Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition/Experiment 34

From BugSigDB


Needs review

Curated date: 2024/04/09

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Subjects

Location of subjects
Denmark
Host species Species from which microbiome was sampled. Contact us to have more species added.
Sus scrofa domesticus
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
Microbiome measurement Microbiome measurement,microbiome measurement
Group 0 name Corresponds to the control (unexposed) group for case-control studies
MagNAPure
Group 1 name Corresponds to the case (exposed) group for case-control studies
QIAStool
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).
Group 0 sample size Number of subjects in the control (unexposed) group
3
Group 1 sample size Number of subjects in the case (exposed) group
3

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).
raw counts
Statistical test
DESeq2
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.1
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
Chao1 Abundance-based estimator of species richness
decreased

Signature 1

Needs review

Curated date: 2024/04/10

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 2E

Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.

Abundance in Group 1: increased abundance in QIAStool

NCBI Quality ControlLinks
Prevotellaceae
Clostridiaceae
Campylobacteraceae
Veillonellaceae
Erysipelotrichaceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/10

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 2E

Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.

Abundance in Group 1: decreased abundance in QIAStool

NCBI Quality ControlLinks
Lachnospiraceae
Oscillospiraceae

Revision editor(s): Aleru Divine