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

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/12
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DOI Digital object identifier for electronic documents.
URI Uniform resource identifier for web resources.
Lin A, Bik EM, Costello EK, Dethlefsen L, Haque R, Relman DA, Singh U
PloS one
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

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

Curated date: 2022/07/19

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, Claregrieve1, WikiWorks


Location of subjects
United States of America
Host species Species from which microbiome was sampled (if applicable)
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
ethnic group , socioeconomic statusEthnicity,race,ethnic group,socioeconomic status

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
Group 1 sample size Number of subjects in the case (exposed) group
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 variable region One or more hypervariable region(s) of the bacterial 16S gene
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance

Statistical Analysis

Statistical test
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?

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
Chao1 Abundance-based estimator of species richness