Development of the oral resistome during the first decade of life/Experiment 1

From BugSigDB


Reviewed Marked as Reviewed by Peace Sandy on 2024-2-23

Curated date: 2023/10/18

Curator: Ojotuleonalo

Revision editor(s): Ojotuleonalo, Peace Sandy

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

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-23

Curated date: 2024/02/23

Curator: Peace Sandy

Revision editor(s): Peace Sandy

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 ControlLinks
Enterococcus wangshanyuanii
Streptococcus himalayensis
Streptococcus marmotae
Streptococcus parauberis
Streptococcus pluranimalium
Streptococcus urinalis

Revision editor(s): Peace Sandy