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

From BugSigDB
Needs review
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Poulsen CS, Kaas RS, Aarestrup FM, Pamp SJ
Journal
Microbiology spectrum
Year
2021
Keywords:
antimicrobial resistance, bacteria, complex samples, freezing, metagenomics, microbial community composition, microbiome, mock community, parasite, sample storage, spiking, synthetic mock community
Storage of biological specimens is crucial in the life and medical sciences. Storage conditions for samples can be different for a number of reasons, and it is unclear what effect this can have on the inferred microbiome composition in metagenomics analyses. Here, we assess the effect of common storage temperatures (deep freezer, -80°C; freezer, -20°C; refrigerator, 5°C; room temperature, 22°C) and storage times (immediate sample processing, 0 h; next day, 16 h; over weekend, 64 h; longer term, 4, 8, and 12 months) as well as repeated sample freezing and thawing (2 to 4 freeze-thaw cycles). We examined two different pig feces and sewage samples, unspiked and spiked with a mock community, in triplicate, respectively, amounting to a total of 438 samples (777 Gbp; 5.1 billion reads). Storage conditions had a significant and systematic effect on the taxonomic and functional composition of microbiomes. Distinct microbial taxa and antimicrobial resistance classes were, in some situations, similarly affected across samples, while others were not, suggesting an impact of individual inherent sample characteristics. With an increasing number of freeze-thaw cycles, an increasing abundance of Firmicutes, Actinobacteria, and eukaryotic microorganisms was observed. We provide recommendations for sample storage and strongly suggest including more detailed information in the metadata together with the DNA sequencing data in public repositories to better facilitate meta-analyses and reproducibility of findings. IMPORTANCE Previous research has reported effects of DNA isolation, library preparation, and sequencing technology on metagenomics-based microbiome composition; however, the effect of biospecimen storage conditions has not been thoroughly assessed. We examined the effect of common sample storage conditions on metagenomics-based microbiome composition and found significant and, in part, systematic effects. Repeated freeze-thaw cycles could be used to improve the detection of microorganisms with more rigid cell walls, including parasites. We provide a data set that could also be used for benchmarking algorithms to identify and correct for unwanted batch effects. Overall, the findings suggest that all samples of a microbiome study should be stored in the same way. Furthermore, there is a need to mandate more detailed information about sample storage and processing be published together with DNA sequencing data at the International Nucleotide Sequence Database Collaboration (ENA/EBI, NCBI, DDBJ) or other repositories.

Experiment 1


Needs review

Curated date: 2024/03/20

Curator: Bolanle

Revision editor(s): Bolanle

Subjects

Location of subjects
Denmark
Host species Species from which microbiome was sampled. Contact us to have more species added.
Sus scrofa domesticus
Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Spiked pig feces(P1) at 0 hour
Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P1) at 64 hours (-80°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P1 sample spiked with a mock community and stored at a temperature of -80°C for 64 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
unchanged

Experiment 2


Needs review

Curated date: 2024/03/23

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P1) at 64 hours (22°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P1 sample spiked with a mock community and stored at a temperature of 22°C for 64 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

incomplete

Curated date: 2024/03/23

Curator: Bolanle

Revision editor(s): Bolanle

Source: text

Description: they were observed at higher abundances following storage at 22°C for 64 h

Abundance in Group 1: increased abundance in Spiked pig feces(P1) at 64 hours (22°C)

NCBI Quality ControlLinks
Actinomycetota
Bacillota

Revision editor(s): Bolanle

Experiment 3


Needs review

Curated date: 2024/03/23

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P1) at 64 hours (5°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P1 sample spiked with a mock community and stored at a temperature of 5°C for 64 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 4


Needs review

Curated date: 2024/03/25

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P1) at 64 hours (-20°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P1 sample spiked with a mock community and stored at a temperature of -20°C for 64 hours

Lab analysis

Statistical Analysis

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

Experiment 5


Needs review

Curated date: 2024/03/25

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P1) at 16 hours (-80°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P1 sample spiked with a mock community and stored at a temperature of -80°C for 16 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 6


Needs review

Curated date: 2024/03/25

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P1) at 16 hours (5°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P1 samplespiked with a mock community and stored at a temperature of 5°C for 16 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 7


Needs review

Curated date: 2024/03/25

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P1) at 16 hours (22°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P1 sample spiked with a mock community and stored at a temperature of 22°C for 16 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 8


Needs review

Curated date: 2024/03/25

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P1) at 16 hours (-20°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P1 sample spiked with a mock community and stored at a temperature of -20°C for 16 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 9


