Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity

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Reviewed Marked as Reviewed by Atrayees on 2023-6-13

Curated date: 2023/03/17

Curator: Ombati

Revision editor(s): LGeistlinger, Chloe, Atrayees, Ombati, Peace Sandy

Subjects

Location of subjects: United States of America

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: Obesity Adiposis,Adiposity,Obese,Obese (finding),obesity,Obesity (disorder),Obesity [Ambiguous],obesity disease,obesity disorder,Obesity NOS,Obesity, unspecified,Overweight and obesity,Obesity

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Individuals with a healthy body mass index

Group 1 name Corresponds to the case (exposed) group for case-control studies: Obese individuals

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Individuals who had a class II or class III obesity

Group 0 sample size Number of subjects in the control (unexposed) group: 293

Group 1 sample size Number of subjects in the case (exposed) group: 294

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 6 months

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: 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): 0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Yes

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: decreased

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-12

Curated date: 2023/03/17

Curator: Ombati

Revision editor(s): Ombati, Chloe, Atrayees

Source: Table S4

Description: Association of genus level 16S data with obesity, adjusted for age, sex, field center, and Hispanic background. This involved the identification of bacterial and fungal taxa associated with birthplace, relocation, and obesity.

Abundance in Group 1: decreased abundance in Obese individuals

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Cloacibacillus
Ruminococcus
unclassified Oscillospiraceae
unclassified Eubacteriales
unclassified Coriobacteriaceae
Anaerotruncus
Oscillospira
Eggerthella
unclassified Rikenellaceae
unclassified Clostridiaceae
Blautia
Akkermansia

Revision editor(s): Ombati, Chloe, Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-12

Curated date: 2023/06/08

Curator: Atrayees

Revision editor(s): Atrayees

Source: Table S4

Description: Association of genus level 16S data with obesity, adjusted for age, sex, field center, and Hispanic background. This involved the identification of bacterial and fungal taxa associated with birthplace, relocation, and obesity.

Abundance in Group 1: increased abundance in Obese individuals

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Acidaminococcus
Megasphaera
Catenibacterium
Prevotella
Streptococcus

Revision editor(s): Atrayees

Experiment 2

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Reviewed Marked as Reviewed by Atrayees on 2023-6-13

Curated date: 2023/03/28

Curator: Ombati

Revision editor(s): LGeistlinger, Atrayees, Ombati, Victoria

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Age Age,age

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Early age

Group 1 name Corresponds to the case (exposed) group for case-control studies: Later age

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Not specified

Group 0 sample size Number of subjects in the control (unexposed) group: 1674

Group 1 sample size Number of subjects in the case (exposed) group: 1674

Lab analysis

Statistical Analysis

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: age, race, sex

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-12

Curated date: 2023/03/28

Curator: Ombati

Revision editor(s): Ombati, Atrayees

Source: Table S5

Description: Association of genus level 16S data with age at relocation among Latin American born individuals, adjusted for age, sex, field center and Hispanic background.

Abundance in Group 1: increased abundance in Later age

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unclassified Eubacteriales
Butyricimonas
Haemophilus
Phascolarctobacterium
Odoribacter
Faecalibacterium
Klebsiella
Prevotella
Paraprevotella
Lachnospira
Lachnobacterium
Desulfovibrio
unclassified Barnesiellaceae
unclassified Lactobacillaceae
unclassified Anaeroplasmataceae
unclassified Oscillospiraceae
unclassified Coriobacteriaceae
unclassified Christensenellaceae
unclassified Enterobacteriaceae

Revision editor(s): Ombati, Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-12

Curated date: 2023/06/12

Curator: Atrayees

Revision editor(s): Atrayees

Source: Table S5

Description: Association of genus level 16S data with age at relocation among Latin American born individuals, adjusted for age, sex, field center and Hispanic background.

Abundance in Group 1: decreased abundance in Later age

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Coprobacillus
Bacteroides
Acidaminococcus
Sutterella
Holdemania
Bifidobacterium
Collinsella
Oscillospira
Megasphaera
Blautia
Parabacteroides
Dorea
Anaerotruncus
Adlercreutzia
Eubacterium

Revision editor(s): Atrayees

Experiment 4

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Atrayees on 2023-6-13

Curated date: 2023/03/28

Curator: Ombati

Revision editor(s): LGeistlinger, Atrayees, Ombati, Victoria

Differences from previous experiment shown

Subjects

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: USB (US born)

Group 1 name Corresponds to the case (exposed) group for case-control studies: LAB

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Latin American Born

Group 0 sample size Number of subjects in the control (unexposed) group: 225

Group 1 sample size Number of subjects in the case (exposed) group: 1532

Lab analysis

Statistical Analysis

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Not specified

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: age

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-13

Curated date: 2023/03/28

Curator: Ombati

Revision editor(s): Ombati, Atrayees

Source: Table S7

Description: Fungal taxa that differ after comparing those born in the mainland USA versus those born in Latin America.

Abundance in Group 1: decreased abundance in LAB

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Cyberlindnera jadinii
Cyberlindnera
Agaricomycetes
Penicillium roqueforti
Panellus
Kluyveromyces marxianus
Alternaria rosae
Xenasmatella ardosiaca
Cladosporium salinae
Erythricium laetum
Erythricium

Revision editor(s): Ombati, Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-13

Curated date: 2023/06/13

Curator: Atrayees

Revision editor(s): Atrayees

Source: Table S7

Description: Fungal taxa that differ after comparing those born in the mainland USA versus those born in Latin America.

Abundance in Group 1: increased abundance in LAB

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Cystofilobasidium
[Candida] railenensis

Revision editor(s): Atrayees

Experiment 5

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Mark reviewed

Needs review

Curated date: 2023/03/28

Curator: Ombati

Revision editor(s): LGeistlinger, Atrayees, Ombati, Victoria

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Obesity Adiposis,Adiposity,Obese,Obese (finding),obesity,Obesity (disorder),Obesity [Ambiguous],obesity disease,obesity disorder,Obesity NOS,Obesity, unspecified,Overweight and obesity,Obesity

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Individuals with a healthy body mass index

Group 1 name Corresponds to the case (exposed) group for case-control studies: Individuals who were obese

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Individuals with class II or class III obesity

Group 0 sample size Number of subjects in the control (unexposed) group: 293

Group 1 sample size Number of subjects in the case (exposed) group: 294

Lab analysis

Statistical Analysis

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): Not specified

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Yes

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: decreased

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-12

Curated date: 2023/03/28

Curator: Ombati

Revision editor(s): Ombati, Atrayees

Source: Table S8

Description: Association of genus level ITS1 data with obesity, adjusted for age, sex, field center, and Hispanic background. Only one met Pvalue < 0.05.

Abundance in Group 1: decreased abundance in Individuals who were obese

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Debaryomyces sp.

Revision editor(s): Ombati, Atrayees

Experiment 6

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Atrayees on 2023-6-13

Curated date: 2023/03/28

Curator: Ombati

Revision editor(s): LGeistlinger, Atrayees, Ombati, Victoria

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Age Age,age

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Early age

Group 1 name Corresponds to the case (exposed) group for case-control studies: Later age

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Individuals who had relocated to the USA at a younger age( 18 and below)

Group 0 sample size Number of subjects in the control (unexposed) group: 1674

Group 1 sample size Number of subjects in the case (exposed) group: 1674

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 2