Cotrimoxazole reduces systemic inflammation in HIV infection by altering the gut microbiome and immune activation/Experiment 1

From BugSigDB


Reviewed Marked as Reviewed by Atrayees on 2023-6-27

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Rimsha, WikiWorks, LGeistlinger

Subjects

Location of subjects
Zimbabwe
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 , Antimicrobial agent [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,antibiotic,antibiotics,Antibiotika,Antibiotikum,antibiotique,antimicrobial,antimicrobial agents,microbicide,microbicides,Antimicrobial agent,antimicrobial agent
Group 0 name Corresponds to the control (unexposed) group for case-control studies
stop cotrimoxazole prophylaxis
Group 1 name Corresponds to the case (exposed) group for case-control studies
continue cotrimoxazole prophylaxis
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
HIV-positive and antiretroviral therapy (ART) treated children who were randomized to continue taking cotrimoxazole prophylaxis
Group 0 sample size Number of subjects in the control (unexposed) group
36
Group 1 sample size Number of subjects in the case (exposed) group
36

Lab analysis

Sequencing type
WMS
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
Not specified
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Statistical test
Zero-Inflated Beta 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

Alpha Diversity

Pielou Quantifies how equal the community is numerically
unchanged
Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-27

Curated date: 2021/01/10

Curator: Michael Lutete

Revision editor(s): WikiWorks, Atrayees

Source: Text, Figure S3, Figure S2

Description: Bacterial species from stool samples that differ between HIV-positive ART-treated Zimbabwean children randomized to continue versus stop cotrimoxazole prophylaxis based on protein families

Abundance in Group 1: increased abundance in continue cotrimoxazole prophylaxis

NCBI Quality ControlLinks
Bacteroides xylanisolvens
Escherichia coli
Odoribacter splanchnicus
Parabacteroides goldsteinii
Parabacteroides johnsonii
Roseburia intestinalis
Alistipes communis

Revision editor(s): WikiWorks, Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-27

Curated date: 2021/01/10

Curator: Michael Lutete

Revision editor(s): Claregrieve1, WikiWorks, Atrayees

Source: Text, Figure S3

Description: Bacterial species from stool samples that differ between HIV-positive ART-treated Zimbabwean children randomized to continue versus stop cotrimoxazole prophylaxis based on protein families

Abundance in Group 1: decreased abundance in continue cotrimoxazole prophylaxis

NCBI Quality ControlLinks
Haemophilus parainfluenzae
Holdemanella biformis
Streptococcus parasanguinis
Faecalibacterium prausnitzii
Streptococcus salivarius
Alistipes onderdonkii
Intestinibacter bartlettii
Eggerthella lenta
Streptococcus mutans
Streptococcus vestibularis

Revision editor(s): Claregrieve1, WikiWorks, Atrayees