Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- Denmark
- 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
- Microbiome measurement Microbiome measurement,microbiome measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- InnuPURE
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- MagNAPure
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- DNA isolation from human fecal samples using MagNA Pure LC DNA isolation Kit III, Roche (MagNAPure).
- 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
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: increased abundance in MagNAPure
| NCBI | Quality Control | Links |
|---|---|---|
| Alcaligenaceae | ||
| Prevotellaceae | ||
| Veillonellaceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: decreased abundance in MagNAPure
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidaceae | ||
| Bifidobacteriaceae | ||
| Pasteurellaceae | ||
| Porphyromonadaceae | ||
| Verrucomicrobiaceae |
Revision editor(s): Aleru Divine
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Easy-DNA
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- DNA isolation from human fecal samples using Easy-DNATM gDNA Purification Kit, Invitrogen (Easy-DNA).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: increased abundance in Easy-DNA
| NCBI | Quality Control | Links |
|---|---|---|
| Veillonellaceae | ||
| Bifidobacteriaceae | ||
| Verrucomicrobiaceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: decreased abundance in Easy-DNA
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Bacteroidaceae | ||
| Porphyromonadaceae | ||
| Alcaligenaceae | ||
| Pasteurellaceae |
Revision editor(s): Aleru Divine
Experiment 3
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- FastDNA
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- DNA isolation from human fecal samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: increased abundance in FastDNA
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacteriaceae | ||
| Verrucomicrobiaceae |
Revision editor(s): Aleru002
Signature 2
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: decreased abundance in FastDNA
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Veillonellaceae | ||
| Bacteroidaceae | ||
| Porphyromonadaceae | ||
| Alcaligenaceae | ||
| Pasteurellaceae |
Revision editor(s): Aleru002
Experiment 4
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- PowerSoil.HMP
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- DNA isolation from human fecal samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: increased abundance in PowerSoil.HMP
| NCBI | Quality Control | Links |
|---|---|---|
| Veillonellaceae | ||
| Prevotellaceae |
Revision editor(s): Aleru002
Signature 2
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: decreased abundance in PowerSoil.HMP
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidaceae | ||
| Bifidobacteriaceae | ||
| Verrucomicrobiaceae | ||
| Porphyromonadaceae | ||
| Alcaligenaceae | ||
| Pasteurellaceae |
Revision editor(s): Aleru002
Experiment 5
Subjects
- 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 human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: increased abundance in QIAStool
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Veillonellaceae | ||
| Verrucomicrobiaceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: decreased abundance in QIAStool
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidaceae | ||
| Bifidobacteriaceae | ||
| Porphyromonadaceae | ||
| Alcaligenaceae | ||
| Pasteurellaceae |
Revision editor(s): Aleru Divine
Experiment 6
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- QIAStool+BB
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: increased abundance in QIAStool+BB
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacteriaceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: decreased abundance in QIAStool+BB
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Veillonellaceae | ||
| Bacteroidaceae | ||
| Verrucomicrobiaceae | ||
| Porphyromonadaceae | ||
| Alcaligenaceae | ||
| Pasteurellaceae |
Revision editor(s): Aleru Divine
Experiment 7
Subjects
- 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
- Easy-DNA
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- DNA isolation from human fecal samples using Easy-DNATM gDNA Purification Kit, Invitrogen (Easy-DNA).
