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

From BugSigDB
Needs review
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM, Pamp SJ
Journal
mSystems
Year
2016
Keywords:
16S rRNA gene profiling, DNA isolation, metagenomics, microbial ecology, microbiome, next-generation sequencing
Explorations of complex microbiomes using genomics greatly enhance our understanding about their diversity, biogeography, and function. The isolation of DNA from microbiome specimens is a key prerequisite for such examinations, but challenges remain in obtaining sufficient DNA quantities required for certain sequencing approaches, achieving accurate genomic inference of microbiome composition, and facilitating comparability of findings across specimen types and sequencing projects. These aspects are particularly relevant for the genomics-based global surveillance of infectious agents and antimicrobial resistance from different reservoirs. Here, we compare in a stepwise approach a total of eight commercially available DNA extraction kits and 16 procedures based on these for three specimen types (human feces, pig feces, and hospital sewage). We assess DNA extraction using spike-in controls and different types of beads for bead beating, facilitating cell lysis. We evaluate DNA concentration, purity, and stability and microbial community composition using 16S rRNA gene sequencing and for selected samples using shotgun metagenomic sequencing. Our results suggest that inferred community composition was dependent on inherent specimen properties as well as DNA extraction method. We further show that bead beating or enzymatic treatment can increase the extraction of DNA from Gram-positive bacteria. Final DNA quantities could be increased by isolating DNA from a larger volume of cell lysate than that in standard protocols. Based on this insight, we designed an improved DNA isolation procedure optimized for microbiome genomics that can be used for the three examined specimen types and potentially also for other biological specimens. A standard operating procedure is available from https://dx.doi.org/10.6084/m9.figshare.3475406. IMPORTANCE Sequencing-based analyses of microbiomes may lead to a breakthrough in our understanding of the microbial worlds associated with humans, animals, and the environment. Such insight could further the development of innovative ecosystem management approaches for the protection of our natural resources and the design of more effective and sustainable solutions to prevent and control infectious diseases. Genome sequence information is an organism (pathogen)-independent language that can be used across sectors, space, and time. Harmonized standards, protocols, and workflows for sample processing and analysis can facilitate the generation of such actionable information. In this study, we assessed several procedures for the isolation of DNA for next-generation sequencing. Our study highlights several important aspects to consider in the design and conduct of sequence-based analysis of microbiomes. We provide a standard operating procedure for the isolation of DNA from a range of biological specimens particularly relevant in clinical diagnostics and epidemiology.

Experiment 1


Needs review

Curated date: 2024/04/05

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.
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

Needs review

Curated date: 2024/04/05

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Alcaligenaceae
Prevotellaceae
Veillonellaceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/05

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Bacteroidaceae
Bifidobacteriaceae
Pasteurellaceae
Porphyromonadaceae
Verrucomicrobiaceae

Revision editor(s): Aleru Divine

Experiment 2


Needs review

Curated date: 2024/04/05

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/05

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Veillonellaceae
Bifidobacteriaceae
Verrucomicrobiaceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/05

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Prevotellaceae
Bacteroidaceae
Porphyromonadaceae
Alcaligenaceae
Pasteurellaceae

Revision editor(s): Aleru Divine

Experiment 3


Needs review

Curated date: 2024/04/05

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/05

Curator: Aleru002

Revision editor(s): Aleru002

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 ControlLinks
Bifidobacteriaceae
Verrucomicrobiaceae

Revision editor(s): Aleru002

Signature 2

Needs review

Curated date: 2024/04/05

Curator: Aleru002

Revision editor(s): Aleru002

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 ControlLinks
Prevotellaceae
Veillonellaceae
Bacteroidaceae
Porphyromonadaceae
Alcaligenaceae
Pasteurellaceae

Revision editor(s): Aleru002

Experiment 4


Needs review

Curated date: 2024/04/05

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/05

Curator: Aleru002

Revision editor(s): Aleru002

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 ControlLinks
Veillonellaceae
Prevotellaceae

Revision editor(s): Aleru002

Signature 2

Needs review

Curated date: 2024/04/05

Curator: Aleru002

Revision editor(s): Aleru002

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 ControlLinks
Bacteroidaceae
Bifidobacteriaceae
Verrucomicrobiaceae
Porphyromonadaceae
Alcaligenaceae
Pasteurellaceae

Revision editor(s): Aleru002

Experiment 5


Needs review

Curated date: 2024/04/05

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/06

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Prevotellaceae
Veillonellaceae
Verrucomicrobiaceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/06

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Bacteroidaceae
Bifidobacteriaceae
Porphyromonadaceae
Alcaligenaceae
Pasteurellaceae

