Association of gut microbiota with the pathogenesis of SARS-CoV-2 Infection in people living with HIV
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
People living with HIV (PLWH) with chronic inflammation may have an increasing risk for coronavirus disease 2019 (COVID-19) severity; however, the impact of their gut microbiota on COVID-19 is not fully elucidated. Here, we analyzed the temporal changes in the gut microbiota composition of hospitalized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected PLWH (PLWH-CoV) and their correlation with COVID-19 severity.
Result The 16S rRNA analysis results using stool samples (along the timeline from disease onset) from 12 hospitalized PLWH-CoV, whose median CD4 + T cell count was 671 cells/µl, were compared to those of 19 healthy people and 25 PLWH. Bacterial diversity in PLWH-CoV is not significantly different from that of healthy people and SARS-CoV-2 non-infected PLWH, but a significant difference in the microbiota diversity was observed in the classification according to the disease severity. Immediately after the disease onset, remarkable changes were observed in the gut microbiota of PLWH-CoV, and the changing with a decrease in some short-chain fatty acid-producing bacteria and an increase in colitis-related pathobiont. In the second week after disease onset, relative amounts of specific bacteria distinguished between disease severity. One month after the disease onset, dysbiosis of the gut microbiota persisted, and the number of Enterobacteriaceae, mainly Escherichia-Shigella, which is potentially pathogenic, increased and were enriched in patients who developed post-acute sequelae of COVID-19 (PASC).
Conclusion The changes in the gut microbiota associated with SARS-CoV-2 infection observed in PLWH in this study indicated a persistent decrease in SCFA-producing bacteria and an intestinal environment with an increase in opportunistic pathogens associated with enteritis. This report demonstrates that the intestinal environment in PLWH tends to show delayed improvement even after COVID-19 recovery, and highlights the importance of the dysbiosis associated with SARS-CoV-2 infection as a potential factor in the COVID-19 severity and the PASC in PLWH.
Experiment 1
Curated date: 2024/03/20
Curator: Ardeybisi
Revision editor(s): Ardeybisi, Svetlana up, Adenike Oladimeji-Kasumu, Scholastica
Subjects
- Location of subjects
- Japan
- 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
- SARS coronavirus HCoV-SARS,Human coronavirus (strain SARS),SARS virus,Severe acute respiratory syndrome coronavirus,SARS coronavirus,sARS coronavirus
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- SARS-CoV-2-uninfected PLWH (< 8 days)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- SARS-CoV-2-infected PLWH (< 8 days)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Hospitalized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected PLWH (People living with HIV) within 7 days of COVID-19 onset (< 8 days)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- None
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
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- body mass index
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 2C
Description: Changes in gut microbiota in SARS-CoV-2 infected PLWH were analyzed using linear discriminant analysis (LDA) effect size in comparison with the SARS-CoV-2 uninfected PLWH within 7 days of COVID-19 onset.
Abundance in Group 1: increased abundance in SARS-CoV-2-infected PLWH (< 8 days)
| NCBI | Quality Control | Links |
|---|---|---|
| Eggerthella | ||
| Ruminococcus sp. | ||
| Alistipes | ||
| Bacteroides | ||
| Bacteroidaceae |
Revision editor(s): Ardeybisi, Adenike Oladimeji-Kasumu
Signature 2
Source: Figure 2C
Description: Changes in gut microbiota in SARS-CoV-2 infected PLWH were analyzed using linear discriminant analysis (LDA) effect size in comparison with the SARS-CoV-2 uninfected PLWH within 7 days of COVID-19 onset.
Abundance in Group 1: decreased abundance in SARS-CoV-2-infected PLWH (< 8 days)
| NCBI | Quality Control | Links |
|---|---|---|
| Agathobacter | ||
| Butyricicoccus | ||
| Dorea | ||
| Eubacterium ruminantium | ||
| Fusicatenibacter | ||
| Megasphaera | ||
| Mitsuokella | ||
| Peptostreptococcaceae bacterium | ||
| Veillonellaceae |
Revision editor(s): Ardeybisi, Adenike Oladimeji-Kasumu
Experiment 2
Curated date: 2024/03/20
Curator: Ardeybisi
Revision editor(s): Ardeybisi, Adenike Oladimeji-Kasumu, Scholastica
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- SARS-CoV-2-uninfected PLWH (8–14 days)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- SARS-CoV-2-infected PLWH (8–14 days)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Hospitalized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected PLWH (People living with HIV) 8 − 14 days after COVID-19 onset
- Group 0 sample size Number of subjects in the control (unexposed) group
- 9
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Curated date: 2024/04/08
Curator: Adenike Oladimeji-Kasumu
Revision editor(s): Adenike Oladimeji-Kasumu
Source: Figure 2D
Description: Changes in gut microbiota in SARS-CoV-2 infected PLWH were analyzed using linear discriminant analysis (LDA) effect size in comparison with the SARS-CoV-2 uninfected PLWH 8−14 days after COVID-19 onset.
