Distinct intestinal microbial signatures linked to accelerated systemic and intestinal biological aging/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-11-14
Subjects
- Location of subjects
- United States of America
- 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
- Ileum Distal intestine,Intestinum ileum,Lower intestine,Posterior intestine,Ileum,ileum
- 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
- Controls/ People living without HIV (PLWOH)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- People living with HIV on Antiretroviral Therapy (PLWH on ART)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- People with HIV infection on Anti-Retroviral Therapy(ART)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 23
- Group 1 sample size Number of subjects in the case (exposed) group
- 25
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V2
- 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
- Linear Regression
- 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)?
- Yes
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, ethnic group, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-11-14
Source: Fig 4D
Description: Log-scale differences in bacterial abundance across ileum (square), between PLWoH and PLWH on ART.
Abundance in Group 1: increased abundance in People living with HIV on Antiretroviral Therapy (PLWH on ART)
| NCBI | Quality Control | Links |
|---|---|---|
| Alloprevotella | ||
| Catenibacterium | ||
| Prevotella sp. | ||
| Prevotella sp. 1-8 |
Revision editor(s): Imaspecial, Fiddyhamma
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-11-14
Source: Fig 4D
Description: Log-scale differences in bacterial abundance across ileum (square), between PLWOH and PLWH on ART
Abundance in Group 1: decreased abundance in People living with HIV on Antiretroviral Therapy (PLWH on ART)
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Bacteroides | ||
| Subdoligranulum | ||
| uncultured Erysipelotrichaceae bacterium | ||
| Coprococcus sp. | ||
| Peptostreptococcaceae | ||
| Romboutsia |
Revision editor(s): Imaspecial, Fiddyhamma
