Subgingival Microbiota during Healthy Pregnancy and Pregnancy Gingivitis

From BugSigDB
Reviewed Marked as Reviewed by Fatima on 2021/09/16
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Balan P, Brandt BW, Chong YS, Crielaard W, Wong ML, Lopez V, He HG, Seneviratne CJ
Journal
JDR clinical and translational research
Year
2021
Keywords:
Singapore, illumina sequencing, oral health, oral microbiota, pregnant women, prenatal care
INTRODUCTION: Previous studies have largely explored the microbial composition and pathogenesis of pregnancy gingivitis. However, the patterns of microbial colonization during pregnancy in the absence of pregnancy gingivitis have rarely been studied. Characterization of the oral microbiome in pregnant women with healthy gingiva is an important initial step in understanding the role of the microbiome in progression to pregnancy gingivitis. OBJECTIVES: In this study, we compared the oral microbiome of pregnant women without gingivitis (healthy pregnancy) with pregnant women having gingivitis and nonpregnant healthy women to understand how pregnancy modifies the oral microbiome and induces progression to pregnancy gingivitis. METHODS: Subgingival plaque samples were collected from Chinese pregnant women with gingivitis (n = 10), healthy pregnant women (n = 10), and nonpregnant healthy women (n = 10). The Illumina MiSeq platform was used to perform 16S rRNA gene sequencing targeting the V4 region. RESULTS: The alpha and beta diversity was significantly different between pregnant and nonpregnant women, but minimal differences were observed between pregnant women with and without gingivitis. Interestingly, the oral bacterial community showed higher abundance of pathogenic taxa during healthy pregnancy as compared with nonpregnant women despite similar gingival and plaque index scores. However, when compared with overt pregnancy gingivitis, pathogenic taxa were less abundant during healthy pregnancy. PICRUSt analysis (phylogenetic investigation of communities by reconstruction of unobserved states) also suggested no difference in the functional capabilities of the microbiome during pregnancy, irrespective of gingival disease status. However, metabolic pathways related to amino acid metabolism were significantly increased in healthy pregnant women as compared with nonpregnant women. CONCLUSION: The presence of pathogenic taxa in healthy pregnancy and pregnancy gingivitis suggests that bacteria may be necessary for initiating disease development but progression to gingivitis may be influenced by the host environmental factors. More efforts are required to plan interventions aimed at sustaining health before the appearance of overt gingivitis. KNOWLEDGE TRANSFER STATEMENT: The results of this study draw attention to the importance of oral health maintenance during pregnancy, as women without any prenatal oral conditions are predisposed to the risk of developing pregnancy gingivitis. Hence, it is important to incorporate comprehensive assessment of oral health in the prenatal health care schedules. Pregnant woman should be screened for oral risks, counseled on proper oral hygiene and expected oral changes, and referred for dental treatment, when necessary.

Experiment 1


Reviewed Marked as Reviewed by Fatima on 2021/09/16

Curated date: 2021/06/16

Curator: Tislam

Revision editor(s): WikiWorks, Fatima, Tislam, Peace Sandy

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
Pregnancy Gestation,PREGN,Pregnancies,Pregnancy,pregnancy
Group 0 name Corresponds to the control (unexposed) group for case-control studies
non pregnant women without gingivitis
Group 1 name Corresponds to the case (exposed) group for case-control studies
pregnant women without gingivitis
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Pregnant women sampled between 21 to 24 wk of gestation without 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

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Statistical test
Mann-Whitney (Wilcoxon)
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

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Fatima on 2021/09/16

Curated date: 2021/06/16

Curator: Tislam

Revision editor(s): Fatima, Tislam

Source: Appendix Figure 1, 2, text

Description: Phylum and Genera showing significant differential abundance in subgingival samples.

