Gut Microbiome Changes Associated With HIV Infection and Sexual Orientation

From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-30
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Zhou J, Zhang Y, Cui P, Luo L, Chen H, Liang B, Jiang J, Ning C, Tian L, Zhong X, Ye L, Liang H, Huang J
Journal
Frontiers in cellular and infection microbiology
Year
2020
Keywords:
16S rRNA gene amplicon sequencing, AIDS, HIV, gut microbiome, sexual orientation
Background: Many studies have explored changes in the gut microbiome associated with HIV infection, but the consistent pattern of changes has not been clarified. Men who have sex with men (MSM) are very likely to be an independent influencing factor of the gut microbiome, but relevant research is still lacking. Methods: We conducted a meta-analysis by screening 12 published studies of 16S rRNA gene amplicon sequencing of gut microbiomes related to HIV/AIDS (six of these studies contain data that is relevant and available to MSM) from NCBI and EBI databases. The analysis of gut microbiomes related to HIV infection status and MSM status included 1,288 samples (HIV-positive (HIV+) individuals, n = 744; HIV-negative (HIV-) individuals, n = 544) and 632 samples (MSM, n = 328; non-MSM, n = 304), respectively. The alpha diversity indexes, beta diversity indexes, differentially enriched genera, differentially enriched species, and differentially enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) functional pathways related to gut microbiomes were calculated. Finally, the overall trend of the above indicators was evaluated. Results: Our results indicate that HIV+ status is associated with decreased alpha diversity of the gut microbiome. MSM status is an important factor that affects the study of HIV-related gut microbiomes; that is, MSM are associated with alpha diversity changes in the gut microbiome regardless of HIV infection, and the changes in the gut microbiome composition of MSM are more significant than those of HIV+ individuals. A consistent change in Bacteroides caccae, Bacteroides ovatus, Bacteroides uniformis, and Prevotella stercorea was found in HIV+ individuals and MSM. The differential expression of the gut microbiome may be accompanied by changes in functional pathways of carbohydrate metabolism, amino acid metabolism, and lipid Metabolism. Conclusions: This study shows that the changes in the gut microbiome are related to HIV and MSM status. Importantly, MSM status may have a far greater impact on the gut microbiome than HIV status.

Experiment 1


Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-23

Curated date: 2023/04/03

Curator: Atrayees

Revision editor(s): Atrayees, Claregrieve1, ChiomaBlessing

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
HIV– individuals
Group 1 name Corresponds to the case (exposed) group for case-control studies
HIV+ individuals
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
HIV positive patients
Group 0 sample size Number of subjects in the control (unexposed) group
544
Group 1 sample size Number of subjects in the case (exposed) group
744

Lab analysis

Sequencing type
16S
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

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
2
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age, body mass index, sex, sexual preference

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Chao1 Abundance-based estimator of species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged
Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
decreased
Richness Number of species
decreased

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-23

Curated date: 2023/04/03

Curator: Atrayees

Revision editor(s): Atrayees, ChiomaBlessing

Source: Figure 8

Description: Differential enrichment of genus or species in HIV+ and HIV– individuals.

Abundance in Group 1: increased abundance in HIV+ individuals

NCBI Quality ControlLinks
Blautia
Bulleidia
Butyricicoccus
Butyricicoccus sp.
Citrobacter
Corynebacterium
Desulfovibrio
Enterococcus
Escherichia
Eubacterium
Fusobacterium
Granulicatella
Megamonas
Megasphaera
Mitsuokella
Mogibacterium
Parvimonas
Peptostreptococcus
Phascolarctobacterium
Prevotella
Pseudoramibacter
Staphylococcus
Turicibacter
[Ruminococcus] torques
Enterocloster citroniae
Dorea formicigenerans
Eggerthella lenta

Revision editor(s): Atrayees, ChiomaBlessing

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-23

Curated date: 2023/04/03

Curator: Atrayees

Revision editor(s): Atrayees, ChiomaBlessing

Source: Figure 8

Description: Differential enrichment of genus or species in HIV+ and HIV– individuals.

Abundance in Group 1: decreased abundance in HIV+ individuals

NCBI Quality ControlLinks
Adlercreutzia
Agrobacterium
Anaerostipes
Bacteroides
Bifidobacterium
Butyrivibrio
Clostridium
Coprococcus
Dorea
Faecalibacterium
Holdemania
Lachnobacterium
Lachnospira
Oscillospira
Roseburia
Ruminococcus
Sneathia
Streptococcus
SMB53SMB53

Revision editor(s): Atrayees, ChiomaBlessing

Experiment 2


Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-23

Curated date: 2024/01/23

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
non-MSM
Group 1 name Corresponds to the case (exposed) group for case-control studies
MSM (men who have sex with men)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Men who have sex with men
Group 0 sample size Number of subjects in the control (unexposed) group
304
Group 1 sample size Number of subjects in the case (exposed) group
328

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased
Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
decreased
Richness Number of species
decreased

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-23

Curated date: 2024/01/23

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Source: Figure 9

Description: Differential enrichment of genus or species in MSM and non-MSM.

Abundance in Group 1: increased abundance in MSM (men who have sex with men)

NCBI Quality ControlLinks
Aggregatibacter
Asteroleplasma
Bulleidia
Butyrivibrio
Catenibacterium
Collinsella
Desulfovibrio
Dialister
Enterococcus
Escherichia
Eubacterium
Megasphaera
Mitsuokella
Mogibacterium
Oribacterium
Peptococcus
Phascolarctobacterium
Prevotella
Slackia
Succinivibrio
Sutterella
Victivallis
Coprococcus eutactus
Dorea formicigenerans

Revision editor(s): ChiomaBlessing

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-23

Curated date: 2024/01/23

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Source: Figure 9

Description: Differential enrichment of genus or species in MSM and non-MSM.

Abundance in Group 1: decreased abundance in MSM (men who have sex with men)

NCBI Quality ControlLinks
Adlercreutzia
Akkermansia
Alistipes
Bacteroides
Bifidobacterium
Bilophila
Blautia
Butyricicoccus
Clostridium
Coprococcus
Faecalibacterium
Holdemania
Methanobrevibacter
Odoribacter
Parabacteroides
Paraprevotella
Porphyromonas
Ruminococcus
SMB53SMB53
Streptococcus

Revision editor(s): ChiomaBlessing