Composition of gut microbiota in infants in China and global comparison
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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
Kuang YS, Li SH, Guo Y, Lu JH, He JR, Luo BJ, Jiang FJ, Shen H, Papasian CJ, Pang H, Xia HM, Deng HW, Qiu X
Journal
Scientific reports
Year
2016
Symbiotic gut microbiota is essential for human health, and its compositional changes have been associated with various complex disorders. However, systematic investigation of the acquisition and development of gut microbial communities during early infancy are relatively rare, particularly for infants from non-Western countries. In this study, we characterize the colonization and development of infant microbiota in healthy Chinese infants and compare the pattern with those from other countries. The fecal microbiota of 2-month-old infants was considerably more diverse than that of neonates, as indicated by higher relative abundances of Veillonella, Clostridium, Bacteroides, Lactobacillus, Collinsella and Prevotella, and reduction of Escherichia and Enterococcus. The fecal microbiota of vaginally delivered infants (both neonates and 2-month-old) had significant enrichment of Bacteroides, Parabacteroides and Megamonas, whereas cesarean delivered infants had enrichment of Prevotella, Streptococcus and Trabulsiella. By global comparison, we identify three different enterotypes, referred as "P-type", "A-type "and "F-type" which were highly abundant in Proteobacteria, Actinobacteria and Firmicutes, respectively. The three enterotypes' compositons vary geographically. All Chinese infants in our study belong to the P-type. These findings may provide novel insights into our understanding of the establishment of infant fecal bacterial communities.
Experiment 4
Reviewed Marked as Reviewed by Folakunmi on 2023-12-20
Differences from previous experiment shown
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
Reviewed Marked as Reviewed by Folakunmi on 2023-12-20
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
Reviewed Marked as Reviewed by Folakunmi on 2023-12-20
Differences from previous experiment shown
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
Reviewed Marked as Reviewed by Folakunmi on 2023-12-20
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
Reviewed Marked as Reviewed by Folakunmi on 2023-12-20
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
Reviewed Marked as Reviewed by Folakunmi on 2023-12-20
Differences from previous experiment shown
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
Reviewed Marked as Reviewed by Folakunmi on 2023-12-20
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
Reviewed Marked as Reviewed by Folakunmi on 2023-12-20
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
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