Prevalent high-risk HPV infection and vaginal microbiota in Nigerian women

From BugSigDB
Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Dareng EO, Ma B, Famooto AO, Adebamowo SN, Offiong RA, Olaniyan O, Dakum PS, Wheeler CM, Fadrosh D, Yang H, Gajer P, Brotman RM, Ravel J, Adebamowo CA
Journal
Epidemiology and infection
Year
2016
Keywords:
HIV/AIDS, human papilloma virus (HPV), public health
In this study, we evaluated the association between high-risk human papillomavirus (hrHPV) and the vaginal microbiome. Participants were recruited in Nigeria between April and August 2012. Vaginal bacterial composition was characterized by deep sequencing of barcoded 16S rRNA gene fragments (V4) on Illumina MiSeq and HPV was identified using the Roche Linear Array® HPV genotyping test. We used exact logistic regression models to evaluate the association between community state types (CSTs) of vaginal microbiota and hrHPV infection, weighted UniFrac distances to compare the vaginal microbiota of individuals with prevalent hrHPV to those without prevalent hrHPV infection, and the Linear Discriminant Analysis effect size (LEfSe) algorithm to characterize bacteria associated with prevalent hrHPV infection. We observed four CSTs: CST IV-B with a low relative abundance of Lactobacillus spp. in 50% of participants; CST III (dominated by L. iners) in 39·2%; CST I (dominated by L. crispatus) in 7·9%; and CST VI (dominated by proteobacteria) in 2·9% of participants. LEfSe analysis suggested an association between prevalent hrHPV infection and a decreased abundance of Lactobacillus sp. with increased abundance of anaerobes particularly of the genera Prevotella and Leptotrichia in HIV-negative women (P < 0·05). These results are hypothesis generating and further studies are required.

Experiment 1


Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Peace Sandy

Subjects

Location of subjects
Nigeria
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
Vagina Vagina,vagina,Distal oviductal region,Distal portion of oviduct,Vaginae
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Human papilloma virus infection HPV,Human Papilloma Virus Infection,Human papilloma Virus infection,human papilloma virus infection,Human papillomavirus caused disease or disorder,Human papillomavirus disease or disorder,Human Papillomavirus Infection,Human Papillomavirus infection,Human papillomavirus infectious disease,Human papilloma virus infection
Group 0 name Corresponds to the control (unexposed) group for case-control studies
HPV-/HIV-
Group 1 name Corresponds to the case (exposed) group for case-control studies
HPV+/HIV-
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
HR-HPV+ confirmed by medical records and HPV genotyping test
Group 0 sample size Number of subjects in the control (unexposed) group
99
Group 1 sample size Number of subjects in the case (exposed) group
12

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
LEfSe
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)?
No
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
2


Signature 1

Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

Curated date: 2021/01/10

Curator: Cynthia Anderson

Revision editor(s): WikiWorks, Atrayees

Source: Fig. 4b

Description: Identified phylotype biomarkers ranked by effect size in HIV–women

Abundance in Group 1: increased abundance in HPV+/HIV-

NCBI Quality ControlLinks
Anaerococcus sp.
Arcanobacterium
Arcanobacterium sp.
Bacteroidales
Bacteroidia
Bacteroidota
Clostridiaceae
Dialister
Dialister micraerophilus
Fusobacteriales
Fusobacteriota
Leptotrichiaceae
Megasphaera
Megasphaera sp.
Peptoniphilus
Peptoniphilus asaccharolyticus
Peptoniphilus sp.
Peptostreptococcaceae
Peptostreptococcus
Peptostreptococcus anaerobius
Prevotella
Prevotella sp.
Prevotellaceae
Sneathia
Sneathia sp.

Revision editor(s): WikiWorks, Atrayees

Signature 2

Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

Curated date: 2021/01/10

Curator: Cynthia Anderson

Revision editor(s): WikiWorks, Atrayees, Merit

Source: Fig. 4b

Description: Identified phylotype biomarkers ranked by effect size in HIV–women

Abundance in Group 1: decreased abundance in HPV+/HIV-

NCBI Quality ControlLinks
Alphaproteobacteria
Halorubrum
Halorubrum sp.
Hyphomicrobiales
Lactobacillus iners
Lysobacterales
Lactobacillus
Lactobacillales

Revision editor(s): WikiWorks, Atrayees, Merit