Development of the oral resistome during the first decade of life
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- Australia
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Mouth Adult mouth,Cavital oralis,Cavitas oris,Cavum oris,Mouth cavity,Oral region,Oral vestibule,Regio oralis,Rima oris,Stoma,Stomatodaeum,Trophic apparatus,Vestibule of mouth,Vestibulum oris,Mouth,mouth
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Dental caries caries,CARIES DENT,Caries, Dental,DECAY DENT,Decay, Dental,DENT CARIES,DENT DECAY,DENT WHITE SPOT,DENT WHITE SPOTS,dental caries,dental caries extending into pulp,dental caries of smooth surface,dental caries pit and fissure,Dental Decay,Dental White Spot,Dental White Spots,Spot, White,Spots, White,White Spot,WHITE SPOT DENT,White Spot, Dental,White Spots,WHITE SPOTS DENT,White Spots, Dental,Dental caries
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- T1 - Timepoint 1 - (T1. edentulous (no teeth))
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- T2 - Timepoint 2
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples (1.6 ± 0.4 years) at T2 (primary/deciduous/baby teeth only)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 139
- Group 1 sample size Number of subjects in the case (exposed) group
- 180
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 Months
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).
- arcsine square-root
- Statistical test
- MaAsLin2
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Signature 1
Source: Figure S4 C
Description: Vector loadings for ARGs, functional pathways and species that contribute to discrimination of individuals by time point/stage of dental development from DIABLO analysis. For each data type, DIABLO was performed on features above 0.01% abundance that had been TSS and CLR transformed. For each data block, displayed are the top ten features (ARG, function and species) with the largest vector loadings.
Abundance in Group 1: decreased abundance in T2 - Timepoint 2
| NCBI | Quality Control | Links |
|---|---|---|
| Enterococcus wangshanyuanii | ||
| Streptococcus himalayensis | ||
| Streptococcus marmotae | ||
| Streptococcus parauberis | ||
| Streptococcus pluranimalium | ||
| Streptococcus urinalis |
Revision editor(s): Peace Sandy
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- T3 - Timepoint 3
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples at T3 (mixed dentition, 8.5 ± 1.2 years old)
- Group 1 sample size Number of subjects in the case (exposed) group
- 211
Lab analysis
Statistical Analysis
Signature 1
Source: Figure S4 C
Description: Vector loadings for ARGs, functional pathways and species that contribute to discrimination of individuals by time point/stage of dental development from DIABLO analysis. For each data type, DIABLO was performed on features above 0.01% abundance that had been TSS and CLR transformed. For each data block, displayed are the top ten features (ARG, function and species) with the largest vector loadings.
Abundance in Group 1: increased abundance in T3 - Timepoint 3
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces sp. | ||
| Actinomyces viscosus |
Revision editor(s): Peace Sandy
Signature 2
Source: Figure S4 C
Description: Vector loadings for ARGs, functional pathways and species that contribute to discrimination of individuals by time point/stage of dental development from DIABLO analysis. For each data type, DIABLO was performed on features above 0.01% abundance that had been TSS and CLR transformed. For each data block, displayed are the top ten features (ARG, function and species) with the largest vector loadings.
Abundance in Group 1: decreased abundance in T3 - Timepoint 3
| NCBI | Quality Control | Links |
|---|---|---|
| Enterococcus wangshanyuanii | ||
| Streptococcus himalayensis | ||
| Streptococcus marmotae | ||
| Streptococcus parauberis | ||
| Streptococcus pluranimalium | ||
| Streptococcus urinalis |
Revision editor(s): Peace Sandy
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- T2 - Timepoint 2
- Group 0 sample size Number of subjects in the control (unexposed) group
- 180
Lab analysis
Statistical Analysis
Signature 1
Source: Figure S4 C
Description: Vector loadings for ARGs, functional pathways and species that contribute to discrimination of individuals by time point/stage of dental development from DIABLO analysis. For each data type, DIABLO was performed on features above 0.01% abundance that had been TSS and CLR transformed.For each data block, displayed are the top ten features (ARG, function and species) with the largest vector loadings.
Abundance in Group 1: increased abundance in T3 - Timepoint 3
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces sp. | ||
| Actinomyces viscosus |
Revision editor(s): Peace Sandy
