Composition of gut microbiota in infants in China and global comparison

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Reviewed Marked as Reviewed by Folakunmi on 2023-12-20
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

Curated date: 2023/10/24

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat

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

Curated date: 2023/10/24

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat

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 ControlLinks
Actinomycetota
Veillonella
Clostridium
Streptococcaceae
Coprobacillaceae
Lactobacillus
Prevotella
Bifidobacterium

Revision editor(s): OdigiriGreat

Experiment 5


Reviewed Marked as Reviewed by Folakunmi on 2023-12-20

Curated date: 2023/10/24

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat, Folakunmi

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

Curated date: 2023/10/25

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat, Folakunmi

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 ControlLinks
Bacteroides
Megamonas
Parabacteroides

Revision editor(s): OdigiriGreat, Folakunmi

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2023-12-20

Curated date: 2023/10/25

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat, Folakunmi

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 ControlLinks
Streptococcus
Trabulsiella

Revision editor(s): OdigiriGreat, Folakunmi

Experiment 6


Reviewed Marked as Reviewed by Folakunmi on 2023-12-20

Curated date: 2023/10/25

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat, Folakunmi

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

Curated date: 2023/10/25

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat, Folakunmi

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 ControlLinks
Bacteroides
Megamonas
Oscillospiraceae

Revision editor(s): OdigiriGreat, Folakunmi

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2023-12-20

Curated date: 2023/10/25

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat, Folakunmi

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 ControlLinks
Clostridium
Prevotella

Revision editor(s): OdigiriGreat, Folakunmi