Lab analysis
Statistical Analysis
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
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: increased abundance in Easy-DNA
| NCBI | Quality Control | Links |
|---|---|---|
| Verrucomicrobiaceae | ||
| Bifidobacteriaceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: decreased abundance in Easy-DNA
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Veillonellaceae | ||
| Bacteroidaceae | ||
| Porphyromonadaceae | ||
| Alcaligenaceae | ||
| Pasteurellaceae |
Revision editor(s): Aleru Divine
Experiment 8
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- FastDNA
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- DNA isolation from human fecal samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: increased abundance in FastDNA
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacteriaceae | ||
| Verrucomicrobiaceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: decreased abundance in FastDNA
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Veillonellaceae | ||
| Bacteroidaceae | ||
| Porphyromonadaceae | ||
| Alcaligenaceae | ||
| Pasteurellaceae |
Revision editor(s): Aleru Divine
Experiment 9
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- PowerSoil.HMP
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- DNA isolation from human fecal samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: increased abundance in PowerSoil.HMP
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacteriaceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: decreased abundance in PowerSoil.HMP
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Veillonellaceae | ||
| Bacteroidaceae | ||
| Verrucomicrobiaceae | ||
| Porphyromonadaceae | ||
| Alcaligenaceae |
Revision editor(s): Aleru Divine
Experiment 10
Subjects
- 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 human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: increased abundance in QIAStool
| NCBI | Quality Control | Links |
|---|---|---|
| Verrucomicrobiaceae | ||
| Veillonellaceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: decreased abundance in QIAStool
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Bacteroidaceae | ||
| Bifidobacteriaceae | ||
| Porphyromonadaceae | ||
| Alcaligenaceae | ||
| Pasteurellaceae |
Revision editor(s): Aleru Divine
Experiment 11
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- QIAStool+BB
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: increased abundance in QIAStool+BB
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacteriaceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: decreased abundance in QIAStool+BB
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Veillonellaceae | ||
| Bacteroidaceae | ||
| Verrucomicrobiaceae | ||
| Porphyromonadaceae | ||
| Alcaligenaceae | ||
| Pasteurellaceae |
Revision editor(s): Aleru Divine
Experiment 12
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Easy-DNA
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- FastDNA
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- DNA isolation from human fecal samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: increased abundance in FastDNA
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Bacteroidaceae | ||
| Porphyromonadaceae | ||
| Alcaligenaceae | ||
| Pasteurellaceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: decreased abundance in FastDNA
| NCBI | Quality Control | Links |
|---|---|---|
| Veillonellaceae | ||
| Bifidobacteriaceae | ||
| Verrucomicrobiaceae |
Revision editor(s): Aleru Divine
Experiment 13
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- PowerSoil.HMP
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- DNA isolation from human fecal samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: increased abundance in PowerSoil.HMP
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Veillonellaceae | ||
| Bacteroidaceae | ||
| Porphyromonadaceae | ||
| Alcaligenaceae | ||
| Pasteurellaceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: decreased abundance in PowerSoil.HMP
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacteriaceae | ||
| Verrucomicrobiaceae |
Revision editor(s): Aleru Divine
Experiment 14
Subjects
- 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 human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: increased abundance in QIAStool
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Veillonellaceae | ||
| Bacteroidaceae | ||
| Porphyromonadaceae | ||
| Alcaligenaceae | ||
| Pasteurellaceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: decreased abundance in QIAStool
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacteriaceae | ||
| Verrucomicrobiaceae |
Revision editor(s): Aleru Divine
Experiment 15
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- QIAStool+BB
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: increased abundance in QIAStool+BB
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Bacteroidaceae | ||
| Porphyromonadaceae | ||
| Alcaligenaceae | ||
| Pasteurellaceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: decreased abundance in QIAStool+BB
| NCBI | Quality Control | Links |
|---|---|---|
| Veillonellaceae | ||
| Bifidobacteriaceae | ||
| Verrucomicrobiaceae |
Revision editor(s): Aleru Divine
Experiment 16
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- FastDNA
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- PowerSoil.HMP
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- DNA isolation from human fecal samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: increased abundance in PowerSoil.HMP
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Veillonellaceae | ||
| Bacteroidaceae | ||
| Porphyromonadaceae | ||
| Alcaligenaceae | ||
| Pasteurellaceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: decreased abundance in PowerSoil.HMP
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacteriaceae | ||
| Verrucomicrobiaceae |
Revision editor(s): Aleru Divine
Experiment 17
Subjects
- 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 human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: increased abundance in QIAStool
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Veillonellaceae | ||
| Bacteroidaceae | ||
| Porphyromonadaceae | ||
| Alcaligenaceae | ||
| Pasteurellaceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: decreased abundance in QIAStool
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacteriaceae | ||
| Verrucomicrobiaceae |
Revision editor(s): Aleru Divine
Experiment 18
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- QIAStool+BB
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: increased abundance in QIAStool+BB
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Veillonellaceae | ||
| Bacteroidaceae | ||
| Bifidobacteriaceae | ||
| Porphyromonadaceae | ||
| Alcaligenaceae | ||
| Pasteurellaceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: decreased abundance in QIAStool+BB
| NCBI | Quality Control | Links |
|---|---|---|
| Verrucomicrobiaceae |
Revision editor(s): Aleru Divine
Experiment 19
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- PowerSoil.HMP
- 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 human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: increased abundance in QIAStool
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Veillonellaceae | ||
| Verrucomicrobiaceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: decreased abundance in QIAStool
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidaceae | ||
| Bifidobacteriaceae | ||
| Porphyromonadaceae | ||
| Alcaligenaceae | ||
| Pasteurellaceae |
Revision editor(s): Aleru Divine
Experiment 20
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- QIAStool+BB
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- DNA isolation from human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: increased abundance in QIAStool+BB
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacteriaceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: decreased abundance in QIAStool+BB
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Veillonellaceae | ||
| Bacteroidaceae | ||
| Verrucomicrobiaceae | ||
| Porphyromonadaceae | ||
| Alcaligenaceae | ||
| Pasteurellaceae |
Revision editor(s): Aleru Divine
Experiment 21
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- QIAStool
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: increased abundance in QIAStool+BB
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacteriaceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2D
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: decreased abundance in QIAStool+BB
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Veillonellaceae | ||
| Bacteroidaceae | ||
| Verrucomicrobiaceae | ||
| Porphyromonadaceae | ||
| Alcaligenaceae | ||
| Pasteurellaceae |
Revision editor(s): Aleru Divine
Experiment 22
Subjects
- 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
- Easy-DNA
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- DNA isolation from human fecal samples using Easy-DNATM gDNA Purification Kit, Invitrogen (Easy-DNA).
