A gut microbiome signature for HIV and metabolic dysfunction-associated steatotic liver disease
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Martínez-Sanz J, Talavera-Rodríguez A, Díaz-Álvarez J, Rosas Cancio-Suárez M, Rodríguez JM, Alba C, Montes ML, Martín-Mateos R, Burgos-Santamaría D, Moreno S, Serrano-Villar S, Sánchez-Conde M
Journal
Frontiers in immunology
Year
2023
Keywords:
HIV, MASLD, NAFLD, gut microbiome, microbiome
INTRODUCTION: Metabolic dysfunction-associated steatotic liver disease (MASLD), has emerged as an increasingly recognized problem among people living with HIV (PLWH). The gut-liver axis is considered to be strongly implicated in the pathogenesis of MASLD. We aimed to characterize the gut microbiota composition in PLWH and MASLD and compare it with that of two control groups: PLWH without MASLD and individuals with MASLD without HIV infection. METHODS: We collected clinical data and stool samples from participants. Bacterial 16S rRNA genes were amplified, sequenced, and clustered into operational taxonomic unit. Alpha diversity was studied by Shannon and Simpson indexes. To study how different the gut microbiota composition is between the different groups, beta diversity estimation was evaluated by principal coordinate analysis (PCoA) using Bray-Curtis dissimilarity. To further analyze differences in microbiome composition we performed a linear discriminant analysis (LDA) effect size (LEfSe). RESULTS: We included 30 HIV+MASLD+, 30 HIV+MASLD- and 20 HIV-MASLD+ participants. Major butyrate producers, including Faecalibacterium, Ruminococcus, and Lachnospira dominated the microbiota in all three groups. Shannon's and Simpson's diversity metrics were higher among MASLD+ individuals (Kruskal-Wallis p = 0.047). Beta diversity analysis showed distinct clustering in MASLD-, with MASLD+ participants overlapping regardless of HIV status (ADONIS significance <0.001). MASLD was associated with increased homogeneity across individuals, in contrast to that observed in the HIV+NAFDL- group, in which the dispersion was higher (Permanova test, p value <0.001; ANOSIM, p value <0.001). MASLD but not HIV determined a different microbiota structure (HIV+MASLD- vs. HIV+MASLD+, q-value = 0.002; HIV-MASLD+ vs. HIV+MASLD+, q-value = 0.930; and HIV-MASLD+ vs. HIV+MASLD-, q-value < 0.001). The most abundant genera in MASLD- were Prevotella, Bacteroides, Dialister, Acidaminococcos, Alloprevotella, and Catenibacterium. In contrast, the most enriched genera in MASLD+ were Ruminococcus, Streptococcus, Holdemanella, Blautia, and Lactobacillus. CONCLUSIONS: We found a microbiome signature linked to MASLD, which had a greater influence on the overall structure of the gut microbiota than HIV status alone.
Experiment 1
Reviewed Marked as Reviewed by Svetlana up on 2024-9-30
Subjects
- Location of subjects
- Spain
- 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
- Non-alcoholic fatty liver disease fatty liver disease, nonalcoholic,fatty liver disease, nonalcoholic, susceptibility to, 1,liver disease, alcoholic, susceptibility to, 1,NAFLD - Nonalcoholic Fatty Liver Disease,NAFLD - nonalcoholic fatty liver disease,NAFLD1,non-alcoholic fatty liver,non-alcoholic fatty liver disease,Nonalcoholic Fatty Liver Disease,nonalcoholic fatty liver disease,Non-alcoholic fatty liver disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HIV- MASLD+
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HIV+ MASLD+
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants living with HIV (PLWH) and Metabolic dysfunction-associated steatotic liver disease (MASLD).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 30
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
- 4
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-9-30
Source: Figure S2
Description: LEfSe analysis graph indicating differentially abundant bacterial genera between the different study groups. Only those genus whose LDA score was greater than 4 have been represented.
Abundance in Group 1: increased abundance in HIV+ MASLD+
Revision editor(s): Aleru Divine
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-9-30
Source: Figure S2
Description: LEfSe analysis graph indicating differentially abundant bacterial genera between the different study groups. Only those genus whose LDA score was greater than 4 have been represented.
Abundance in Group 1: decreased abundance in HIV+ MASLD+
Revision editor(s): Aleru Divine
Experiment 2
Reviewed Marked as Reviewed by Svetlana up on 2024-9-30
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HIV+ MASLD-
- Group 0 sample size Number of subjects in the control (unexposed) group
- 30
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-9-30
Source: Figure S2
Description: LEfSe analysis graph indicating differentially abundant bacterial genera between the different study groups. Only those genus whose LDA score was greater than 4 have been represented.
Abundance in Group 1: increased abundance in HIV+ MASLD+
Revision editor(s): Aleru Divine
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-9-30
Source: Figure S2
Description: LEfSe analysis graph indicating differentially abundant bacterial genera between the different study groups. Only those genus whose LDA score was greater than 4 have been represented.
Abundance in Group 1: decreased abundance in HIV+ MASLD+
Revision editor(s): Aleru Divine
Experiment 3
Reviewed Marked as Reviewed by Svetlana up on 2024-9-30
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HIV- MASLD+
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with Metabolic dysfunction-associated steatotic liver disease (MASLD) without HIV infection.
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-9-30
Source: Figure S2
Description: LEfSe analysis graph indicating differentially abundant bacterial genera between the different study groups. Only those genus whose LDA score was greater than 4 have been represented.
Abundance in Group 1: increased abundance in HIV- MASLD+
Revision editor(s): Aleru Divine
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-9-30
Source: Figure S2
Description: LEfSe analysis graph indicating differentially abundant bacterial genera between the different study groups. Only those genus whose LDA score was greater than 4 have been represented.
Abundance in Group 1: decreased abundance in HIV- MASLD+
Revision editor(s): Aleru Divine
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