Ethnicity influences the gut microbiota of individuals sharing a geographical location: a cross-sectional study from a middle-income country

From BugSigDB
Reviewed Marked as Reviewed by Fatima on 2022/08/9
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Dwiyanto J, Hussain MH, Reidpath D, Ong KS, Qasim A, Lee SWH, Lee SM, Foo SC, Chong CW, Rahman S
Journal
Scientific reports
Year
2021
No studies have investigated the influence of ethnicity in a multi-ethnic middle-income country with a long-standing history of co-habitation. Stool samples from 214 Malaysian community members (46 Malay, 65 Chinese, 49 Indian, and 54 Jakun) were collected. The gut microbiota of the participants was investigated using 16S amplicon sequencing. Ethnicity exhibited the largest effect size across participants (PERMANOVA Pseudo-F = 4.24, R2 = 0.06, p = 0.001). Notably, the influence of ethnicity on the gut microbiota was retained even after controlling for all demographic, dietary factors and other covariates which were significantly associated with the gut microbiome (PERMANOVA Pseudo-F = 1.67, R2 = 0.02, p = 0.002). Our result suggested that lifestyle, dietary, and uncharacterized differences collectively drive the gut microbiota variation across ethnicity, making ethnicity a reliable proxy for both identified and unidentified lifestyle and dietary variation across ethnic groups from the same community.

Experiment 1


Reviewed Marked as Reviewed by Fatima on 2022/08/9

Curated date: 2022/07/12

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, Fatima, WikiWorks, Victoria

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
Ethnic group Ethnicity,race,Ethnic group,ethnic group
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Chinese
Group 1 name Corresponds to the case (exposed) group for case-control studies
Malay
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Malay ethnic group living in the Segamat Malaysian community.
Group 0 sample size Number of subjects in the control (unexposed) group
65
Group 1 sample size Number of subjects in the case (exposed) group
46

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V3-V4
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
raw counts
Statistical test
Linear Regression
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
.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
unchanged

Signature 1

Reviewed Marked as Reviewed by Fatima on 2022/08/9

Curated date: 2022/07/12

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101

Source: Figure 4.

Description: Multi-ethnic comparison of (a) gut enterotype profiles analyzed using Dirichlet Multinomial Model, and (b) Prevotella: Bacteroides ratio analyzed using a linear mixed model (likelihood ratio test p<0.05).

Abundance in Group 1: increased abundance in Malay

NCBI Quality ControlLinks
Prevotella

Revision editor(s): Kaluifeanyi101

Signature 2

Reviewed Marked as Reviewed by Fatima on 2022/08/9

Curated date: 2022/07/12

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, Fatima

Source: Figure 4, text

Description: Multi-ethnic comparison of (a) gut enterotype profiles analyzed using Dirichlet Multinomial Model, and (b) Prevotella: Bacteroides ratio analyzed using a linear mixed model (likelihood ratio test p<0.05).

Abundance in Group 1: decreased abundance in Malay

NCBI Quality ControlLinks
Bacteroides

Revision editor(s): Kaluifeanyi101, Fatima

Experiment 2


Reviewed Marked as Reviewed by Fatima on 2022/08/9

Curated date: 2022/07/13

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, Fatima, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
India
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
India ethnic group living in the Segamat Malaysian community.
Group 1 sample size Number of subjects in the case (exposed) group
49

Lab analysis

Statistical Analysis

Alpha Diversity

Pielou Quantifies how equal the community is numerically
unchanged
Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged

Signature 1

Reviewed Marked as Reviewed by Fatima on 2022/08/9

Curated date: 2022/07/13

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101

Source: Figure 4

Description: Multi-ethnic comparison of (a) gut enterotype profiles analyzed using Dirichlet Multinomial Model, and (b) Prevotella: Bacteroides ratio analyzed using a linear mixed model (likelihood ratio test p<0.05).

Abundance in Group 1: increased abundance in India

NCBI Quality ControlLinks
Prevotella

Revision editor(s): Kaluifeanyi101

Signature 2

Reviewed Marked as Reviewed by Fatima on 2022/08/9

Curated date: 2022/07/13

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101

Source: Figure 4

Description: Multi-ethnic comparison of (a) gut enterotype profiles analyzed using Dirichlet Multinomial Model, and (b) Prevotella: Bacteroides ratio analyzed using a linear mixed model (likelihood ratio test p<0.05).