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Experiment 23
Subjects
- 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 human fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen (QIAStool).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- unchanged
Experiment 24
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Easy-DNA
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Experiment 25
Subjects
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Sus scrofa domesticus
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- InnuPURE
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- MagNAPure
- 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 MagNA Pure LC DNA isolation Kit III, Roche (MagNAPure).
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Figure 2E
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: increased abundance in MagNAPure
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Oscillospiraceae | ||
| Clostridiaceae | ||
| Lachnospiraceae | ||
| Veillonellaceae | ||
| Erysipelotrichaceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2E
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: decreased abundance in MagNAPure
| NCBI | Quality Control | Links |
|---|---|---|
| Campylobacteraceae |
Revision editor(s): Aleru Divine
Experiment 26
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Easy-DNA
- 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 Easy-DNATM gDNA Purification Kit, Invitrogen (Easy-DNA).
Lab analysis
Statistical Analysis
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
Source: Figure 2E
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: increased abundance in Easy-DNA
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Oscillospiraceae | ||
| Lachnospiraceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2E
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: decreased abundance in Easy-DNA
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridiaceae | ||
| Campylobacteraceae | ||
| Veillonellaceae | ||
| Erysipelotrichaceae |
Revision editor(s): Aleru Divine
Experiment 27
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- FastDNA
- 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 MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Figure 2E
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: increased abundance in FastDNA
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillospiraceae | ||
| Clostridiaceae | ||
| Lachnospiraceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2E
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: decreased abundance in FastDNA
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Campylobacteraceae | ||
| Veillonellaceae | ||
| Erysipelotrichaceae |
Revision editor(s): Aleru Divine
Experiment 28
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- PowerSoil.HMP
- 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 PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Figure 2E
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: increased abundance in PowerSoil.HMP
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillospiraceae | ||
| Lachnospiraceae | ||
| Erysipelotrichaceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2E
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: decreased abundance in PowerSoil.HMP
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Clostridiaceae | ||
| Campylobacteraceae | ||
| Veillonellaceae |
Revision editor(s): Aleru Divine
Experiment 29
Subjects
- 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).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
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 Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Oscillospiraceae | ||
| Clostridiaceae | ||
| Veillonellaceae | ||
| Erysipelotrichaceae |
Revision editor(s): Aleru Divine
Signature 2
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 Control | Links |
|---|---|---|
| Lachnospiraceae | ||
| Campylobacteraceae |
Revision editor(s): Aleru Divine
Experiment 30
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- QIAStool+BB
- 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 +Bead Beating (QIAStool+BB).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
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+BB
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillospiraceae | ||
| Clostridiaceae | ||
| Lachnospiraceae | ||
| Erysipelotrichaceae |
Revision editor(s): Aleru Divine
Signature 2
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+BB
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Campylobacteraceae | ||
| Veillonellaceae |
Revision editor(s): Aleru Divine
Experiment 31
Subjects
- 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
- Easy-DNA
- 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 Easy-DNATM gDNA Purification Kit, Invitrogen (Easy-DNA).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Figure 2E
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: increased abundance in Easy-DNA
| NCBI | Quality Control | Links |
|---|---|---|
| Campylobacteraceae | ||
| Prevotellaceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2E
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: decreased abundance in Easy-DNA
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillospiraceae | ||
| Clostridiaceae | ||
| Lachnospiraceae | ||
| Veillonellaceae | ||
| Erysipelotrichaceae |
Revision editor(s): Aleru Divine
Experiment 32
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- FastDNA
- 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 MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Figure 2E
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: increased abundance in FastDNA
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillospiraceae | ||
| Clostridiaceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2E
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: decreased abundance in FastDNA
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Lachnospiraceae | ||
| Campylobacteraceae | ||
| Veillonellaceae | ||
| Erysipelotrichaceae |
Revision editor(s): Aleru Divine
Experiment 33
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- PowerSoil.HMP
- 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 PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP)
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Figure 2E
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: increased abundance in PowerSoil.HMP
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillospiraceae | ||
| Lachnospiraceae | ||
| Campylobacteraceae | ||
| Erysipelotrichaceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2E
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: decreased abundance in PowerSoil.HMP
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridiaceae | ||
| Prevotellaceae | ||
| Veillonellaceae |
Revision editor(s): Aleru Divine
Experiment 34
Subjects
- 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).
