Oral and Gut Microbial Diversity and Immune Regulation in Patients with HIV on Antiretroviral Therapy/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-15
Curated date: 2021/12/21
Curator: Joyessa
Revision editor(s): WikiWorks, Joyessa, Jacquelynshevin, Peace Sandy, Victoria
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
- Oral cavity , Feces Bucca,Buccal cavity,Cavity of mouth,Oral cavity,oral cavity,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
- PLWH >50 years old with no/mild periodontitis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- PLWH >50 years old with severe periodontitis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with severe periodontal disease
- Group 0 sample size Number of subjects in the control (unexposed) group
- 4
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 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).
- raw counts
- Statistical test
- DESeq2
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, race, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-15
Source: Table S5 and Table S6
Description: Differentially abundant fungal taxa in saliva and subgingival plaque from patients with severe vs. no/mild periodontal disease (DESeq2, p<0.05, padj (FDR)<0.05)
Abundance in Group 1: increased abundance in PLWH >50 years old with severe periodontitis
| NCBI | Quality Control | Links |
|---|---|---|
| Candida albicans | ||
| Candida parapsilosis | ||
| Prevotella | ||
| Fusobacterium | ||
| Rothia | ||
| Kingella | ||
| Veillonella | ||
| Moryella | ||
| Streptococcus | ||
| Haemophilus |
Revision editor(s): Jacquelynshevin, Peace Sandy
Signature 2
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-15
Source: Table S5 and Table S6
Description: Differentially abundant fungal taxa in saliva and subgingival plaque from patients with severe vs. no/mild periodontal disease (DESeq2, p<0.05, padj (FDR)<0.05)
Abundance in Group 1: decreased abundance in PLWH >50 years old with severe periodontitis
| NCBI | Quality Control | Links |
|---|---|---|
| Candida dubliniensis | ||
| Debaryomyces hansenii | ||
| Exserohilum turcicum | ||
| Tausonia pullulans | ||
| Saccharomyces cerevisiae | ||
| Megasphaera | ||
| Veillonella |
Revision editor(s): Jacquelynshevin, Peace Sandy
