Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth

From BugSigDB
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-22
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Feehily C, Crosby D, Walsh CJ, Lawton EM, Higgins S, McAuliffe FM, Cotter PD
Journal
NPJ biofilms and microbiomes
Year
2020
An association between the vaginal microbiota and preterm birth (PTB) has been reported in several research studies. Population shifts from high proportions of lactobacilli to mixed species communities, as seen with bacterial vaginosis, have been linked to a twofold increased risk of PTB. Despite the increasing number of studies using next-generation sequencing technologies, primarily involving 16S rRNA-based approaches, to investigate the vaginal microbiota during pregnancy, no distinct microbial signature has been associated with PTB. Shotgun metagenomic sequencing offers a powerful tool to reveal community structures and their gene functions at a far greater resolution than amplicon sequencing. In this study, we employ shotgun metagenomic sequencing to compare the vaginal microbiota of women at high risk of preterm birth (n = 35) vs. a low-risk control group (n = 14). Although microbial diversity and richness did not differ between groups, there were significant differences in terms of individual species. In particular, Lactobacillus crispatus was associated with samples from a full-term pregnancy, whereas one community state-type was associated with samples from preterm pregnancies. Furthermore, by predicting gene functions, the functional potential of the preterm microbiota was different from that of full-term equivalent. Taken together, we observed a discrete structural and functional difference in the microbial composition of the vagina in women who deliver preterm. Importance: with an estimated 15 million cases annually, spontaneous preterm birth (PTB) is the leading cause of death in infants under the age of five years. The ability to accurately identify pregnancies at risk of spontaneous PTB is therefore of utmost importance. However, no single cause is attributable. Microbial infection is a known risk factor, yet the role of vaginal microbes is poorly understood. Using high-resolution DNA-sequencing techniques, we investigate the microbial communities present in the vaginal tracts of women deemed high risk for PTB. We confirm that Lactobacillus crispatus is strongly linked to full-term pregnancies, whereas other microbial communities associate with PTB. Importantly, we show that the specific functions of the microbes present in PTB samples differs from FTB samples, highlighting the power of our sequencing approach. This information enables us to begin understanding the specific microbial traits that may be influencing PTB, beyond the presence or absence of microbial taxa.

Experiment 1


Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-22

Curated date: 2023/10/06

Curator: Joan Chuks

Revision editor(s): Joan Chuks, ChiomaBlessing, Victoria

Subjects

Location of subjects
Ireland
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
Posterior fornix of vagina , External cervical os Pars posterior fornicis vaginae,Posterior fornix,Posterior part of fornix of vagina,Posterior fornix of vagina,posterior fornix of vagina,External os,External os of uterus,Ostium of uterus,Ostium uteri,External cervical os,external cervical os
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Spontaneous preterm birth Spontaneous preterm birth,spontaneous preterm birth
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Full-term Birth
Group 1 name Corresponds to the case (exposed) group for case-control studies
Preterm Birth
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Pregnant women who delivered before 37 weeks’ gestation.
Group 0 sample size Number of subjects in the control (unexposed) group
41
Group 1 sample size Number of subjects in the case (exposed) group
8
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
Women currently on antibiotic treatment.

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).
raw counts
Statistical test
Linear Regression
T-Test
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.25
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
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged
Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-22

Curated date: 2023/10/07

Curator: Joan Chuks

Revision editor(s): Joan Chuks, ChiomaBlessing

Source: Figure 2b + Figure 2C

Description: Differentially abundant species for Preterm Birth (PTB) within the delivery outcome group compared to Full-term birth (FTB)

Abundance in Group 1: increased abundance in Preterm Birth

NCBI Quality ControlLinks
Aerococcus christensenii
Coriobacteriales bacterium DNF00809
Dialister micraerophilus
Fannyhessea vaginae
Gardnerella greenwoodii 00703Dmash
Gardnerella vaginalis
Gardnerella vaginalis 1500E
Hallella colorans
Hoylesella timonensis
Lachnospiraceae bacterium
Megasphaera genomosp. type_1 str. 28L
Prevotella amnii
Prevotella bivia
Prevotella histicola
Scardovia wiggsiae
Sneathia sanguinegens
Sneathia vaginalis
Tissierellia bacterium KA00581
unclassified Stomatobaculum
Prevotella sp. S7-1-8