Revision editor(s): Aleru Divine

Experiment 6


Needs review

Curated date: 2024/04/05

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/06

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Bifidobacteriaceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/06

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Prevotellaceae
Veillonellaceae
Bacteroidaceae
Verrucomicrobiaceae
Porphyromonadaceae
Alcaligenaceae
Pasteurellaceae

Revision editor(s): Aleru Divine

Experiment 7


Needs review

Curated date: 2024/04/05

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/06

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Verrucomicrobiaceae
Bifidobacteriaceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/06

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Prevotellaceae
Veillonellaceae
Bacteroidaceae
Porphyromonadaceae
Alcaligenaceae
Pasteurellaceae

Revision editor(s): Aleru Divine

Experiment 8


Needs review

Curated date: 2024/04/05

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/06

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Bifidobacteriaceae
Verrucomicrobiaceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/06

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Prevotellaceae
Veillonellaceae
Bacteroidaceae
Porphyromonadaceae
Alcaligenaceae
Pasteurellaceae

Revision editor(s): Aleru Divine

Experiment 9


Needs review

Curated date: 2024/04/05

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/06

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Bifidobacteriaceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/06

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Prevotellaceae
Veillonellaceae
Bacteroidaceae
Verrucomicrobiaceae
Porphyromonadaceae
Alcaligenaceae

Revision editor(s): Aleru Divine

Experiment 10


Needs review

Curated date: 2024/04/05

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/06

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Verrucomicrobiaceae
Veillonellaceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/06

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Prevotellaceae
Bacteroidaceae
Bifidobacteriaceae
Porphyromonadaceae
Alcaligenaceae
Pasteurellaceae

Revision editor(s): Aleru Divine

Experiment 11


Needs review

Curated date: 2024/04/05

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/06

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Bifidobacteriaceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/06

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Prevotellaceae
Veillonellaceae
Bacteroidaceae
Verrucomicrobiaceae
Porphyromonadaceae
Alcaligenaceae
Pasteurellaceae

Revision editor(s): Aleru Divine

Experiment 12


Needs review

Curated date: 2024/04/05

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/07

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Prevotellaceae
Bacteroidaceae
Porphyromonadaceae
Alcaligenaceae
Pasteurellaceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/07

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Veillonellaceae
Bifidobacteriaceae
Verrucomicrobiaceae

Revision editor(s): Aleru Divine

Experiment 13


Needs review

Curated date: 2024/04/05

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/07

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Prevotellaceae
Veillonellaceae
Bacteroidaceae
Porphyromonadaceae
Alcaligenaceae
Pasteurellaceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/07

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Bifidobacteriaceae
Verrucomicrobiaceae

Revision editor(s): Aleru Divine

Experiment 14


Needs review

Curated date: 2024/04/05

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/07

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Prevotellaceae
Veillonellaceae
Bacteroidaceae
Porphyromonadaceae
Alcaligenaceae
Pasteurellaceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/07

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Bifidobacteriaceae
Verrucomicrobiaceae

Revision editor(s): Aleru Divine

Experiment 15


Needs review

Curated date: 2024/04/05

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/07

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Prevotellaceae
Bacteroidaceae
Porphyromonadaceae
Alcaligenaceae
Pasteurellaceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/07

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Veillonellaceae
Bifidobacteriaceae
Verrucomicrobiaceae

Revision editor(s): Aleru Divine

Experiment 16


Needs review

Curated date: 2024/04/05

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/07

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Prevotellaceae
Veillonellaceae
Bacteroidaceae
Porphyromonadaceae
Alcaligenaceae
Pasteurellaceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/07

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Bifidobacteriaceae
Verrucomicrobiaceae

Revision editor(s): Aleru Divine

Experiment 17


Needs review

Curated date: 2024/04/05

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/07

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Prevotellaceae
Veillonellaceae
Bacteroidaceae
Porphyromonadaceae
Alcaligenaceae
Pasteurellaceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/07

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Bifidobacteriaceae
Verrucomicrobiaceae

Revision editor(s): Aleru Divine

Experiment 18


Needs review

Curated date: 2024/04/05

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/07

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Prevotellaceae
Veillonellaceae
Bacteroidaceae
Bifidobacteriaceae
Porphyromonadaceae
Alcaligenaceae
Pasteurellaceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/07

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Verrucomicrobiaceae

Revision editor(s): Aleru Divine

Experiment 19


Needs review

Curated date: 2024/04/05

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/07

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Prevotellaceae
Veillonellaceae
Verrucomicrobiaceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/07

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Bacteroidaceae
Bifidobacteriaceae
Porphyromonadaceae
Alcaligenaceae
Pasteurellaceae

Revision editor(s): Aleru Divine

Experiment 20


Needs review

Curated date: 2024/04/05

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/07

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Bifidobacteriaceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/07

