Kindergarten Biogeography of Microorganisms
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB40975 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Biogeography of Microorganisms in Kindergarten Reveals Higher Pathogenic Burden in Children Hands.
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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
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.
2010-11-26 | GSE24582 | GEO
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. 10 patients, 5 males and 5 females. Four different locations along the colorectum.
2010-05-07 | E-GEOD-18933 | biostudies-arrayexpress
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
Project description:Effect of certain microorganisms on mouse gut microbial communities in aged group.
2021-09-24 | GSE180087 | GEO
Project description:Polystachya biogeography using Next-Generation Sequencing
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Project description:16S amplicon analysis of floor dust samples collected from a kindergarten over an 11 month period
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