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

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

Curated date: 2022/07/12

Curator: Kaluifeanyi101

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

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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

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Bacteroides

Revision editor(s): Kaluifeanyi101, Fatima

Experiment 2

Your review change was submittedDuplicate this Experiment Add a new Signature

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

Curated date: 2022/07/13

Curator: Kaluifeanyi101

Revision editor(s): WikiWorks, Fatima, Kaluifeanyi101, 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 Control	Links
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 Control	Links
Bacteroides

Revision editor(s): Kaluifeanyi101

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

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

Curated date: 2022/07/13

Curator: Kaluifeanyi101

Revision editor(s): WikiWorks, Fatima, Kaluifeanyi101, 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 Control	Links
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 Control	Links
Bacteroides

Revision editor(s): Kaluifeanyi101

Experiment 4

Your review change was submittedDuplicate this Experiment Add a new Signature

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

Curated date: 2022/07/13

Curator: Kaluifeanyi101

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

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Oscillospiraceae
unclassified Eubacteriales

Revision editor(s): Kaluifeanyi101, Fatima

Experiment 5

Your review change was submittedDuplicate this Experiment Add a new Signature

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

Curated date: 2022/07/13

Curator: Kaluifeanyi101

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

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Bifidobacterium longum
Bifidobacterium catenulatum

Revision editor(s): Kaluifeanyi101

Signature 2