Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Variations in Gut Microbiome Profiles Under Different DNA Extraction Methods: A Multidimensional Evaluation

PROVIDER: PRJNA807123 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR18048118_1.fastq.gz	Fastqsanger.gz
	SRR18048118_2.fastq.gz	Fastqsanger.gz
	SRR18048119_1.fastq.gz	Fastqsanger.gz
	SRR18048119_2.fastq.gz	Fastqsanger.gz
	SRR18048120_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 120

Similar Datasets

Microbiome analysis of soybean nodule

Project description:Metagenomic analysis of soybean nodule with different DNA extraction methods

| PRJEB83845 | ENA

Homo sapiens

Project description:H sapiens brain genome sequencing with different DNA extraction methods

| PRJNA291342 | ENA

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.

2010-01-01 | GSE18420 | GEO

Project description:Impact of DNA extraction methods and comparison of different sampling spots of the cattle microbiome

| PRJNA718141 | ENA

Project description:Evaluation of DNA extraction methods in microbial community profiling associated with deadwood decomposition

| PRJNA1104661 | ENA

marine metagenome

Project description:Evaluation of filtration and DNA extraction methods for environmental DNA biodiversity assessments across multiple trophic levels.

| PRJNA358589 | ENA

Multi-level microbial fingerprinting in anaerobic digestion reveals consistent fingerprinting profiles

Project description:The anaerobic digestion microbiomes has been puzzling us since the dawn of molecular methods for mixed microbial community analysis. Monitoring of the anaerobic digestion microbiome can either take place via a holistic evaluation of the microbial community through fingerprinting or by targeted monitoring of selected taxa. Here, we compared four different microbial community fingerprinting methods, i.e., amplicon sequencing, metaproteomics, metabolomics and phenotypics, in their ability to reflect the full-scale anaerobic digestion microbiome. The phenotypic fingerprinting reflects a, for anaerobic digestion, novel, single cell-based approach of direct microbial community fingerprinting. Three different digester types, i.e., sludge digesters, digesters treating agro-industrial waste and dry anaerobic digesters reflected different operational parameters. The α-diversity analysis yielded inconsistent results, especially for richness, across the different methods. In contrast, β-diversity analysis resulted in comparable profiles, even when translated into phyla or functions, with clear separation of the three digester types. In-depth analysis of each method's features i.e., operational taxonomic units, metaproteins, metabolites, and phenotypic traits, yielded certain similar features yet, also some clear differences between the different methods, which was related to the complexity of the anaerobic digestion process. In conclusion, phenotypic fingerprinting is a reliable, fast method for holistic monitoring of the anaerobic digestion microbiome, and the complementary identification of key features through other methods could give rise to a direct interpretation of anaerobic digestion process performance.

2021-05-26 | PXD024788 | Pride

Evaluation of lysis methods for the extraction of bacterial DNA for analysis of the broiler chicken cecal microbiota

Project description:Methods for the extraction of bacterial DNA

| PRJEB25932 | ENA

Project description:Evaluation of fecal DNA extraction protocols for human gut microbiome studies

| PRJEB37658 | ENA

Comparing and optimizing protein extraction methods for the analyses of human fecal microbiome via metaproteomics approach

Project description:Metaproteomic analysis offers critical insights into gut microbiome function; however, efficient microbial protein extraction from fecal samples remains challenging due to the complexity of different types of bacterial cell walls in the microbiome. In this study, we systematically compared three representative detergent-based lysis buffers (SDS_urea, DDM_urea, SDS_DDM_urea) for metaproteomics sample preparation. After multiple levels of analyses, we identified SDS_DDM_urea as the most efficient option for extracting diverse microbial proteins, peptides, and identifying microbial species. Applying this optimized method to samples from a dietary intervention study (Summer Harvest Adventure), we found minimal group-level microbial diversity shifts during this type of intervention, but substantial individual-specific variations reflected by metaproteomics results. Functional analyses also revealed microbial protein changes, especially proteins related to metabolic adaptations, including enhanced carbohydrate metabolism, amino acid biosynthesis, vitamin transport, and increased expression of membrane-associated proteins. Our results highlighted the personalized microbiome response to dietary interventions and underscored the importance of selecting appropriate protein extraction methods to accurately capture microbiome functional dynamics in microbiome analyses via metaproteomics.

2025-05-10 | PXD063844 |

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data