2 is a DExD/H-box helicase responsible for U4/U6 unwinding, a critical step in spliceosomal activation. Brr2 contains an N-terminal domain and two tandem sets of a helicase-like domain followed by a Sec63 domain with unknown function. We determined the crystal structure of the second Sec63 domain, which unexpectedly resembles domains 4 and 5 of DNA helicase Hel308. The helicase-like domain upstream of Sec63 has clear sequence similarity with domains 1-3 of Hel308. In addition modeling indicates that Brr2 is composed of an N-terminal domain and two consecutive Hel308-like modules (Hel308-I and II). Together this provides our first glimpse of the overall structure of this large and unique spliceosomal ATPase and helicase. Our structural model and mutagenesis data suggest that Brr2 shares a similar helicase mechanism to Hel308, that differs from many DEAD-box proteins. We demonstrate that Hel308-II interacts with Prp8 and Snu114 in vitro and in vivo, potentially serving as a mediator for the regulation of Brr2â??s activity by Prp8. We further find that the C-terminal region of Prp8 (Prp8-CTR) facilitates the binding of the Brr2/Prp8-CTR complex to U4/U6, suggesting a potential role of Prp8-CTR as an auxiliary substrate binding and specificity domain for Brr2. Splicing specific microarrays were used to assess the genome-wide defects in pre-mRNA splicing that result from a deletion of the second Sec63 domain of yeast Brr2.

2010-05-18 | E-GEOD-16135 | biostudies-arrayexpress

OncomiR-21 triggers growth arrest of endothelial cells via a complex network involving p21 CDK2 CDC25A and NFIB

Project description:miRNA transcription in senescent human umbilical vein endothelial cells (HUVEC) compared to young HUVECs.

2013-01-17 | E-MEXP-3596 | biostudies-arrayexpress

Peripheral blood mononuclear cells, control vs. Kashin-Beck Disease

Project description:Objective: To investigate the differences between the gene expression profiles in peripheral blood mononuclear cells (PBMC) from normal controls and patients with Kashin-Beck disease (KBD). Methods: Twenty KBD patients and 12 normal subjects were selected from a KBD-endemic area and divided into four pairs of KBD vs. control (KBD, n=5 per pair; control, n=3 per pair). RNAs were respectively isolated from KBD PBMCs and normal PBMCs. Gene expression profiles were analyzed by oligonucleotide microarray. Two-condition experiment, control vs. KBD PBM cells. Biological replicates: 4 control replicates, 4 KBD replicates.

2011-09-22 | E-GEOD-32127 | biostudies-arrayexpress

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