Needs review

Curated date: 2024/03/25

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Spiked pig feces(P1) at 16 hours (-80°C)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P1) at 64 hours (22°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P1 sample spiked with a mock community and stored at a temperature of 64 hours (22°C)

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 10


Needs review

Curated date: 2024/03/25

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P1) at 64 hours (-80°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P1 sample spiked with a mock community and stored at a temperature of 64 hours (-80°C)

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 11


Needs review

Curated date: 2024/03/25

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P1) at 64 hours (-20°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P1 samplespiked with a mock community and stored at a temperature of 64 hours (-20°C)

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 12


Needs review

Curated date: 2024/03/25

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P1) at 16 hours (-20°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P1 sample spiked with a mock community and stored at a temperature of 16 hours (-20°C)

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 13


Needs review

Curated date: 2024/03/25

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P1) at 64 hours (5°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P1 sample spiked with a mock community and stored at a temperature of 64 hours (5°C)

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 14


Needs review

Curated date: 2024/03/25

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P1) at 16 hours (22°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P1 sample spiked with a mock community and stored at a temperature of 16 hours (22°C)

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 15


Needs review

Curated date: 2024/03/25

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P1) at 16 hours (5°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P1 sample spiked with a mock community and stored at a temperature of 16 hours (5°C)

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 16


Needs review

Curated date: 2024/03/25

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Spiked pig feces(P1) at 64 hours (-80°C)

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 17


Needs review

Curated date: 2024/03/25

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P1) at 16 hours (22°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P1 sample spiked with a mock community and stored at a temperature of 16 hours (22°C)

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 18


Needs review

Curated date: 2024/03/25

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P1) at 64 hours (22°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P1 sample spiked with a mock community and stored at a temperature of 64 hours (22°C)

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 19


Needs review

Curated date: 2024/03/25

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Spiked pig feces(P1) at 16 hours (5°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P1 sample spiked with a mock community and stored at a temperature of 64 hours (22°C)

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 20


Needs review

Curated date: 2024/03/25

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Spiked pig feces(P1) at 16 hours (-20°C)

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 21


Needs review

Curated date: 2024/03/25

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Spiked pig feces(P1) at 64 hours (22°C)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P1) at 64 hours (5°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P1 sample spiked with a mock community and stored at a temperature of 64 hours (5°C)

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 22


Needs review

Curated date: 2024/03/25

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Spiked pig feces(P1) at 64 hours (-20°C)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P1) at 64 hours (22°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P1 sample spiked with a mock community and stored at a temperature of 64 hours (22°C)

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 23


Needs review

Curated date: 2024/03/25

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Spiked pig feces(P1) at 16 hours (22°C)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P1) at 64 hours (-20°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P1 sample spiked with a mock community and stored at a temperature of 64 hours (-20°C)

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 24


Needs review

Curated date: 2024/03/25

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Spiked pig feces(P1) at 16 hours (-80°C)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P1) at 16 hours (22°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P1 sample spiked with a mock community and stored at a temperature of 16 hours (22°C)

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 25


Needs review

Curated date: 2024/03/25

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Spiked pig feces(P1) at 16 hours (-20°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P1 sample spiked with a mock community and stored at a temperature of 16 hours (22°C)

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 26


Needs review

Curated date: 2024/03/25

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Spiked pig feces(P1) at 64 hours (-20°C)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P1) at 64 hours (5°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P1 sample spiked with a mock community and stored at a temperature of 64 hours (5°C)

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 27


Needs review

Curated date: 2024/03/25

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Spiked pig feces(P1) at 64 hours (-80°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P1 sample spiked with a mock community and stored at a temperature of 64 hours (5°C)

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 28


Needs review

Curated date: 2024/03/25

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Spiked pig feces(P1) at 16 hours (-20°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P1 sample spiked with a mock community and stored at a temperature of 64 hours (5°C)

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 29


Needs review

Curated date: 2024/03/25

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Spiked pig feces(P1) at 16 hours (5°C)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P1) at 64 hours (-20°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P1 sample spiked with a mock community and stored at a temperature of 64 hours (-20°C)

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 30


Needs review

Curated date: 2024/03/25

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Spiked pig feces(P1) at 64 hours (-80°C)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P1) at 16 hours (-20°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P1 sample spiked with a mock community and stored at a temperature of 16 hours (-20°C)

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 31


Needs review

Curated date: 2024/03/25

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P1) at 64 hours (-20°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P1 sample spiked with a mock community and stored at a temperature of 64 hours (-20°C)

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 32


Needs review

Curated date: 2024/03/25

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Spiked pig feces(P1) at 16 hours (-20°C)

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 33


Needs review

Curated date: 2024/03/26

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

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 pig feces(P1) at 0 hour
Group 1 name Corresponds to the case (exposed) group for case-control studies
Unspiked pig feces(P1) at 16 hours (-80°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Unspiked P1 sample stored at a temperature of -80°C for 16 hours

Lab analysis

Statistical Analysis

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: 2024/03/27

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: Prevotella (class Bacteroidia), the most abundant genus in pig feces, was more abundant for P1 frozen samples than in samples undergoing immediate DNA isolation, Phascolarctobacterium (class Negativicutes), also had higher abundance in stored samples than for samples processed immediately.

Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 16 hours (-80°C)

NCBI Quality ControlLinks
Prevotella
Phascolarctobacterium

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/03/27

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.

Abundance in Group 1: decreased abundance in Unspiked pig feces(P1) at 16 hours (-80°C)

NCBI Quality ControlLinks
Treponema
Faecalibacterium
Roseburia

Revision editor(s): Bolanle

Experiment 34


Needs review

Curated date: 2024/03/26

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
Unspiked pig feces(P1) at 64 hours (-80°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Unspiked P1 sample stored at a temperature of -80°C for 64 hours

Lab analysis

Statistical Analysis

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: 2024/03/27

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: Prevotella (class Bacteroidia), the most abundant genus in pig feces, was abundant for P1 frozen samples than in samples undergoing immediate DNA isolation, Phascolarctobacterium (class Negativicutes), also had higher abundance in stored samples than for samples processed immediately

Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 64 hours (-80°C)

NCBI Quality ControlLinks
Prevotella
Phascolarctobacterium

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/03/27

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.

Abundance in Group 1: decreased abundance in Unspiked pig feces(P1) at 64 hours (-80°C)

NCBI Quality ControlLinks
Treponema
Faecalibacterium
Roseburia

Revision editor(s): Bolanle

Experiment 35


Needs review

Curated date: 2024/03/26

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
Unspiked pig feces(P1) at 16 hours (-20°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Unspiked P1 sample stored at a temperature of -20°C for 16 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/03/30

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: Prevotella (class Bacteroidia), the most abundant genus in pig feces, was abundant for P1 frozen samples than in samples undergoing immediate DNA isolation, Phascolarctobacterium (class Negativicutes), also had higher abundance in stored samples than for samples processed immediately

Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 16 hours (-20°C)

NCBI Quality ControlLinks
Prevotella
Phascolarctobacterium

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/03/30

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.

Abundance in Group 1: decreased abundance in Unspiked pig feces(P1) at 16 hours (-20°C)

NCBI Quality ControlLinks
Treponema
Faecalibacterium
Roseburia

Revision editor(s): Bolanle

Experiment 36


Needs review

Curated date: 2024/03/26

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
Unspiked pig feces(P1) at 64 hours (-20°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Unspiked P1 sample stored at a temperature of -20°C for 64 hours

Lab analysis

Statistical Analysis

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: 2024/03/30

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: higher abundance with increasing temperature and time was detected in samples processed immediately.

Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 64 hours (-20°C)

NCBI Quality ControlLinks
Prevotella
Phascolarctobacterium

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/03/30

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.

Abundance in Group 1: decreased abundance in Unspiked pig feces(P1) at 64 hours (-20°C)

NCBI Quality ControlLinks
Treponema
Faecalibacterium
Roseburia

Revision editor(s): Bolanle

Experiment 37


Needs review

Curated date: 2024/03/26

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
Unspiked pig feces(P1) at 16 hours (5°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Unspiked P1 sample stored at a temperature of 5°C for 16 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/03/30

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description:

Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 16 hours (5°C)

NCBI Quality ControlLinks
Prevotella
Phascolarctobacterium

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/04/01

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description:

Abundance in Group 1: decreased abundance in Unspiked pig feces(P1) at 16 hours (5°C)

NCBI Quality ControlLinks
Treponema
Faecalibacterium
Roseburia

Revision editor(s): Bolanle

Experiment 38


Needs review

Curated date: 2024/03/26

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
Unspiked pig feces(P1) at 64 hours (5°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Unspiked P1 sample stored at a temperature of 5°C for 64 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/01

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: higher abundance with increasing temperature and time was detected in samples processed immediately.

Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 64 hours (5°C)

NCBI Quality ControlLinks
Prevotella
Phascolarctobacterium

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/04/01

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.

Abundance in Group 1: decreased abundance in Unspiked pig feces(P1) at 64 hours (5°C)

NCBI Quality ControlLinks
Treponema
Faecalibacterium
Roseburia

Revision editor(s): Bolanle

Experiment 39


Needs review

Curated date: 2024/03/26

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
Unspiked pig feces(P1) at 16 hours (22°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Unspiked P1 sample stored at a temperature of 22°C for 16 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/01

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.

