Subgingival Microbiota during Healthy Pregnancy and Pregnancy Gingivitis/Experiment 3

From BugSigDB


Needs review

Curated date: 2021/06/24

Curator: Tislam

Revision editor(s): Fatima, Tislam, WikiWorks

Subjects

Location of subjects
Singapore
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
Subgingival dental plaque Subgingival plaque,Subgingival dental plaque,subgingival dental plaque
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Gingivitis acute gingivitis,chronic gingivitis,gingiva inflammation,gingivitis,inflammation of gingiva,Gingivitis
Group 0 name Corresponds to the control (unexposed) group for case-control studies
pregnant women without gingivitis
Group 1 name Corresponds to the case (exposed) group for case-control studies
pregnant women with gingivitis
Group 0 sample size Number of subjects in the control (unexposed) group
10
Group 1 sample size Number of subjects in the case (exposed) group
10
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
6 months

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V4
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Statistical test
LEfSe
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
.05
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
Yes
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
2

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
unchanged
Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
unchanged
Richness Number of species
unchanged

Signature 1

Needs review

Curated date: 2021/06/24

Curator: Tislam

Revision editor(s): Tislam

Source: Figure 3, text

Description: Linear discriminant analysis effect size. Differentially abundant taxonomic profile of subgingival plaque (SGP) microbiota in pregnant women with gingivitis versus pregnant women without gingivitis

Abundance in Group 1: increased abundance in pregnant women with gingivitis

NCBI Quality ControlLinks
Veillonellaceae
Leptotrichia
TM7 phylum sp. oral taxon 349
Metamycoplasma faucium
Lachnospiraceae bacterium oral taxon 500
TM7 phylum sp. oral taxon 346
Treponema sp. oral taxon 258
[Eubacterium] saphenum
Catonella morbi
Treponema maltophilum
Filifactor alocis
Fretibacterium fastidiosum
Tannerella forsythia
Treponema lecithinolyticum
Treponema sp. oral taxon 238
Prevotella sp. oral taxon 304
Aggregatibacter actinomycetemcomitans
Treponema sp. oral taxon 270
Treponema denticola
Fretibacterium sp.

Revision editor(s): Tislam

Signature 2

Needs review

Curated date: 2021/06/24

Curator: Tislam

Revision editor(s): Tislam

Source: Figure 3, text

Description: Linear discriminant analysis effect size. Differentially abundant taxonomic profile of subgingival plaque (SGP) microbiota in pregnant women with gingivitis versus pregnant women without gingivitis

Abundance in Group 1: decreased abundance in pregnant women with gingivitis

NCBI Quality ControlLinks
Veillonella parvula
Actinomyces naeslundii
Streptococcus salivarius
Granulicatella adiacens
Rothia dentocariosa
SR1 bacterium oral taxon 875
Actinomyces sp. oral taxon 448
Actinomyces sp. oral taxon 172
Kingella oralis
Oribacterium sp. oral taxon 108
Leptotrichia sp. oral taxon 221
Selenomonas sp. oral taxon 478
Propionibacterium sp. oral taxon 194
Actinomyces graevenitzii
Lancefieldella parvula

Revision editor(s): Tislam