Abundance in Group 1: increased abundance in SARS-CoV-2-infected PLWH (8–14 days)
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnoanaerobaculum | ||
| Peptoniphilus | ||
| Mogibacterium | ||
| Dielma | ||
| Eggerthellaceae | ||
| Corynebacterium | ||
| Bacteroides | ||
| Bacteroidaceae |
Revision editor(s): Adenike Oladimeji-Kasumu
Signature 2
Curated date: 2024/04/08
Curator: Adenike Oladimeji-Kasumu
Revision editor(s): Adenike Oladimeji-Kasumu
Source: Figure 2D
Description: Changes in gut microbiota in SARS-CoV-2 infected PLWH were analyzed using linear discriminant analysis (LDA) effect size in comparison with the SARS-CoV-2 uninfected PLWH 8−14 days after COVID-19 onset.
Abundance in Group 1: decreased abundance in SARS-CoV-2-infected PLWH (8–14 days)
| NCBI | Quality Control | Links |
|---|---|---|
| Megasphaera | ||
| Acidaminococcus | ||
| Veillonellaceae | ||
| Selenomonadales | ||
| Lachnoclostridium | ||
| Agathobacter | ||
| Anaerostipes |
Revision editor(s): Adenike Oladimeji-Kasumu
Experiment 3
Curated date: 2024/03/21
Curator: Ardeybisi
Revision editor(s): Ardeybisi, Adenike Oladimeji-Kasumu, Scholastica
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- SARS-CoV-2-uninfected PLWH (>1 M)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- SARS-CoV-2-infected PLWH (>1 M)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Hospitalized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected PLWH (People living with HIV) over 1 month after COVID-19 onset
- Group 0 sample size Number of subjects in the control (unexposed) group
- 7
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Curated date: 2024/04/08
Curator: Adenike Oladimeji-Kasumu
Revision editor(s): Adenike Oladimeji-Kasumu
Source: Figure 2E
Description: Changes in gut microbiota in SARS-CoV-2 infected PLWH were analyzed using linear discriminant analysis (LDA) effect size in comparison with the SARS-CoV-2 uninfected PLWH over 1 month after COVID-19 onset.
Abundance in Group 1: increased abundance in SARS-CoV-2-infected PLWH (>1 M)
| NCBI | Quality Control | Links |
|---|---|---|
| Candidatus Saccharimonas | ||
| Dickeya | ||
| Enterobacteriaceae | ||
| Enterobacteriaceae bacterium | ||
| Gammaproteobacteria | ||
| Rhizobiaceae | ||
| Enterobacterales | ||
| Escherichia/Shigella sp. |
Revision editor(s): Adenike Oladimeji-Kasumu
Signature 2
Curated date: 2024/04/08
Curator: Adenike Oladimeji-Kasumu
Revision editor(s): Adenike Oladimeji-Kasumu, Scholastica
Source: Figure 2E
Description: Changes in gut microbiota in SARS-CoV-2 infected PLWH were analyzed using linear discriminant analysis (LDA) effect size in comparison with the SARS-CoV-2 uninfected PLWH over 1 month after COVID-19 onset.
Abundance in Group 1: decreased abundance in SARS-CoV-2-infected PLWH (>1 M)
| NCBI | Quality Control | Links |
|---|---|---|
| Agathobacter | ||
| Clostridia | ||
| Fusicatenibacter | ||
| Roseburia | ||
| Ruminococcaceae UCG_002Ruminococcaceae UCG_002 | ||
| Eubacteriales |
Revision editor(s): Adenike Oladimeji-Kasumu, Scholastica
Experiment 4
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Illness severity status Illness severity status,illness severity status
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Mildly ill SARS-CoV-2-infected PLWH (8–14 days)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Moderately/severely ill SARS-CoV-2-infected PLWH (8–14 days)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Moderately (n = 4) and severely (n = 1) ill hospitalized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected PLWH (People living with HIV) within 7 days of COVID-19 onset (8–14 days)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 6
- Group 1 sample size Number of subjects in the case (exposed) group
- 5
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Figure 3F
Description: Changes in the gut microbiota in PLWH-CoV (8-14 days) analyzed by linear discriminant analysis (LDA) effect size, compared by disease severity (mild, n = 6 vs. moderate/severe, n = 5)
Abundance in Group 1: increased abundance in Moderately/severely ill SARS-CoV-2-infected PLWH (8–14 days)
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerotruncus | ||
| Ruminococcaceae UCG_009Ruminococcaceae UCG_009 |
Revision editor(s): Scholastica
Signature 2
Source: Figure 3F
Description: Changes in the gut microbiota in PLWH-CoV (8-14 days) analyzed by linear discriminant analysis (LDA) effect size, compared by disease severity (mild, n = 6 vs. moderate/severe, n = 5)
Abundance in Group 1: decreased abundance in Moderately/severely ill SARS-CoV-2-infected PLWH (8–14 days)
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella9Prevotella9 | ||
| Alloprevotella | ||
| Collinsella | ||
| Coriobacteriaceae | ||
| Pasteurellaceae | ||
| Pasteurellales | ||
| Blautia | ||
| Dorea | ||
| Clostridia | ||
| Eubacteriales | ||
| unclassified Pasteurellaceae |
Revision editor(s): Scholastica
