Reducing bias in microbiome research: Comparing methods from sample collection to sequencing/Experiment 8

From BugSigDB


Reviewed Marked as Reviewed by Svetlana up on 2025-4-14

Curated date: 2025/04/12

Curator: Shulamite

Revision editor(s): Shulamite, KateRasheed

Subjects

Location of subjects
Netherlands
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
Mechanical disruption blood kit (MD-BK)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Enzymatical disruption blood kit (ED-BK)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Enzymatical disruption blood kit refers to enzymatical disruption (ED) that was purified with the Maxwell RSC Blood DNA kit (BK).
Group 0 sample size Number of subjects in the control (unexposed) group
14
Group 1 sample size Number of subjects in the case (exposed) group
14
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
3 Months

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
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
Mann-Whitney (Wilcoxon)
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)?
Yes

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged
Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-4-14

Curated date: 2025/04/12

Curator: Shulamite

Revision editor(s): Shulamite

Source: Fig 8A

Description: Boxplots show the relative abundance of the top most abundant phyla. The Wilcoxon test was used to calculate the adjusted p-values of the differences between the DNA extraction methods.

Abundance in Group 1: increased abundance in Enzymatical disruption blood kit (ED-BK)

NCBI Quality ControlLinks
Bacteroidota

Revision editor(s): Shulamite

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-4-14

Curated date: 2025/04/12

Curator: Shulamite

Revision editor(s): Shulamite

Source: Fig 8A

Description: Boxplots show the relative abundance of the top most abundant phyla. The Wilcoxon test was used to calculate the adjusted p-values of the differences between the DNA extraction methods.

Abundance in Group 1: decreased abundance in Enzymatical disruption blood kit (ED-BK)

NCBI Quality ControlLinks
Actinomycetota
Bacillota

Revision editor(s): Shulamite