Effect of ethnicity and socioeconomic variation to the gut microbiota composition among pre-adolescent in Malaysia

Study information

Reviewed Marked as Reviewed by Fatima on 2022/07/6

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

26290472

DOI Digital object identifier for electronic documents.

10.1038/srep13338

URI

https://pubmed.ncbi.nlm.nih.gov/26290472/

Authors

Chong CW, Ahmad AF, Lim YA, Teh CS, Yap IK, Lee SC, Chin YT, Loke P, Chua KH

Journal

Scientific reports

Year

2015

Gut microbiota plays an important role in mammalian host metabolism and physiological functions. The functions are particularly important in young children where rapid mental and physical developments are taking place. Nevertheless, little is known about the gut microbiome and the factors that contribute to microbial variation in the gut of South East Asian children. Here, we compared the gut bacterial richness and composition of pre-adolescence in Northern Malaysia. Our subjects covered three distinct ethnic groups with relatively narrow range of socioeconomic discrepancy. These included the Malays (n = 24), Chinese (n = 17) and the Orang Asli (indigenous) (n = 20). Our results suggested a strong ethnicity and socioeconomic-linked bacterial diversity. Highest bacterial diversity was detected from the economically deprived indigenous children while the lowest diversity was recorded from the relatively wealthy Chinese children. In addition, predicted functional metagenome profiling suggested an over-representation of pathways pertinent to bacterial colonisation and chemotaxis in the former while the latter exhibited enriched gene pathways related to sugar metabolism.

Experiment 1

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Reviewed Marked as Reviewed by Fatima on 2022/07/6

Curated date: 2022/06/24

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, Fatima, Claregrieve1, Peace Sandy

Subjects

Location of subjects: Malaysia

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: Socioeconomic status class,Socioeconomic status,socioeconomic status,socioeconomic factors

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Chinese Children (High SES, household income>RM500)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Malays Children (Moderate SES. house income=<RM500)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Gut microbiota from fecal samples of 24 Malays children whose household income =<RM500. Note: Poverty line = RM 764($254).

Group 0 sample size Number of subjects in the control (unexposed) group: 17

Group 1 sample size Number of subjects in the case (exposed) group: 24

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

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V3-V5

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances

Statistical test: PERMANOVA

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)?: Yes

Alpha Diversity

Pielou Quantifies how equal the community is numerically: unchanged

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

Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa: unchanged

Richness Number of species: increased

Experiment 2

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Reviewed Marked as Reviewed by Folakunmi on 2024-2-17

Curated date: 2022/06/24

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, Fatima, Claregrieve1, Folakunmi

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Chinese Children (High SES, household income >RM500)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Orang Asli Children (low SES, household income<RM500)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Gut microbiota from fecal samples of 20 Orang Asli children whose household income <RM500.

Group 1 sample size Number of subjects in the case (exposed) group: 20

Lab analysis

Statistical Analysis

Alpha Diversity

Pielou Quantifies how equal the community is numerically: increased

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

Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa: increased

Richness Number of species: increased

Signature 1

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/7

Curated date: 2022/06/24

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, Claregrieve1

Source: Table 3

Description: Differential microbial abundance between Chinese and Orang Asli children.

Abundance in Group 1: increased abundance in Orang Asli Children (low SES, household income<RM500)

NCBI	Quality Control	Links
Aeromonadales
unclassified Bacteroidota
unclassified Deltaproteobacteria
unclassified Eubacteriales
unclassified Oscillospiraceae

Revision editor(s): Kaluifeanyi101, Claregrieve1

Signature 2

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/7

Curated date: 2022/06/24

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, Claregrieve1

Source: Table 3

Description: Differential microbial abundance between Chinese and Orang Asli children.

Abundance in Group 1: decreased abundance in Orang Asli Children (low SES, household income<RM500)

NCBI	Quality Control	Links
Alistipes

Revision editor(s): Kaluifeanyi101, Claregrieve1

Experiment 3

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Reviewed Marked as Reviewed by Folakunmi on 2024-2-17

Curated date: 2022/06/24

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, Folakunmi

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Malays children (Moderate SES, household income =>RM500)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Orang Asli children (low SES, household income <RM500)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Gut microbiota from fecal samples of 20 Orang Asli children whose household income<RM500. 45% of the households earn < RM500 Note: Poverty line = RM 764($254).

Group 0 sample size Number of subjects in the control (unexposed) group: 24

Lab analysis

Statistical Analysis

Alpha Diversity

Pielou Quantifies how equal the community is numerically: increased

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

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

Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa: increased

Signature 1

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/7

Curated date: 2022/06/24

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, Claregrieve1

Source: Table 3

Description: Differential microbial abundance between Malay and Orang Asli children.

Abundance in Group 1: increased abundance in Orang Asli children (low SES, household income <RM500)

NCBI	Quality Control	Links
Aeromonadales
Spirochaetota
unclassified Bacteria
unclassified Bacteroidota
unclassified Clostridia
unclassified Deltaproteobacteria
unclassified Oscillospiraceae