Abundance in Group 1: decreased abundance in India

NCBI Quality ControlLinks
Bacteroides

Revision editor(s): Kaluifeanyi101

Experiment 3


Reviewed Marked as Reviewed by Fatima on 2022/08/9

Curated date: 2022/07/13

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, Fatima, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Jakun
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Jakun ethnic group living in the Segamat Malaysian community.
Group 1 sample size Number of subjects in the case (exposed) group
54
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
Unspecified

Lab analysis

Statistical Analysis

Alpha Diversity

Pielou Quantifies how equal the community is numerically
unchanged
Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged

Signature 1

Reviewed Marked as Reviewed by Fatima on 2022/08/9

Curated date: 2022/07/13

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101

Source: Figure 4

Description: Description: Multi-ethnic comparison of (a) gut enterotype profiles analyzed using Dirichlet Multinomial Model, and (b) Prevotella: Bacteroides ratio analyzed using a linear mixed model (likelihood ratio test p<0.05).

Abundance in Group 1: increased abundance in Jakun

NCBI Quality ControlLinks
Prevotella

Revision editor(s): Kaluifeanyi101

Signature 2

Reviewed Marked as Reviewed by Fatima on 2022/08/9

Curated date: 2022/07/13

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101

Source: Figure 4

Description: Description: Multi-ethnic comparison of (a) gut enterotype profiles analyzed using Dirichlet Multinomial Model, and (b) Prevotella: Bacteroides ratio analyzed using a linear mixed model (likelihood ratio test p<0.05).

Abundance in Group 1: decreased abundance in Jakun

NCBI Quality ControlLinks
Bacteroides

Revision editor(s): Kaluifeanyi101

Experiment 4


Reviewed Marked as Reviewed by Fatima on 2022/08/9

Curated date: 2022/07/13

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, Fatima, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
India
Group 1 name Corresponds to the case (exposed) group for case-control studies
Malay
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Malay ethnic group living in the Segamat Malaysian community.
Group 0 sample size Number of subjects in the control (unexposed) group
49
Group 1 sample size Number of subjects in the case (exposed) group
46
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
Not specified

Lab analysis

Statistical Analysis

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
diet, demographics, health, hygiene

Alpha Diversity

Pielou Quantifies how equal the community is numerically
unchanged
Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged

Signature 1

Reviewed Marked as Reviewed by Fatima on 2022/08/9

Curated date: 2022/07/13

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, Fatima

Source: FIGURE 5

Description: Taxa were significantly differentially abundant across ethnicity in Segamat as analyzed using ALDEx2 generalized linear model (FDR<0.1). Description: IM Indian–Malay, JI Jakun–Indian.

Abundance in Group 1: increased abundance in Malay

NCBI Quality ControlLinks
Oscillospiraceae
unclassified Eubacteriales

Revision editor(s): Kaluifeanyi101, Fatima

Experiment 5


Reviewed Marked as Reviewed by Fatima on 2022/08/9

Curated date: 2022/07/13

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101, Fatima, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Jakun
Group 1 name Corresponds to the case (exposed) group for case-control studies
India
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
India ethnic group living in the Segamat Malaysian community.
Group 0 sample size Number of subjects in the control (unexposed) group
54
Group 1 sample size Number of subjects in the case (exposed) group
49

Lab analysis

Statistical Analysis

Alpha Diversity

Pielou Quantifies how equal the community is numerically
unchanged
Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged

Signature 1

Reviewed Marked as Reviewed by Fatima on 2022/08/9

Curated date: 2022/07/13

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101

Source: FIGURE 5

Description: Taxa were significantly differentially abundant across ethnicity in Segamat as analyzed using ALDEx2 generalized linear model (FDR<0.1). Description: JI Jakun–Indian.

Abundance in Group 1: increased abundance in India

NCBI Quality ControlLinks
Bifidobacterium longum
Bifidobacterium catenulatum

Revision editor(s): Kaluifeanyi101

Signature 2

Reviewed Marked as Reviewed by Fatima on 2022/08/9

Curated date: 2022/07/13

Curator: Kaluifeanyi101

Revision editor(s): Kaluifeanyi101

Source: FIGURE 5

Description: Taxa were significantly differentially abundant across ethnicity in Segamat as analyzed using ALDEx2 generalized linear model (FDR<0.1). Description: JI Jakun–Indian.

Abundance in Group 1: decreased abundance in India

NCBI Quality ControlLinks
Klebsiella quasipneumoniae

Revision editor(s): Kaluifeanyi101