Abundance in Group 1: decreased abundance in Unspiked pig feces(P1) at 16 hours (22°C)

NCBI Quality ControlLinks
Prevotella
Treponema

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/04/01

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: higher abundance with increasing temperature and time was detected in samples processed immediately.

Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 16 hours (22°C)

NCBI Quality ControlLinks
Faecalibacterium
Phascolarctobacterium
Roseburia

Revision editor(s): Bolanle

Experiment 40


Needs review

Curated date: 2024/03/26

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
Unspiked pig feces(P1) at 64 hours (22°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Unspiked P1 sample stored at a temperature of 22°C for 64 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/01

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: higher abundance with increasing temperature and time was detected in samples processed immediately.

Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 64 hours (22°C)

NCBI Quality ControlLinks
Faecalibacterium
Phascolarctobacterium

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/04/01

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.

Abundance in Group 1: decreased abundance in Unspiked pig feces(P1) at 64 hours (22°C)

NCBI Quality ControlLinks
Prevotella
Treponema
Roseburia

Revision editor(s): Bolanle

Experiment 41


Needs review

Curated date: 2024/03/26

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
Unspiked pig feces(P1) at 16 hours (-80°C)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Unspiked pig feces(P1) at 64 hours (-80°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Unspiked P1 sample stored at a temperature of -80°C for 64 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/01

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: higher abundance with increasing temperature and time was detected in samples processed immediately.

Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 64 hours (-80°C)

NCBI Quality ControlLinks
Treponema
Faecalibacterium

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/04/01

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.

Abundance in Group 1: decreased abundance in Unspiked pig feces(P1) at 64 hours (-80°C)

NCBI Quality ControlLinks
Prevotella
Phascolarctobacterium
Roseburia

Revision editor(s): Bolanle

Experiment 42


Needs review

Curated date: 2024/03/26

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
Unspiked pig feces(P1) at 16 hours (-20°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Unspiked P1 sample stored at a temperature of -20°C for 16 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/01

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: higher abundance with increasing temperature and time was detected in samples processed immediately.

Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 16 hours (-20°C)

NCBI Quality ControlLinks
Phascolarctobacterium
Roseburia
Treponema
Faecalibacterium

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/04/01

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.

Abundance in Group 1: decreased abundance in Unspiked pig feces(P1) at 16 hours (-20°C)

NCBI Quality ControlLinks
Prevotella

Revision editor(s): Bolanle

Experiment 43


Needs review

Curated date: 2024/03/26

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
Unspiked pig feces(P1) at 64 hours (-20°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Unspiked P1 sample stored at a temperature of -20°C for 64 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/02

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: higher abundance with increasing temperature and time was detected in samples processed immediately.

Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 64 hours (-20°C)

NCBI Quality ControlLinks
Phascolarctobacterium

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/04/02

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.

Abundance in Group 1: decreased abundance in Unspiked pig feces(P1) at 64 hours (-20°C)

NCBI Quality ControlLinks
Prevotella
Treponema
Faecalibacterium
Roseburia

Revision editor(s): Bolanle

Experiment 44


Needs review

Curated date: 2024/03/26

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
Unspiked pig feces(P1) at 16 hours (5°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Unspiked P1 sample stored at a temperature of 5°C for 16 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/02

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: higher abundance with increasing temperature and time was detected in samples processed immediately.

Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 16 hours (5°C)

NCBI Quality ControlLinks
Treponema
Faecalibacterium
Roseburia

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/04/02

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.

Abundance in Group 1: decreased abundance in Unspiked pig feces(P1) at 16 hours (5°C)

NCBI Quality ControlLinks
Prevotella
Phascolarctobacterium

Revision editor(s): Bolanle

Experiment 45


Needs review

Curated date: 2024/03/26

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
Unspiked pig feces(P1) at 64 hours (5°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Unspiked P1 sample stored at a temperature of 5°C for 64 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/02

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: higher abundance with increasing temperature and time was detected in samples processed immediately.

Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 64 hours (5°C)

NCBI Quality ControlLinks
Treponema
Faecalibacterium
Phascolarctobacterium
Roseburia

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/04/02

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.

Abundance in Group 1: decreased abundance in Unspiked pig feces(P1) at 64 hours (5°C)

NCBI Quality ControlLinks
Prevotella

Revision editor(s): Bolanle

Experiment 46


Needs review

Curated date: 2024/03/26

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
Unspiked pig feces(P1) at 16 hours (22°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Unspiked P1 sample stored at a temperature of 22°C for 16 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/02

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: higher abundance with increasing temperature and time was detected in samples processed immediately.

Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 16 hours (22°C)

NCBI Quality ControlLinks
Treponema
Faecalibacterium
Roseburia

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/04/02

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.

Abundance in Group 1: decreased abundance in Unspiked pig feces(P1) at 16 hours (22°C)

NCBI Quality ControlLinks
Prevotella
Phascolarctobacterium

Revision editor(s): Bolanle

Experiment 47


Needs review

Curated date: 2024/03/26

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
Unspiked pig feces(P1) at 64 hours (22°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Unspiked P1 sample stored at a temperature of 22°C for 64 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/02

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: higher abundance with increasing temperature and time was detected in samples processed imm

Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 64 hours (22°C)

NCBI Quality ControlLinks
Treponema
Faecalibacterium

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/04/02

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: lower abundance with increasing temperature and time was detected in samples processed immediately

Abundance in Group 1: decreased abundance in Unspiked pig feces(P1) at 64 hours (22°C)

NCBI Quality ControlLinks
Prevotella

Revision editor(s): Bolanle

Experiment 48


Needs review

Curated date: 2024/03/26

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
Unspiked pig feces(P1) at 64 hours (-80°C)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Unspiked pig feces(P1) at 16 hours (-20°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Unspiked P1 sample stored at a temperature of -20°C for 16 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/02

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: higher abundance with increasing temperature and time was detected in samples processed immediately.

Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 16 hours (-20°C)

NCBI Quality ControlLinks
Faecalibacterium
Roseburia

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/04/02

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.

Abundance in Group 1: decreased abundance in Unspiked pig feces(P1) at 16 hours (-20°C)

NCBI Quality ControlLinks
Prevotella
Treponema
Phascolarctobacterium

Revision editor(s): Bolanle

Experiment 49


Needs review

Curated date: 2024/03/26

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
Unspiked pig feces(P1) at 64 hours (-20°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Unspiked P1 sample stored at a temperature of -20°C for 64 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/02

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: higher abundance with increasing temperature and time was detected in samples processed immediately.

Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 64 hours (-20°C)

NCBI Quality ControlLinks
Treponema
Faecalibacterium
Roseburia

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/04/02

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.

Abundance in Group 1: decreased abundance in Unspiked pig feces(P1) at 64 hours (-20°C)

NCBI Quality ControlLinks
Prevotella
Phascolarctobacterium

Revision editor(s): Bolanle

Experiment 50


Needs review

Curated date: 2024/03/26

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
Unspiked pig feces(P1) at 16 hours (5°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Unspiked P1 sample stored at a temperature of 5°C for 16 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/02

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: higher abundance with increasing temperature and time was detected in samples processed immediately.

Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 16 hours (5°C)

NCBI Quality ControlLinks
Treponema
Faecalibacterium
Roseburia

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/04/02

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.

Abundance in Group 1: decreased abundance in Unspiked pig feces(P1) at 16 hours (5°C)

NCBI Quality ControlLinks
Prevotella
Phascolarctobacterium

Revision editor(s): Bolanle

Experiment 51


Needs review

Curated date: 2024/03/26

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
Unspiked pig feces(P1) at 64 hours (5°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Unspiked P1 sample stored at a temperature of 5°C for 64 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/02

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: higher abundance with increasing temperature and time was detected in samples processed immediately.

Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 64 hours (5°C)

NCBI Quality ControlLinks
Faecalibacterium
Roseburia

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/04/02

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.

Abundance in Group 1: decreased abundance in Unspiked pig feces(P1) at 64 hours (5°C)

NCBI Quality ControlLinks
Prevotella
Treponema
Phascolarctobacterium

Revision editor(s): Bolanle

Experiment 52


Needs review

Curated date: 2024/03/26

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
Unspiked pig feces(P1) at 16 hours (22°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Unspiked P1 sample stored at a temperature of 22°C for 16 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/02

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: higher abundance with increasing temperature and time was detected in samples processed immediately.

Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 16 hours (22°C)

NCBI Quality ControlLinks
Treponema
Faecalibacterium
Phascolarctobacterium
Roseburia

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/04/02

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.

Abundance in Group 1: decreased abundance in Unspiked pig feces(P1) at 16 hours (22°C)

NCBI Quality ControlLinks
Prevotella

Revision editor(s): Bolanle

Experiment 53


Needs review

Curated date: 2024/03/26

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
Unspiked pig feces(P1) at 64 hours (22°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Unspiked P1 sample stored at a temperature of 22°C for 64 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/02

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: higher abundance with increasing temperature and time was detected in samples processed immediately.

Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 64 hours (22°C)

NCBI Quality ControlLinks
Treponema
Faecalibacterium
Phascolarctobacterium
Roseburia

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/04/02

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: lower abundance with increasing temperature and time was detected in samples processed immediately.

