Reducing bias in microbiome research: Comparing methods from sample collection to sequencing/Experiment 4

From BugSigDB


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

Curated date: 2025/04/04

Curator: Shulamite

Revision editor(s): Shulamite

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
Sample collection protocol Sample collection protocol,sample collection protocol
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Frozen OMNIgene GUT control (-80-OMCON)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Room temperature OMNIgene GUT buffer (RT-OMBUF)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
OMNIgene·GUT tube with a stabilization buffer and stored at RT for 3–5 days before freezing at −80°C
Group 0 sample size Number of subjects in the control (unexposed) group
65
Group 1 sample size Number of subjects in the case (exposed) group
65
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
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)?
Yes
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
4

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: 2025/04/04

Curator: Shulamite

Revision editor(s): Shulamite

Source: Supplementary Fig 2d

Description: LEfSe analysis showing the significantly distinguishing taxa between the different storage methods based on an LDA score >4.0. Showing the effect of storage at RT, with or without a stabilization buffer in green, compared to the control samples in red.

Abundance in Group 1: increased abundance in Room temperature OMNIgene GUT buffer (RT-OMBUF)

NCBI Quality ControlLinks
Bacteroidaceae
Bacteroidales
Bacteroides
Bacteroidia
Bacteroidota
Phocaeicola vulgatus

Revision editor(s): Shulamite

Signature 2

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

Curated date: 2025/04/04

Curator: Shulamite

Revision editor(s): Shulamite

Source: Supplementary Fig 2d

Description: LEfSe analysis showing the significantly distinguishing taxa between the different storage methods based on an LDA score >4.0. Showing the effect of storage at RT, with or without a stabilization buffer in green, compared to the control samples in red.

Abundance in Group 1: decreased abundance in Room temperature OMNIgene GUT buffer (RT-OMBUF)

NCBI Quality ControlLinks
Actinomycetota
Bacillota
Bifidobacteriaceae
Bifidobacteriales
Bifidobacterium
Blautia
Clostridia
Coriobacteriales
Coriobacteriia
Lachnospiraceae
Lachnospirales
Acidimicrobiia

Revision editor(s): Shulamite