Human gut metagenome
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Similar Datasets
Project description:The effects from DNA extraction methods on the evaluation of microbial diversity associated with human colonic tissue
| PRJNA118215 | ENA
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.
2010-01-01 | GSE18420 | GEO
Project description:An improved methodology to overcome key issues associated with the methods of human fecal metagenomic DNA extraction
| PRJNA295000 | ENA
Project description:An improved methodology to overcome key issues associated with the methods of human fecal metagenomic DNA extraction
| PRJNA294995 | ENA
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
Project description:Evaluating Methods for the Optimal Extraction of Microbial Nucleic Acids for Analysis of the Human Gut Microbiota
| PRJNA255266 | ENA
Project description:Toward standards in clinical microbiome studies: comparison of DNA extraction methods and bioinformatic pipelines
| PRJEB34118 | ENA