Relationship between the Cervical Microbiome, HIV Status, and Precancerous Lesions/Experiment 3

From BugSigDB


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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

Subjects

Location of subjects
United Republic of Tanzania
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
Uterine cervix Canalis cervicis uteri,Caudal segment of uterus,Cervical canal,Cervical canal of uterus,Cervix,Cervix of uterus,Cervix uteri,Neck of uterus,Uterine cervix,uterine cervix
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
HIV infection [X]Human immunodeficiency virus disease,[X]Human immunodeficiency virus disease (disorder),[X]Unspecified human immunodeficiency virus [HIV] disease,[X]Unspecified human immunodeficiency virus [HIV] disease (disorder),HIV - Human immunodeficiency virus infection,HIV INFECT,HIV Infection,HIV infection,HIV Infections,HIV infectious disease,HTLV III INFECT,HTLV III Infections,HTLV III LAV INFECT,HTLV III LAV Infections,HTLV WIII INFECTIONS,HTLV WIII LAV INFECTIONS,HTLV-III Infection,HTLV-III Infections,HTLV-III-LAV Infection,HTLV-III-LAV Infections,HUMAN IMMUNO VIRUS DIS,human immunodeficiency virus,Human immunodeficiency virus [HIV] disease,HUMAN IMMUNOdeficiency VIRUS [HIV] INFECTION,Human immunodeficiency virus caused disease or disorder,Human immunodeficiency virus disease,Human immunodeficiency virus disease (disorder),Human immunodeficiency virus disease or disorder,Human immunodeficiency virus infection,Human immunodeficiency virus infection (disorder),Human immunodeficiency virus infection, NOS,Human immunodeficiency virus infectious disease,human immunodeficiency virus infectious disease,Infection, HIV,Infection, HTLV-III,Infection, HTLV-III-LAV,Infections, HIV,Infections, HTLV-III,Infections, HTLV-III-LAV,LYMPHOTROPIC VIRUS TYPE III INFECTIONS HUMAN T,T LYMPHOTROPIC VIRUS TYPE III INFECT HUMAN,T Lymphotropic Virus Type III Infections, Human,T-Lymphotropic Virus Type III Infections, Human,Unspecified human immunodeficiency virus [HIV] disease (disorder),hIV infection
Group 0 name Corresponds to the control (unexposed) group for case-control studies
HIV-
Group 1 name Corresponds to the case (exposed) group for case-control studies
HIV+
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
HIV+ comfirmed by Standard Diagnostics HIV-1/2 3.0 detection kit
Group 0 sample size Number of subjects in the control (unexposed) group
95
Group 1 sample size Number of subjects in the case (exposed) group
39

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)
0.1
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
Yes

Alpha Diversity

Chao1 Abundance-based estimator of species richness
increased

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, Merit

Source: figure 6c

Description: LEfSe linear discriminant analysis (LDA) scores.

Abundance in Group 1: increased abundance in HIV+

NCBI Quality ControlLinks
Actinomycetaceae
Actinomycetales
Aerococcus
Alphaproteobacteria
Bacillota
Bifidobacteriaceae
Carnobacteriaceae
Clostridia
Gemella
Granulicatella
Haemophilus influenzae
Mollicutes
Moryella
Mycoplasmataceae
Mycoplasmatales
Mycoplasmatota
Peptostreptococcaceae
Peptostreptococcus
Peptostreptococcus anaerobius
Rhizobiaceae
Staphylococcus
Streptococcus
Streptococcus anginosus

Revision editor(s): WikiWorks, Merit

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

Source: figure 6c

Description: LEfSe linear discriminant analysis (LDA) scores.

Abundance in Group 1: decreased abundance in HIV+

NCBI Quality ControlLinks
Arcanobacterium
Ureaplasma
Limosilactobacillus reuteri
Actinomycetes
Bifidobacteriales
Bifidobacterium

Revision editor(s): WikiWorks