Revision editor(s): Joan Chuks, ChiomaBlessing

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-22

Curated date: 2023/10/07

Curator: Joan Chuks

Revision editor(s): Joan Chuks, ChiomaBlessing

Source: Figure 2b + Figure 2C

Description: Differentially abundant species for Preterm Birth (PTB) within the delivery outcome group compared to Full-term birth (FTB)

Abundance in Group 1: decreased abundance in Preterm Birth

NCBI Quality ControlLinks
Bifidobacterium breve
Lactobacillus crispatus
Lactobacillus gasseri ATCC 33323 = JCM 1131
Lactobacillus johnsonii

Revision editor(s): Joan Chuks, ChiomaBlessing

Experiment 2


Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-22

Curated date: 2023/10/26

Curator: Joan Chuks

Revision editor(s): Joan Chuks, ChiomaBlessing, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Low-risk controls
Group 1 name Corresponds to the case (exposed) group for case-control studies
Risk Group
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Pregnant women with either a history of previous spontaneous preterm birth (risk_PTB) or women with risk factors for preterm birth but who delivered full term (risk_FTB)
Group 0 sample size Number of subjects in the control (unexposed) group
14
Group 1 sample size Number of subjects in the case (exposed) group
35

Lab analysis

Statistical Analysis

Statistical test
Linear Regression


Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-22

Curated date: 2023/10/27

Curator: Joan Chuks

Revision editor(s): Joan Chuks

Source: Figure 2C

Description: Differentially abundant species within the Risk group.

Abundance in Group 1: increased abundance in Risk Group

NCBI Quality ControlLinks
Bifidobacterium breve

Revision editor(s): Joan Chuks

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-22

Curated date: 2023/10/27

Curator: Joan Chuks

Revision editor(s): Joan Chuks

Source: Figure 2C

Description: Differentially abundant species within the Risk group

Abundance in Group 1: decreased abundance in Risk Group

NCBI Quality ControlLinks
Caloramator mitchellensis
Mycobacterium sp. 852013-50091_SCH5140682
Stenotrophomonas maltophilia

Revision editor(s): Joan Chuks

Experiment 3


Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-22

Curated date: 2023/10/27

Curator: Joan Chuks

Revision editor(s): Joan Chuks, ChiomaBlessing, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
No Previous Preterm birth
Group 1 name Corresponds to the case (exposed) group for case-control studies
Previous Preterm birth
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Pregnant women with a history of previous spontaneous preterm birth (PTB)
Group 0 sample size Number of subjects in the control (unexposed) group
20
Group 1 sample size Number of subjects in the case (exposed) group
29

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-22

Curated date: 2023/10/27

Curator: Joan Chuks

Revision editor(s): Joan Chuks

Source: Figure 2C

Description: Differentially abundant species for Previous Preterm birth(PTB) group

Abundance in Group 1: increased abundance in Previous Preterm birth

NCBI Quality ControlLinks
Bacteroides cellulosilyticus
Caloramator mitchellensis
Mycobacterium sp. 852013-50091_SCH5140682
Stenotrophomonas maltophilia
Lacticaseibacillus rhamnosus
Virgibacillus profundi
Desulfuromonas acetexigens

Revision editor(s): Joan Chuks

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-22

Curated date: 2023/10/27

Curator: Joan Chuks

Revision editor(s): Joan Chuks

Source: Figure 2C

Description: Differentially abundant species for Previous Preterm birth(PTB) group

Abundance in Group 1: decreased abundance in Previous Preterm birth

NCBI Quality ControlLinks
Bifidobacterium breve
Bifidobacterium longum subsp. infantis

Revision editor(s): Joan Chuks