Lab analysis
Statistical Analysis
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
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 Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Clostridiaceae | ||
| Campylobacteraceae | ||
| Veillonellaceae | ||
| Erysipelotrichaceae |
Revision editor(s): Aleru Divine
Signature 2
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 Control | Links |
|---|---|---|
| Lachnospiraceae | ||
| Oscillospiraceae |
Revision editor(s): Aleru Divine
Experiment 35
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- QIAStool+BB
- 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 +Bead Beating (QIAStool+BB).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
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+BB
| NCBI | Quality Control | Links |
|---|---|---|
| Campylobacteraceae | ||
| Clostridiaceae |
Revision editor(s): Aleru Divine
Signature 2
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+BB
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Oscillospiraceae | ||
| Lachnospiraceae | ||
| Veillonellaceae | ||
| Erysipelotrichaceae |
Revision editor(s): Aleru Divine
Experiment 36
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Easy-DNA
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- FastDNA
- 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 MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Figure 2E
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: increased abundance in FastDNA
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillospiraceae | ||
| Clostridiaceae | ||
| Lachnospiraceae | ||
| Veillonellaceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2E
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: decreased abundance in FastDNA
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Campylobacteraceae | ||
| Erysipelotrichaceae |
Revision editor(s): Aleru Divine
Experiment 37
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- PowerSoil.HMP
- 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 PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Figure 2E
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: increased abundance in PowerSoil.HMP
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillospiraceae | ||
| Clostridiaceae | ||
| Lachnospiraceae | ||
| Campylobacteraceae | ||
| Veillonellaceae | ||
| Erysipelotrichaceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2E
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: decreased abundance in PowerSoil.HMP
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae |
Revision editor(s): Aleru Divine
Experiment 38
Subjects
- 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).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
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 Control | Links |
|---|---|---|
| Campylobacteraceae | ||
| Erysipelotrichaceae | ||
| Veillonellaceae | ||
| Clostridiaceae |
Revision editor(s): Aleru Divine
Signature 2
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 Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Oscillospiraceae | ||
| Lachnospiraceae |
Revision editor(s): Aleru Divine
Experiment 39
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- QIAStool+BB
- 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 +Bead Beating (QIAStool+BB).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
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+BB
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridiaceae | ||
| Campylobacteraceae | ||
| Erysipelotrichaceae |
Revision editor(s): Aleru Divine
Signature 2
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+BB
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Oscillospiraceae | ||
| Lachnospiraceae | ||
| Veillonellaceae |
Revision editor(s): Aleru Divine
Experiment 40
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- FastDNA
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- PowerSoil.HMP
- 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 PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Figure 2E
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: increased abundance in PowerSoil.HMP
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillospiraceae | ||
| Lachnospiraceae | ||
| Campylobacteraceae | ||
| Veillonellaceae | ||
| Erysipelotrichaceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2E
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: decreased abundance in PowerSoil.HMP
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Clostridiaceae |
Revision editor(s): Aleru Divine
Experiment 41
Subjects
- 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).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
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 Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Campylobacteraceae | ||
| Veillonellaceae | ||
| Erysipelotrichaceae |
Revision editor(s): Aleru Divine
Signature 2
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 Control | Links |
|---|---|---|
| Oscillospiraceae | ||
| Clostridiaceae | ||
| Lachnospiraceae |
Revision editor(s): Aleru Divine
Experiment 42
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- QIAStool+BB
- 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 +Bead Beating (QIAStool+BB).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
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+BB
| NCBI | Quality Control | Links |
|---|---|---|
| Campylobacteraceae | ||
| Erysipelotrichaceae |
Revision editor(s): Aleru Divine
Signature 2
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+BB
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Oscillospiraceae | ||
| Clostridiaceae | ||
