HIV-Positive Patients on Antiretroviral Therapy Have an Altered Mucosal Intestinal but Not Oral Microbiome/Experiment 1
From BugSigDB
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
- Saliva , Mouth mucosa , Intestinal brush border layer Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva,Buccal mucosa,Mouth mucosa,Mouth mucous membrane,Mouth organ mucosa,Mucosa of mouth,Mucosal lining of mouth,Mucous membrane of mouth,Oral mucosa,Oral mucous membrane,Oral part of viscerocranial mucosa,Tunica mucosa oris,mouth mucosa,Brush border microvillus layer of intestine,Intestinal brush border,Intestinal brush border layer,intestinal brush border layer
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- HIV enteropathy HIV Enteropathy,HIV enteropathy,hIV enteropathy
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy Control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HIV Positive Patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- compositional and functional shifts in the intestinal and oral microbiome in HIV-positive patients on antiretroviral therapy compared to HIV-negative individuals
- Group 0 sample size Number of subjects in the control (unexposed) group
- 12
- Group 1 sample size Number of subjects in the case (exposed) group
- 5
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- N/A
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4-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
- Kruskall-Wallis
- PERMANOVA
- 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, sex, Matched on: "Hispanic" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.Hispanic, Matched on: "Non-Hispanic" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.Non-Hispanic
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: fig.S1
Description: Bacterial composition at phylum and genus levels in the gut samples, Linear discriminant analysis (LDA) effect size (LEfSe) analysis was performed among intestinal samples to determine the bacterial taxa that were differentially enriched. Bacteria from the genera were more abundant in samples from HIV-positive patients.
Abundance in Group 1: increased abundance in HIV Positive Patients
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella | ||
| Fusobacterium | ||
| Eubacterium | ||
| Collinsella | ||
| Megasphaera | ||
| Mogibacterium | ||
| Mitsuokella |
Revision editor(s): Eve10111
Signature 2
Source: fig.S1
Description: Bacterial composition at phylum and genus levels in the gut samples, Linear discriminant analysis (LDA) effect size (LEfSe) analysis was performed among intestinal samples to determine the bacterial taxa that were differentially enriched. Bacteria from the genera were more abundant in samples from HIV-positive patients.
Abundance in Group 1: decreased abundance in HIV Positive Patients
| NCBI | Quality Control | Links |
|---|---|---|
| Ruminococcus | ||
| Blautia | ||
| Clostridium |
Revision editor(s): Eve10111
