Comparison of DNA extraction methods for human gut microbial community profiling/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2025-4-9
Subjects
- Location of subjects
- Republic of Korea
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Nucleic acid extraction protocol Nucleic acid extraction protocol,nucleic acid extraction protocol
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No bead-beating method for QS kit
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Bead-beating method for QS kit
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Bead beating facilitates DNA recovery by lysing both Gram-negative and Gram-positive bacteria.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 1
- Group 1 sample size Number of subjects in the case (exposed) group
- 1
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2.0
Alpha Diversity
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-4-9
Source: Supplementary Fig. S7b
Description: Differential microbial abundance between the no-bead-beating and bead-beating groups for the QS kit, as determined by LEfSe analysis.
Abundance in Group 1: increased abundance in Bead-beating method for QS kit
Revision editor(s): Ameenatoloko, Montana-D
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-4-9
Source: Supplementary Fig. S7b
Description: Differential microbial abundance between the no-bead-beating and bead-beating groups for the QS kit, as determined by LEfSe analysis.
Abundance in Group 1: decreased abundance in Bead-beating method for QS kit
Revision editor(s): Ameenatoloko
