Altered gut microbiota correlate with different immune responses to HAART in HIV-infected individuals/Experiment 3
From BugSigDB
Reviewed Marked as Reviewed by Peace Sandy on 2024-10-22
Subjects
- Location of subjects
- China
- 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
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- 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
- immunological non-responders (INR) HIV infected individual
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Immunological Responder (IR) HIV infected individual
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Immunological Responder HIV infected individual (IR) was defined as patients whose CD4+ T-cell counts/μl equal or is more than 500 or less than 200 after 2 years of receiving complete viral suppression therapy respectively. All HIV-positive subjects were on two nucleoside reverse transcriptase inhibitors (NRTIs) + nonnucleoside reverse transcriptase inhibitors (NNRTIs) or the protease inhibitor-based therapy: Zidovudine/Tenofovir Disoproxil Fumarate (AZT/TDF) + Lamivudine (3TC) + Efavirenz (EFV) or Lopinavir/ritonavir (LPV/r).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 30
- Group 1 sample size Number of subjects in the case (exposed) group
- 28
- 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
- V3-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)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-10-22
Source: Additional file 4, figure S4 f
Description: Taxonomic differences of fecal microbiota between the immunological non-responders (INR) and Immunological Responder (IR) HIV infected individual.
Abundance in Group 1: increased abundance in Immunological Responder (IR) HIV infected individual
| NCBI | Quality Control | Links |
|---|---|---|
| Solobacterium | ||
| Dielma | ||
| Blautia | ||
| Escherichia/Shigella sp. |
Revision editor(s): Patience Onah
Signature 2
Reviewed Marked as Reviewed by Peace Sandy on 2024-10-22
Source: Additional file 4, figure S4 f
Description: Taxonomic differences of fecal microbiota between the immunological non-responders (INR) and Immunological Responder (IR) HIV infected
Abundance in Group 1: decreased abundance in Immunological Responder (IR) HIV infected individual
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerostipes | ||
| Eubacterium ruminantium | ||
| Alloprevotella | ||
| Eubacterium | ||
| Ruminiclostridium sp. |
Revision editor(s): Patience Onah