Abundance in Group 1: decreased abundance in Unspiked pig feces(P1) at 64 hours (22°C)

NCBI Quality ControlLinks
Prevotella

Revision editor(s): Bolanle

Experiment 54


Needs review

Curated date: 2024/03/26

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
Unspiked pig feces(P1) at 16 hours (-20°C)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Unspiked pig feces(P1) at 64 hours (-20°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Unspiked P1 sample stored at a temperature of -20°C for 64 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/02

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: higher abundance with increasing temperature and time was detected in samples processed immediately.

Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 64 hours (-20°C)

NCBI Quality ControlLinks
Treponema

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/04/02

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.

Abundance in Group 1: decreased abundance in Unspiked pig feces(P1) at 64 hours (-20°C)

NCBI Quality ControlLinks
Prevotella
Phascolarctobacterium
Faecalibacterium
Roseburia

Revision editor(s): Bolanle

Experiment 55


Needs review

Curated date: 2024/03/26

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
Unspiked pig feces(P1) at 16 hours (5°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Unspiked P1 sample stored at a temperature of 5°C for 16 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/02

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: higher abundance with increasing temperature and time was detected in samples processed immediately.

Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 16 hours (5°C)

NCBI Quality ControlLinks
Treponema
Faecalibacterium
Roseburia

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/04/02

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.

Abundance in Group 1: decreased abundance in Unspiked pig feces(P1) at 16 hours (5°C)

NCBI Quality ControlLinks
Prevotella
Phascolarctobacterium

Revision editor(s): Bolanle

Experiment 56


Needs review

Curated date: 2024/03/26

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
Unspiked pig feces(P1) at 64 hours (5°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Unspiked P1 sample stored at a temperature of 5°C for 64 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/02

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: higher abundance with increasing temperature and time was detected in samples processed immediately.

Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 64 hours (5°C)

NCBI Quality ControlLinks
Treponema
Faecalibacterium
Phascolarctobacterium
Roseburia

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/04/02

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.

Abundance in Group 1: decreased abundance in Unspiked pig feces(P1) at 64 hours (5°C)

NCBI Quality ControlLinks
Prevotella

Revision editor(s): Bolanle

Experiment 57


Needs review

Curated date: 2024/03/26

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
Unspiked pig feces(P1) at 16 hours (22°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Unspiked P1 sample stored at a temperature of 22°C for 16 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/03

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: higher abundance with increasing temperature and time was detected in samples processed immediately.

Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 16 hours (22°C)

NCBI Quality ControlLinks
Treponema
Faecalibacterium
Phascolarctobacterium
Roseburia

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/04/03

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately

Abundance in Group 1: decreased abundance in Unspiked pig feces(P1) at 16 hours (22°C)

NCBI Quality ControlLinks
Prevotella

Revision editor(s): Bolanle

Experiment 58


Needs review

Curated date: 2024/03/26

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
Unspiked pig feces(P1) at 64 hours (22°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Unspiked P1 sample stored at a temperature of 22°C for 64 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/03

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: higher abundance with increasing temperature and time was detected in samples processed immediately.

Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 64 hours (22°C)

NCBI Quality ControlLinks
Treponema
Faecalibacterium
Phascolarctobacterium
Roseburia

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/04/03

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately

Abundance in Group 1: decreased abundance in Unspiked pig feces(P1) at 64 hours (22°C)

NCBI Quality ControlLinks
Prevotella

Revision editor(s): Bolanle

Experiment 59


Needs review

Curated date: 2024/03/26

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Not specified
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Spiked pig feces(P1) at 16 hours (5°C)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P1) at 64 hours (5°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P1 samplespiked with a mock community and stored at a temperature of 64 hours (5°C)

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 60


Needs review

Curated date: 2024/03/26

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P1) at 16 hours (22°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P1 sample spiked with a mock community and stored at a temperature of 16 hours (22°C)

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 61


Needs review

Curated date: 2024/03/26

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Spiked pig feces(P1) at 64 hours (5°C)

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 62


Needs review

Curated date: 2024/03/26

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

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 pig feces(P1) at 64 hours (-20°C)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Unspiked pig feces(P1) at 16 hours (5°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Unspiked P1 sample stored at a temperature of 5°C for 16 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/03

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: higher abundance with increasing temperature and time was detected in samples processed immediately.

Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 16 hours (5°C)

NCBI Quality ControlLinks
Treponema
Faecalibacterium

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/04/03

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately

Abundance in Group 1: decreased abundance in Unspiked pig feces(P1) at 16 hours (5°C)

NCBI Quality ControlLinks
Prevotella
Phascolarctobacterium
Roseburia

Revision editor(s): Bolanle

Experiment 63


Needs review

Curated date: 2024/03/26

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Not specified
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Spiked pig feces(P1) at 16 hours (22°C)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P1) at 64 hours (22°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P1 sample spiked with a mock community and stored at a temperature of 64 hours (22°C)

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 64


Needs review

Curated date: 2024/03/26

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

Subjects

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 pig feces(P1) at 64 hours (-20°C)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Unspiked pig feces(P1) at 64 hours (5°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Unspiked P1 sample stored at a temperature of 5°C for 64 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/03

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: higher abundance with increasing temperature and time was detected in samples processed immediately.

Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 64 hours (5°C)

NCBI Quality ControlLinks
Faecalibacterium
Phascolarctobacterium
Roseburia

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/04/03

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately

Abundance in Group 1: decreased abundance in Unspiked pig feces(P1) at 64 hours (5°C)

NCBI Quality ControlLinks
Prevotella
Treponema

Revision editor(s): Bolanle

Experiment 65


Needs review

Curated date: 2024/03/26

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
Unspiked pig feces(P1) at 16 hours (22°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Unspiked P1 sample stored at a temperature of 22°C for 16 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/03

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: higher abundance with increasing temperature and time was detected in samples processed immediately.

Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 16 hours (22°C)

NCBI Quality ControlLinks
Treponema
Faecalibacterium
Phascolarctobacterium
Roseburia

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/04/03

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately

Abundance in Group 1: decreased abundance in Unspiked pig feces(P1) at 16 hours (22°C)

NCBI Quality ControlLinks
Prevotella

Revision editor(s): Bolanle

Experiment 66


Needs review

Curated date: 2024/03/26

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
Unspiked pig feces(P1) at 64 hours (22°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Unspiked P1 sample stored at a temperature of 22°C for 64 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/03

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: higher abundance with increasing temperature and time was detected in samples processed immediately

Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 64 hours (22°C)

NCBI Quality ControlLinks
Treponema
Phascolarctobacterium
Faecalibacterium
Roseburia

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/04/03

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately

Abundance in Group 1: decreased abundance in Unspiked pig feces(P1) at 64 hours (22°C)

NCBI Quality ControlLinks
Prevotella

Revision editor(s): Bolanle

Experiment 67


Needs review

Curated date: 2024/03/26

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
Unspiked pig feces(P1) at 16 hours (5°C)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Unspiked pig feces(P1) at 64 hours (5°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Unspiked P1 sample stored at a temperature of 5°C for 64 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/03

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: higher abundance with increasing temperature and time was detected in samples processed immediately

Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 64 hours (5°C)

NCBI Quality ControlLinks
Treponema
Faecalibacterium
Roseburia

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/04/03

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately

Abundance in Group 1: decreased abundance in Unspiked pig feces(P1) at 64 hours (5°C)

NCBI Quality ControlLinks
Prevotella
Phascolarctobacterium

Revision editor(s): Bolanle

Experiment 68


Needs review

Curated date: 2024/03/26

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
Unspiked pig feces(P1) at 16 hours (22°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Unspiked P1 sample stored at a temperature of 22°C for 16 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/03

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: higher abundance with increasing temperature and time was detected in samples processed immediately

Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 16 hours (22°C)

NCBI Quality ControlLinks
Treponema
Faecalibacterium
Phascolarctobacterium
Roseburia

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/04/03

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately

Abundance in Group 1: decreased abundance in Unspiked pig feces(P1) at 16 hours (22°C)

NCBI Quality ControlLinks
Prevotella

Revision editor(s): Bolanle

Experiment 69


Needs review

Curated date: 2024/03/26

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
Unspiked pig feces(P1) at 64 hours (22°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Unspiked P1 sample stored at a temperature of 22°C for 64 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/03

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: higher abundance with increasing temperature and time was detected in samples processed immediately

Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 64 hours (22°C)

NCBI Quality ControlLinks
Faecalibacterium
Phascolarctobacterium
Roseburia

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/04/03

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately

Abundance in Group 1: decreased abundance in Unspiked pig feces(P1) at 64 hours (22°C)

NCBI Quality ControlLinks
Prevotella
Treponema

Revision editor(s): Bolanle

Experiment 70


Needs review

Curated date: 2024/03/26

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
Unspiked pig feces(P1) at 64 hours (5°C)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Unspiked pig feces(P1) at 16 hours (22°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Unspiked P1 sample stored at a temperature of 22°C for 16 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/03

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: higher abundance with increasing temperature and time was detected in samples processed immediately

Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 16 hours (22°C)

