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

From BugSigDB
Reviewed Marked as Reviewed by Fatima on 2022/07/6
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
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


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


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

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 ControlLinks
Aeromonadales
unclassified Bacteroidota
unclassified Deltaproteobacteria
unclassified Eubacteriales
unclassified Oscillospiraceae

Revision editor(s): Kaluifeanyi101, Claregrieve1

Signature 2

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 ControlLinks
Alistipes

Revision editor(s): Kaluifeanyi101, Claregrieve1

Experiment 3


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

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 ControlLinks
Aeromonadales
Spirochaetota
unclassified Bacteria
unclassified Bacteroidota
unclassified Clostridia
unclassified Deltaproteobacteria
unclassified Oscillospiraceae

Revision editor(s): Kaluifeanyi101, Claregrieve1

Signature 2

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: decreased abundance in Orang Asli children (low SES, household income <RM500)

NCBI Quality ControlLinks
Bacteroidales
Selenomonadales

Revision editor(s): Kaluifeanyi101, Claregrieve1