Microbial gut evaluation in an angolan paediatric population with sickle cell 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
Delgadinho M, Ginete C, Santos B, Mendes J, Miranda A, Vasconcelos J, Brito M
Journal
Journal of cellular and molecular medicine
Year
2022
Keywords:
16S rRNA, foetal haemoglobin, microbiome, sickle cell disease
Sickle cell disease (SCD) is one of the most common genetic conditions worldwide. It can contribute up to 90% of under-5 mortality in sub-Saharan Africa. Clinical manifestations are very heterogeneous, and the intestinal microbiome appears to be crucial in the modulation of inflammation, cell adhesion and induction of aged neutrophils, the main interveners of recurrent vaso-occlusive crisis. Enterocyte injury, increased permeability, altered microbial composition and bacterial overgrowth have all been documented as microbial and pathophysiologic changes in the gut microbiome of SCD patients in recent studies. Our aim was to sequence the bacterial 16S rRNA gene in order to characterize the gut microbiome of Angolan children with SCA and healthy siblings as a control. A total of 72 stool samples were obtained from children between 3 and 14 years old. Our data showed that the two groups exhibit some notable differences in microbiota relative abundance at different classification levels. Children with SCA have a higher number of the phylum Actinobacteria. As for the genus level, Clostridium cluster XI bacteria was more prevalent in the SCA children, whereas the siblings had a higher abundance of Blautia, Aestuariispira, Campylobacter, Helicobacter, Polaribacter and Anaerorhabdus. In this study, we have presented the first microbiota analysis in an Angolan paediatric population with SCD and provided a detailed view of the microbial differences between patients and healthy controls. There is still much to learn before fully relying on the therapeutic approaches for gut modulation, which is why more research in this field is crucial to making this a reality.
Experiment 1
Reviewed Marked as Reviewed by Svetlana up on 2024-11-27
Subjects
- Location of subjects
- Angola
- 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
- Sickle cell anemia drepanocytosis,Hb SC disease,Hb-S/Hb-C disease,Hb-SS disease without crisis,HbS disease,Hemoglobin S disease,Hemoglobin S disease without crisis,hemoglobin SC disease,sickle cell anemia,Sickle cell disease,sickle cell disease,sickle-cell/Hb-C disease without crisis,sickling disorder due to Hemoglobin S,Sickle cell anemia
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy Siblings
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Sickle Cell Anaemia Children
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Angolan children between 3 and 14 years with Sickle Cell Anemia
- 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
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
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
- Welch's T-Test
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-11-27
Source: Figure 4
Description: Differential abundance in the microbiota of sickle cell anaemia (SCA) children compared to their siblings(controls).
Abundance in Group 1: increased abundance in Sickle Cell Anaemia Children
Revision editor(s): Aleru Divine
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-11-27
Source: Figure 4
Description: Differential abundance in the microbiota of sickle cell anaemia (SCA) children compared to their siblings(controls).
Abundance in Group 1: decreased abundance in Sickle Cell Anaemia Children
Revision editor(s): Aleru Divine
Experiment 2
Reviewed Marked as Reviewed by Svetlana up on 2024-11-27
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Sickle cell disease associated with an other hemoglobin anomaly Double heterozygotes sickling disorder,sickle cell disease associated with an other hemoglobin anomaly,Sickle cell disease associated with an other hemoglobin anomaly
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Foetal haemoglobin level < 5%
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Foetal haemoglobin level > 5%
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Sickle Cell Anemia(SCA) children with Foetal haemoglobin level > 5%
- Group 0 sample size Number of subjects in the control (unexposed) group
- 27
- 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
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-11-27
Source: Figure 7B
Description: Differential abundance in the microbiota of sickle cell anaemia (SCA) children with < 5% of HbF compared SCA children with < 5% of HbF.
Abundance in Group 1: increased abundance in Foetal haemoglobin level > 5%
| NCBI | Quality Control | Links |
|---|---|---|
| Ruminococcus |
Revision editor(s): Aleru Divine
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-11-27
Source: Figure 7B
Description: Differential abundance in the microbiota of sickle cell anaemia (SCA) children with < 5% of HbF compared SCA children with < 5% of HbF.
Abundance in Group 1: decreased abundance in Foetal haemoglobin level > 5%
| NCBI | Quality Control | Links |
|---|---|---|
| Kandleria |
Revision editor(s): Aleru Divine
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