NCBI Quality ControlLinks
Treponema
Faecalibacterium

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/04/03

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately

Abundance in Group 1: decreased abundance in Unspiked pig feces(P1) at 16 hours (22°C)

NCBI Quality ControlLinks
Prevotella
Phascolarctobacterium
Roseburia

Revision editor(s): Bolanle

Experiment 71


Needs review

Curated date: 2024/03/26

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
Unspiked pig feces(P1) at 64 hours (22°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Unspiked P1 sample stored at a temperature of 22°C for 64 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/03

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: higher abundance with increasing temperature and time was detected in samples processed immediately

Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 64 hours (22°C)

NCBI Quality ControlLinks
Treponema
Faecalibacterium

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/04/03

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately

Abundance in Group 1: decreased abundance in Unspiked pig feces(P1) at 64 hours (22°C)

NCBI Quality ControlLinks
Prevotella
Phascolarctobacterium
Roseburia

Revision editor(s): Bolanle

Experiment 72


Needs review

Curated date: 2024/03/26

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
Unspiked pig feces(P1) at 16 hours (22°C)

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2024/04/03

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: higher abundance with increasing temperature and time was detected in samples processed immediately

Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 64 hours (22°C)

NCBI Quality ControlLinks
Treponema
Faecalibacterium

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/04/03

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately

Abundance in Group 1: decreased abundance in Unspiked pig feces(P1) at 64 hours (22°C)

NCBI Quality ControlLinks
Prevotella
Phascolarctobacterium
Roseburia

Revision editor(s): Bolanle

Experiment 73


Needs review

Curated date: 2024/03/26

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Not specified
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Spiked pig feces(P2) at 0 hour
Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P2) at 64 hours (-80°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P2 sample spiked with a mock community and stored at a temperature of -80°C for 64 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 74


Needs review

Curated date: 2024/03/26

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P2) at 64 hours (22°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P2 sample spiked with a mock community and stored at a temperature of 22°C for 64 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 75


Needs review

Curated date: 2024/03/26

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P2) at 64 hours (5°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P2 sample spiked with a mock community and stored at a temperature of 5°C for 64 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 76


Needs review

Curated date: 2024/03/26

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P2) at 64 hours (-20°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P2 sample spiked with a mock community and stored at a temperature of -20°C for 64 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 77


Needs review

Curated date: 2024/03/26

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P2) at 16 hours (-80°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P2 sample spiked with a mock community and stored at a temperature of -80°C for 16 hours

Lab analysis

Statistical Analysis

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

Experiment 78


Needs review

Curated date: 2024/03/26

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P2) at 16 hours (5°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P2 sample spiked with a mock community and stored at a temperature of 5°C for 16 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 79


Needs review

Curated date: 2024/03/26

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P2) at 16 hours (22°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P2 sample spiked with a mock community and stored at a temperature of 22°C for 16 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 80


Needs review

Curated date: 2024/03/26

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P2) at 16 hours (-20°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P2 sample spiked with a mock community and stored at a temperature of -20°C for 16 hours

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 81


Needs review

Curated date: 2024/03/26

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Spiked pig feces(P2) at 16 hours (-80°C)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P2) at 64 hours (22°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P2 sample spiked with a mock community and stored at a temperature of 64 hours (22°C)

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 82


Needs review

Curated date: 2024/03/26

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P2) at 64 hours (-80°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P2 sample spiked with a mock community and stored at a temperature of 64 hours (-80°C)

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 83


Needs review

Curated date: 2024/03/26

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P2) at 64 hours (-20°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P2 sample spiked with a mock community and stored at a temperature of 64 hours (-20°C)

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 84


Needs review

Curated date: 2024/03/26

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P2) at 16 hours (-20°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P2 sample spiked with a mock community and stored at a temperature of 16 hours (-20°C)

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 85


Needs review

Curated date: 2024/03/26

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P2) at 64 hours (5°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P2 sample spiked with a mock community and stored at a temperature of 64 hours (5°C)

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 86


Needs review

Curated date: 2024/03/26

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P2) at 16 hours (22°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P2 sample spiked with a mock community and stored at a temperature of 16 hours (22°C)

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 87


Needs review

Curated date: 2024/03/26

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Spiked pig feces(P2) at 16 hours (5°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
P2 sample spiked with a mock community and stored at a temperature of 16 hours (5°C)

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 88


Needs review

Curated date: 2024/03/26

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Spiked pig feces(P2) at 64 hours (-80°C)

Lab analysis

Statistical Analysis

Alpha Diversity

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

Experiment 89


Needs review

Curated date: 2024/03/26

Curator: Bolanle

Revision editor(s):