| Lachnospiraceae | ||
| Veillonellaceae |
Revision editor(s): Aleru Divine
Experiment 43
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- PowerSoil.HMP
- 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).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
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 Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Clostridiaceae | ||
| Veillonellaceae |
Revision editor(s): Aleru Divine
Signature 2
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 Control | Links |
|---|---|---|
| Oscillospiraceae | ||
| Lachnospiraceae | ||
| Campylobacteraceae | ||
| Erysipelotrichaceae |
Revision editor(s): Aleru Divine
Experiment 44
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- QIAStool+BB
- 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 +Bead Beating (QIAStool+BB).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
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+BB
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridiaceae |
Revision editor(s): Aleru Divine
Signature 2
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+BB
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Oscillospiraceae | ||
| Lachnospiraceae | ||
| Campylobacteraceae | ||
| Veillonellaceae | ||
| Erysipelotrichaceae |
Revision editor(s): Aleru Divine
Experiment 45
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- QIAStool
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
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+BB
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnospiraceae |
Revision editor(s): Aleru Divine
Signature 2
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+BB
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Oscillospiraceae | ||
| Clostridiaceae | ||
| Campylobacteraceae | ||
| Veillonellaceae | ||
| Erysipelotrichaceae |
Revision editor(s): Aleru Divine
Experiment 46
Subjects
- 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
- Easy-DNA
- 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 Easy-DNATM gDNA Purification Kit, Invitrogen (Easy-DNA).
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Experiment 47
Subjects
- 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).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Experiment 48
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Easy-DNA
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Experiment 49
Subjects
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Not specified
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Not specified
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- InnuPURE
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- MagNAPure
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- DNA isolation from sewage samples using MagNA Pure LC DNA isolation Kit III, Roche (MagNAPure).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Figure 2F
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: increased abundance in MagNAPure
| NCBI | Quality Control | Links |
|---|---|---|
| Moraxellaceae | ||
| Neisseriaceae | ||
| Verrucomicrobiaceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2F
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: decreased abundance in MagNAPure
| NCBI | Quality Control | Links |
|---|---|---|
| Campylobacteraceae | ||
| Oscillospiraceae | ||
| Bacteroidaceae | ||
| Lachnospiraceae | ||
| Opitutaceae |
Revision editor(s): Aleru Divine
Experiment 50
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Easy-DNA
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- DNA isolation from sewage samples using Easy-DNATM gDNA Purification Kit, Invitrogen (Easy-DNA).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Figure 2F
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: increased abundance in Easy-DNA
| NCBI | Quality Control | Links |
|---|---|---|
| Moraxellaceae | ||
| Campylobacteraceae | ||
| Oscillospiraceae | ||
| Bacteroidaceae | ||
| Neisseriaceae | ||
| Lachnospiraceae | ||
| Verrucomicrobiaceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2F
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: decreased abundance in Easy-DNA
| NCBI | Quality Control | Links |
|---|---|---|
| Opitutaceae |
Revision editor(s): Aleru Divine
Experiment 51
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- FastDNA
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- DNA isolation from sewage samples using MP FastDNATM Spin Kit, MP Biomedicals (FastDNA).
Lab analysis
Statistical Analysis
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
Source: Figure 2F
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: increased abundance in FastDNA
| NCBI | Quality Control | Links |
|---|---|---|
| Moraxellaceae | ||
| Neisseriaceae | ||
| Verrucomicrobiaceae | ||
| Opitutaceae | ||
| Bacteroidaceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2F
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: decreased abundance in FastDNA
| NCBI | Quality Control | Links |
|---|---|---|
| Campylobacteraceae | ||
| Oscillospiraceae | ||
| Lachnospiraceae |
Revision editor(s): Aleru Divine
Experiment 52
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- PowerSoil.HMP
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- DNA isolation from sewage samples using PowerSoil® DNA Isolation kit, MoBio Laboratories Inc. (PowerSoil.HMP).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Figure 2F
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: increased abundance in PowerSoil.HMP
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillospiraceae | ||
| Bacteroidaceae | ||
| Neisseriaceae | ||
| Verrucomicrobiaceae | ||
| Opitutaceae |