Composition of gut microbiota in infants in China and global comparison

Study information

Needs review

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

27827448

DOI Digital object identifier for electronic documents.

10.1038/srep36666

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

Edit History Delete

Mark reviewed

Your review change was submittedDuplicate this Experiment Add a new Signature

Needs review

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

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: 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

Edit History Delete

Mark reviewed

Your review change was submitted

Needs review

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 Control	Links
Actinomycetota
Veillonella
Clostridium
Streptococcaceae
Coprobacillaceae
Lactobacillus
Prevotella
Bifidobacterium

Revision editor(s): OdigiriGreat

Experiment 5

Edit History Delete

Mark reviewed

Your review change was submittedDuplicate this Experiment Add a new Signature

Needs review

Curated date: 2023/10/24

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Cesarean delivery

Group 1 name Corresponds to the case (exposed) group for case-control studies: Vaginal delivery

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

Edit History Delete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2023/10/25

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat

Source: Figure 5

Description: Comparison of the microbial community of vaginal and cesarean delivery subjects for neonates (a) and 2-month-old infants (b)

Abundance in Group 1: increased abundance in Vaginal delivery

NCBI	Quality Control	Links
Bacteroides
Megamonas
Parabacteroides

Revision editor(s): OdigiriGreat

Signature 2

Edit History Delete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2023/10/25

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat

Source: Figure 5

Description: Comparison of the microbial community of vaginal and cesarean delivery subjects for neonates (a) and 2-month-old infants (b)

Abundance in Group 1: decreased abundance in Vaginal delivery

NCBI	Quality Control	Links
Streptococcus
Trabulsiella

Revision editor(s): OdigiriGreat

Experiment 6

Edit History Delete

Mark reviewed

Your review change was submittedDuplicate this Experiment Add a new Signature

Needs review

Curated date: 2023/10/25

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat

Differences from previous experiment shown

Subjects

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Two months infants that were delivered virginally