Distinct distal gut microbiome diversity and composition in healthy children from Bangladesh and the United States

Study information

Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/12

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

23349750

DOI Digital object identifier for electronic documents.

10.1371/journal.pone.0053838

URI

https://pubmed.ncbi.nlm.nih.gov/23349750/

Authors

Lin A, Bik EM, Costello EK, Dethlefsen L, Haque R, Relman DA, Singh U

Journal

PloS one

Year

2013

BACKGROUND: Our current understanding of the composition and stability of the human distal gut microbiota is based largely on studies of infants and adults living in developed countries. In contrast, little is known about the gut microbiota and its variation over time in older children and adolescents, especially in developing countries. METHODOLOGY/PRINCIPAL FINDINGS: We compared the diversity, composition, and temporal stability of the fecal microbiota of healthy children, ages 9 to 14 years, living in an urban slum in Bangladesh with that of children of the same age range in an upper-middle class suburban community in the United States. We analyzed >8,000 near full-length 16S rRNA gene sequences and over 845,000 pyrosequencing reads of the 16S rRNA V1-V3 region. The distal gut of Bangladeshi children harbored significantly greater bacterial diversity than that of U.S. children, including novel lineages from several bacterial phyla. Bangladeshi and U.S. children had distinct fecal bacterial community membership and structure; the microbiota of Bangladeshi children was enriched in Prevotella, Butyrivibrio, and Oscillospira and depleted in Bacteroides relative to U.S. children (although similar to Bangladeshi adults). Furthermore, community membership and structure in Bangladeshi children was significantly less stable month-to-month than U.S. children. CONCLUSIONS/SIGNIFICANCE: Together, these results suggest that differing environmental or genetic factors may shape the microbiota of healthy children in the two countries. Further investigation is necessary to understand the mechanisms and factors that underlie these differences, and to incorporate these findings into new strategies for the prevention and treatment of childhood and adolescent diseases.

Experiment 1

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/12

Curated date: 2022/07/19

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, Claregrieve1, WikiWorks

Subjects

Location of subjects: Bangladesh; United States of America

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: Ethnic group , Socioeconomic status Ethnicity,race,Ethnic group,ethnic group,class,Socioeconomic status,socioeconomic status,socioeconomic factors

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

Group 1 name Corresponds to the case (exposed) group for case-control studies: Bangladesh Children (Household income < $61)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Fecal specimens from 6 Bangladeshi children (ages 8–13), in low socioeconomic conditions with an average monthly income per family of,5,000 takas (the U.S. $61).

Group 0 sample size Number of subjects in the control (unexposed) group: 4

Group 1 sample size Number of subjects in the case (exposed) group: 6

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 3 months

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V1-V3

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Roche454

Statistical Analysis

Statistical test: ANOSIM

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.1

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Yes

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: age, sex

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: increased

Chao1 Abundance-based estimator of species richness: increased

Signature 1

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/12

Curated date: 2022/07/19

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, Claregrieve1

Source: Table 3

Description: Differential microbial abundance between Bangladeshi children and US children

Abundance in Group 1: increased abundance in Bangladesh Children (Household income < $61)

NCBI	Quality Control	Links
Butyrivibrio
Eubacteriales

Revision editor(s): Kaluifeanyi101, Claregrieve1

Signature 2

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/23

Curated date: 2022/07/20

Curator: Kaluifeanyi101

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Source: Table 3

Description: Differential microbial abundance between Bangladeshi children and US children

Abundance in Group 1: decreased abundance in Bangladesh Children (Household income < $61)

NCBI	Quality Control	Links
Bacteroides thetaiotaomicron
Faecalibacterium prausnitzii

Revision editor(s): Kaluifeanyi101, Claregrieve1