Composition of gut microbiota in infants in China and global comparison
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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
Experiment 4
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
- Gut microbiome measurement Gut microbiome measurement,gut microbiome measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Neonates
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 2-month-old infants
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples from 2-month-old infants
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
- Group 1 sample size Number of subjects in the case (exposed) group
- 14
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V5
- 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).
- relative abundances
- Statistical test
- 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
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Richness Number of species
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Source: Figure 3
Description: Comparison of microbial community composition at the phylum (a) and genus (b) levels for neonates and 2-month-old infants.
Abundance in Group 1: increased abundance in 2-month-old infants
NCBI | Quality Control | Links |
---|---|---|
Actinomycetota | ||
Veillonella | ||
Clostridium | ||
Streptococcaceae | ||
Coprobacillaceae | ||
Lactobacillus | ||
Prevotella | ||
Bifidobacterium |
Revision editor(s): OdigiriGreat
Experiment 5
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Delivery method DeliveryMethod,Delivery method,delivery method
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Cesarean delivered neonates
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Vaginally delivered neonates
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- samples from neonates delivered by Vagina
- 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
- 6
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Figure 5
Description: Comparison of the microbial community of vaginal and cesarean delivery subjects for neonates
Abundance in Group 1: increased abundance in Vaginally delivered neonates
NCBI | Quality Control | Links |
---|---|---|
Bacteroides | ||
Megamonas | ||
Parabacteroides |
Revision editor(s): OdigiriGreat, Folakunmi
Signature 2
Source: Figure 5
Description: Comparison of the microbial community of vaginal and cesarean delivery subjects for neonates
Abundance in Group 1: decreased abundance in Vaginally delivered neonates
NCBI | Quality Control | Links |
---|---|---|
Streptococcus | ||
Trabulsiella |
Revision editor(s): OdigiriGreat, Folakunmi
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Cesarean delivered 2-month-olds
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Vaginally delivered 2-month-olds
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Two months infants that were delivered vaginally
- 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
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Richness Number of species
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Source: Figure 5, within text result (Effects of delivery modes on infant gut microbiota, line 12)
Description: Comparison of the microbial community of vaginal and cesarean delivery subjects for 2-month-old infants
Abundance in Group 1: increased abundance in Vaginally delivered 2-month-olds
NCBI | Quality Control | Links |
---|---|---|
Bacteroides | ||
Megamonas | ||
Oscillospiraceae |
Revision editor(s): OdigiriGreat, Folakunmi
Signature 2
Source: Figure 5
Description: Comparison of the microbial community of vaginal and cesarean delivery subjects for 2-month-old infants
Abundance in Group 1: decreased abundance in Vaginally delivered 2-month-olds
NCBI | Quality Control | Links |
---|---|---|
Clostridium | ||
Prevotella |
Revision editor(s): OdigiriGreat, Folakunmi