Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns/Experiment 162

From BugSigDB


Needs review

Curated date: 2024/03/31

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.
Not specified
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Microbiome Microbiome,microbiome
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Unspiked sewage samples (S1) at 64 hours (-80°C)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Unspiked sewage samples (S1) at 16 hours (5°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Unspiked S1 sample stored at a temperature of 5°C for 16 hours
Group 0 sample size Number of subjects in the control (unexposed) group
1
Group 1 sample size Number of subjects in the case (exposed) group
1

Lab analysis

Sequencing type
WMS
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
Not specified
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)
0.01
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
No

Alpha Diversity

Pielou Quantifies how equal the community is numerically
decreased
Chao1 Abundance-based estimator of species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased

Signature 1

Needs review

Curated date: 2024/04/27

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: : Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked sewage sample S1

Abundance in Group 1: increased abundance in Unspiked sewage samples (S1) at 16 hours (5°C)

NCBI Quality ControlLinks
Arcobacter
Acinetobacter
Parabacteroides
Prevotella

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/04/28

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked sewage sample S1

Abundance in Group 1: decreased abundance in Unspiked sewage samples (S1) at 16 hours (5°C)

NCBI Quality ControlLinks
Aeromonas

Revision editor(s): Bolanle