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Prevotellaceae
Veillonellaceae
Bacteroidaceae
Verrucomicrobiaceae
Porphyromonadaceae
Alcaligenaceae
Pasteurellaceae

Revision editor(s): Aleru Divine

Experiment 21


Needs review

Curated date: 2024/04/05

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/07

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Bifidobacteriaceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/07

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Prevotellaceae
Veillonellaceae
Bacteroidaceae
Verrucomicrobiaceae
Porphyromonadaceae
Alcaligenaceae
Pasteurellaceae

Revision editor(s): Aleru Divine

Experiment 22


Needs review

Curated date: 2024/04/05

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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


Needs review

Curated date: 2024/04/05

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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


Needs review

Curated date: 2024/04/05

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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


Needs review

Curated date: 2024/04/09

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

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 MagNAPure

NCBI Quality ControlLinks
Prevotellaceae
Oscillospiraceae
Clostridiaceae
Lachnospiraceae
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 MagNAPure

NCBI Quality ControlLinks
Campylobacteraceae

Revision editor(s): Aleru Divine

Experiment 26


Needs review

Curated date: 2024/04/09

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

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 Easy-DNA

NCBI Quality ControlLinks
Prevotellaceae
Oscillospiraceae
Lachnospiraceae

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 Easy-DNA

NCBI Quality ControlLinks
Clostridiaceae
Campylobacteraceae
Veillonellaceae
Erysipelotrichaceae

Revision editor(s): Aleru Divine

Experiment 27


Needs review

Curated date: 2024/04/09

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

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 FastDNA

NCBI Quality ControlLinks
Oscillospiraceae
Clostridiaceae
Lachnospiraceae

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 FastDNA

NCBI Quality ControlLinks
Prevotellaceae
Campylobacteraceae
Veillonellaceae
Erysipelotrichaceae

Revision editor(s): Aleru Divine

Experiment 28


Needs review

Curated date: 2024/04/09

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

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 PowerSoil.HMP

NCBI Quality ControlLinks
Oscillospiraceae
Lachnospiraceae
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 PowerSoil.HMP

NCBI Quality ControlLinks
Prevotellaceae
Clostridiaceae
Campylobacteraceae
Veillonellaceae

Revision editor(s): Aleru Divine

Experiment 29


Needs review

Curated date: 2024/04/09

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

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
Oscillospiraceae
Clostridiaceae
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
Campylobacteraceae

Revision editor(s): Aleru Divine

Experiment 30


Needs review

Curated date: 2024/04/09

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

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+BB

NCBI Quality ControlLinks
Oscillospiraceae
Clostridiaceae
Lachnospiraceae
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+BB

NCBI Quality ControlLinks
Prevotellaceae
Campylobacteraceae
Veillonellaceae

Revision editor(s): Aleru Divine

Experiment 31


Needs review

Curated date: 2024/04/09

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

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 Easy-DNA

NCBI Quality ControlLinks
Campylobacteraceae
Prevotellaceae

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 Easy-DNA

NCBI Quality ControlLinks
Oscillospiraceae
Clostridiaceae
Lachnospiraceae
Veillonellaceae
Erysipelotrichaceae

Revision editor(s): Aleru Divine

Experiment 32


Needs review

Curated date: 2024/04/09

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

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 FastDNA

NCBI Quality ControlLinks
Oscillospiraceae
Clostridiaceae

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 FastDNA

NCBI Quality ControlLinks
Prevotellaceae
Lachnospiraceae
Campylobacteraceae
Veillonellaceae
Erysipelotrichaceae

Revision editor(s): Aleru Divine

Experiment 33


Needs review

Curated date: 2024/04/09

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

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 PowerSoil.HMP

NCBI Quality ControlLinks
Oscillospiraceae
Lachnospiraceae
Campylobacteraceae
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 PowerSoil.HMP

NCBI Quality ControlLinks
Clostridiaceae
Prevotellaceae
Veillonellaceae

Revision editor(s): Aleru Divine

Experiment 34


Needs review

Curated date: 2024/04/09

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

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

Experiment 35


Needs review

Curated date: 2024/04/09

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

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+BB

NCBI Quality ControlLinks
Campylobacteraceae
Clostridiaceae

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+BB

NCBI Quality ControlLinks
Prevotellaceae
Oscillospiraceae
Lachnospiraceae
Veillonellaceae
Erysipelotrichaceae

Revision editor(s): Aleru Divine

Experiment 36


Needs review

Curated date: 2024/04/22

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/24

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 FastDNA

NCBI Quality ControlLinks
Oscillospiraceae
Clostridiaceae
Lachnospiraceae
Veillonellaceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/24