Abundance in Group 1: increased abundance in pregnant women without gingivitis

NCBI Quality ControlLinks
Bacteroides
Fusobacteriia
Fusobacterium
Spirochaetota
Treponema
Candidatus Saccharibacteria

Revision editor(s): Fatima, Tislam

Signature 2

Reviewed Marked as Reviewed by Fatima on 2021/09/16

Curated date: 2021/06/16

Curator: Tislam

Revision editor(s): Fatima, Tislam

Source: Appendix Figure 2, text

Description: Phylum and Genera showing significant differential abundance in subgingival samples.

Abundance in Group 1: decreased abundance in pregnant women without gingivitis

NCBI Quality ControlLinks
Bergeyella
Gemella
Haemophilus
Streptococcus
Terrahaemophilus

Revision editor(s): Fatima, Tislam

Experiment 2


Reviewed Marked as Reviewed by Fatima on 2021/09/16

Curated date: 2021/06/17

Curator: Tislam

Revision editor(s): WikiWorks, Fatima, Tislam, Victoria

Differences from previous experiment shown

Subjects

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 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Not specified

Lab analysis

Statistical Analysis

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

Reviewed Marked as Reviewed by Fatima on 2021/09/16

Curated date: 2021/06/24

Curator: Tislam

Revision editor(s): Fatima, Tislam

Source: Appendix Figure 1, 2, text

Description: Genera showing significant differential abundance in subgingival samples.

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

NCBI Quality ControlLinks
Bacteroides
Campylobacter
Candidatus Saccharibacteria
Filifactor
Fretibacterium
Spirochaetota
Tannerella
Treponema

Revision editor(s): Fatima, Tislam

Experiment 3


Needs review

Curated date: 2021/06/24

Curator: Tislam

Revision editor(s): WikiWorks, Fatima, Tislam, Victoria

Differences from previous experiment shown

Subjects

Lab analysis

Statistical Analysis

Statistical test
LEfSe
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

Experiment 4


Needs review

Curated date: 2021/07/07

Curator: Tislam

Revision editor(s): WikiWorks, LGeistlinger, Tislam, Victoria

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Pregnancy Gestation,PREGN,Pregnancies,Pregnancy,pregnancy
Group 0 name Corresponds to the control (unexposed) group for case-control studies
non pregnant women
Group 1 name Corresponds to the case (exposed) group for case-control studies
pregnant women
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
pregnant women

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2021/07/07

Curator: Tislam

Revision editor(s): Tislam

Source: Figure 3, text

Description: Linear discriminant analysis effect size. pregnant women without gingivitis versus nonpregnant women without gingivitis

Abundance in Group 1: increased abundance in pregnant women

NCBI Quality ControlLinks
Actinomyces graevenitzii
Alloprevotella sp.
Alloprevotella tannerae
Bergeyella
Campylobacter
Capnocytophaga haemolytica
Fretibacterium fastidiosum
Fretibacterium sp.
Fusobacterium periodonticum
Pseudoleptotrichia goodfellowii D28
Leptotrichia shahii
Leptotrichia sp.
Megasphaera micronuciformis
Metamycoplasma faucium
Oribacterium
Peptostreptococcus
Porphyromonas gingivalis
Segatella baroniae
Prevotella dentalis
Prevotella denticola
Prevotella melaninogenica
Prevotella micans
Prevotella sp.
Scardovia wiggsiae
Selenomonas sp.
Selenomonas sputigena
Tannerella forsythia
Treponema denticola
Treponema sp.
Veillonella parvula
Veillonella sp.
[Eubacterium] saphenum

Revision editor(s): Tislam

Signature 2

Needs review

Curated date: 2021/07/07

Curator: Tislam

Revision editor(s): Tislam

Source: Figure 3, text

Description: pregnant women without gingivitis versus nonpregnant women without gingivitis

Abundance in Group 1: decreased abundance in pregnant women

NCBI Quality ControlLinks
Bergeyella sp. oral taxon 322
Gemella morbillorum
Haemophilus sp.
Neisseria bacilliformis
Rothia aeria
Streptococcus sp.
Terrahaemophilus aromaticivorans

Revision editor(s): Tislam