Evolution in fecal bacterial/viral composition in infants of two central African countries (Gabon and Republic of the Congo) during their first month of life
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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.
URI
Authors
Brazier L, Elguero E, Koumavor CK, Renaud N, Prugnolle F, Thomas F, Ategbo S, Engoba M, Obengui EM, Leroy P, Durand F, Renaud P, Becquart
Journal
PloS one
Year
2017
Few studies have analyzed the gut microbiota of child in unindustrialized countries, but none during the first month of life. Stool samples were collected from healthy newborns in hospitals of Gabon (n = 6) and Republic of the Congo (n = 9) at different time points during the first month of life: meconium, day 2 (D02), day 7 (D07) and day 28 (D28). In addition, one fecal sample was collected from each mother after delivery. Metagenomic sequencing was performed to determine the bacterial communities, and multiplex real-time PCR was used to detect the presence of seven enteric viruses (rotavirus a, adenovirus, norovirus I and II, sapovirus, astrovirus, enterovirus) in these samples. Bacterial diversity was high in the first days of life, and was dominated by the genus Prevotella. Then, it rapidly decreased and remained low up to D28 when the gut flora was composed almost exclusively of strictly anaerobic bacteria. Each infant's fecal bacterial microbiota composition was significantly closer to that of their mother than to that of any other woman in the mothers' group, suggesting an intrauterine, placental or amniotic fluid origin of such bacteria. Moreover, bacterial communities differed according to the delivery mode. Overall, the bacterial microbiota communities displayed a similar diversification and expansion in newborns within and between countries during the first four weeks of life. Moreover, six of the fifteen infants of this study harbored enteric viruses (rotavirus, enterovirus and adenovirus) in fecal samples, but never in the meconium. A maternal source for the viruses detected at D02 and D07 can be excluded because none of them was found also in the child's mother. These findings improve our knowledge on the gut bacterial and viral communities of infants from two Sub-Saharan countries during their first month of life.
Experiment 1
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Subjects
- Location of subjects
- Gabon
- 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
- Meconium Meconium,meconium
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Cesarean section caesarean section,Cesarean section,cesarean section
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- vaginal delivery
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- two-day aged babies c-section
- 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
- 8
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- Linear 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
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Source: figure 4 &text
Description: Signatures include bacterial genera with a read frequency higher than 5% in at least one child. Viruses were tested and not found in meconium samples. preterm, normal and postterm included
Abundance in Group 1: increased abundance in two-day aged babies c-section
| NCBI | Quality Control | Links |
|---|---|---|
| Klebsiella | ||
| Sarcina |
Revision editor(s): WikiWorks
Experiment 2
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Differences from previous experiment shown
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 Shaimaa Elsafoury on 2021/02/09
Source: figure 4 &text
Description: Signatures include bacterial genera with a read frequency higher than 5% in at least one child. Viruses were tested and not found in meconium samples. preterm, normal and postterm included
Abundance in Group 1: decreased abundance in two-day aged babies c-section
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides |
Revision editor(s): WikiWorks
Experiment 3
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Differences from previous experiment shown
Subjects
- Location of subjects
- Gabon
- 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
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- seven-day aged babies c-section
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 Shaimaa Elsafoury on 2021/02/09
Source: figure 4 &text
Description: Signatures include bacterial genera with a read frequency higher than 5% in at least one child. Viruses were tested and not found in meconium samples. preterm, normal and postterm included
Abundance in Group 1: increased abundance in seven-day aged babies c-section
| NCBI | Quality Control | Links |
|---|---|---|
| Klebsiella | ||
| Sarcina |
Revision editor(s): WikiWorks
Experiment 4
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Differences from previous experiment shown
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 Shaimaa Elsafoury on 2021/02/09
Source: figure 4 &text
Description: Signatures include bacterial genera with a read frequency higher than 5% in at least one child. Viruses were tested and not found in meconium samples. preterm, normal and postterm included
Abundance in Group 1: decreased abundance in seven-day aged babies c-section
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Collinsella |
Revision editor(s): WikiWorks
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