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 FastDNA

NCBI Quality ControlLinks
Prevotellaceae
Campylobacteraceae
Erysipelotrichaceae

Revision editor(s): Aleru Divine

Experiment 37


Needs review

Curated date: 2024/04/22

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/24

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 PowerSoil.HMP

NCBI Quality ControlLinks
Oscillospiraceae
Clostridiaceae
Lachnospiraceae
Campylobacteraceae
Veillonellaceae
Erysipelotrichaceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/24

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 PowerSoil.HMP

NCBI Quality ControlLinks
Prevotellaceae

Revision editor(s): Aleru Divine

Experiment 38


Needs review

Curated date: 2024/04/22

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/24

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
Campylobacteraceae
Erysipelotrichaceae
Veillonellaceae
Clostridiaceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/24

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
Prevotellaceae
Oscillospiraceae
Lachnospiraceae

Revision editor(s): Aleru Divine

Experiment 39


Needs review

Curated date: 2024/04/22

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/24

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+BB

NCBI Quality ControlLinks
Clostridiaceae
Campylobacteraceae
Erysipelotrichaceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/24

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+BB

NCBI Quality ControlLinks
Prevotellaceae
Oscillospiraceae
Lachnospiraceae
Veillonellaceae

Revision editor(s): Aleru Divine

Experiment 40


Needs review

Curated date: 2024/04/22

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/24

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 PowerSoil.HMP

NCBI Quality ControlLinks
Oscillospiraceae
Lachnospiraceae
Campylobacteraceae
Veillonellaceae
Erysipelotrichaceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/24

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 PowerSoil.HMP

NCBI Quality ControlLinks
Prevotellaceae
Clostridiaceae

Revision editor(s): Aleru Divine

Experiment 41


Needs review

Curated date: 2024/04/22

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/24

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
Campylobacteraceae
Veillonellaceae
Erysipelotrichaceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/24

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
Oscillospiraceae
Clostridiaceae
Lachnospiraceae

Revision editor(s): Aleru Divine

Experiment 42


Needs review

Curated date: 2024/04/22

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/24

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+BB

NCBI Quality ControlLinks
Campylobacteraceae
Erysipelotrichaceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/24

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+BB

NCBI Quality ControlLinks
Prevotellaceae
Oscillospiraceae
Clostridiaceae
Lachnospiraceae
Veillonellaceae

Revision editor(s): Aleru Divine

Experiment 43


Needs review

Curated date: 2024/04/22

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/24

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
Veillonellaceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/24

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
Oscillospiraceae
Lachnospiraceae
Campylobacteraceae
Erysipelotrichaceae

Revision editor(s): Aleru Divine

Experiment 44


Needs review

Curated date: 2024/04/22

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/24

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+BB

NCBI Quality ControlLinks
Clostridiaceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/24

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+BB

NCBI Quality ControlLinks
Prevotellaceae
Oscillospiraceae
Lachnospiraceae
Campylobacteraceae
Veillonellaceae
Erysipelotrichaceae

Revision editor(s): Aleru Divine

Experiment 45


Needs review

Curated date: 2024/04/22

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/24

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+BB

NCBI Quality ControlLinks
Lachnospiraceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/24

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+BB

NCBI Quality ControlLinks
Prevotellaceae
Oscillospiraceae
Clostridiaceae
Campylobacteraceae
Veillonellaceae
Erysipelotrichaceae

Revision editor(s): Aleru Divine

Experiment 46


Needs review

Curated date: 2024/04/22

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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


Needs review

Curated date: 2024/04/22

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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


Needs review

Curated date: 2024/04/22

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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


Needs review

Curated date: 2024/04/25

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/27

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Moraxellaceae
Neisseriaceae
Verrucomicrobiaceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/27

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Campylobacteraceae
Oscillospiraceae
Bacteroidaceae
Lachnospiraceae
Opitutaceae

Revision editor(s): Aleru Divine

Experiment 50


Needs review

Curated date: 2024/04/25

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/27

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Moraxellaceae
Campylobacteraceae
Oscillospiraceae
Bacteroidaceae
Neisseriaceae
Lachnospiraceae
Verrucomicrobiaceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/27

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Opitutaceae

Revision editor(s): Aleru Divine

Experiment 51


Needs review

Curated date: 2024/04/25

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/27

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Moraxellaceae
Neisseriaceae
Verrucomicrobiaceae
Opitutaceae
Bacteroidaceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/27

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Campylobacteraceae
Oscillospiraceae
Lachnospiraceae

Revision editor(s): Aleru Divine

Experiment 52


Needs review

Curated date: 2024/04/25

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Needs review

Curated date: 2024/04/27

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Oscillospiraceae
Bacteroidaceae
Neisseriaceae
Verrucomicrobiaceae
Opitutaceae