Characterizing both bacteria and fungi improves understanding of the Arabidopsis root microbiome/Experiment 1
Curated date: 2023/10/06
Curator: Spykelionel
Revision editor(s): LGeistlinger, Peace Sandy, Spykelionel, Victoria
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Arabidopsis thaliana
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Accessory nerve root Accessory nerve root,Accessory portion of spinal accessory nerve,Bulbar accessory nerve,Bulbar part of accessory nerve,C11n,Cranial accessory nerve,Cranial part of accessory nerve,Cranial part of the accessory nerve,Cranial portion of eleventh cranial nerve,Internal branch of accessory nerve,Nerve XI (cranialis),Pars vagalis of nervus accessorius,Radices craniales nervi accessorii,Root of accessory nerve,accessory nerve root
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Root Root,root
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control group (Leaves)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Test group (Roots)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The leaf microbiome, representing the microbial communities associated with the leaves of the Arabidopsis plants.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 4
- Group 1 sample size Number of subjects in the case (exposed) group
- 4
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- NIL
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V5-V7
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- Linear Regression
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.1
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Confounders controlled for: "Block Effects" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.Block Effects, Confounders controlled for: "Sequencing run" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.Sequencing run
Alpha Diversity
- Richness Number of species
- increased
Signature 1
Source: Table 1
Description: The top 10 differentially enriched genera from each kingdom and their preferred habitats. The estimates (coefficients) and P - values are from a generalized linear (Poisson) model, fit to determine the effect of the factor organ while taking into account differences in sequencing effort among samples. Note: the ‘Unassigned’ categories include diverse taxa, which themselves may be differentially enriched (or depleted) in the root relative to the leaf microbiome.
Abundance in Group 1: increased abundance in Test group (Roots)
| NCBI | Quality Control | Links |
|---|---|---|
| Massilia | ||
| Mortierella | ||
| Tetracladium |
Revision editor(s): Spykelionel, Peace Sandy
Signature 2
Source: Table 1
Description: The top 10 differentially enriched genera from each kingdom and their preferred habitats. The estimates (coefficients) and P - values are from a generalized linear (Poisson) model, fit to determine the effect of the factor organ while taking into account differences in sequencing effort among samples. Note: the ‘Unassigned’ categories include diverse taxa, which themselves may be differentially enriched (or depleted) in the root relative to the leaf microbiome.
Abundance in Group 1: decreased abundance in Test group (Roots)
| NCBI | Quality Control | Links |
|---|---|---|
| Janthinobacterium | ||
| Pseudomonas | ||
| Alternaria | ||
| Articulospora | ||
| Cladosporium | ||
| Plectosphaerella |
Revision editor(s): Spykelionel, Peace Sandy
