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

From BugSigDB
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-12
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Kaplan RC, Wang Z, Usyk M, Sotres-Alvarez D, Daviglus ML, Schneiderman N, Talavera GA, Gellman MD, Thyagarajan B, Moon JY, Vázquez-Baeza Y, McDonald D, Williams-Nguyen JS, Wu MC, North KE, Shaffer J, Sollecito CC, Qi Q, Isasi CR, Wang T, Knight R, Burk RD
Journal
Genome biology
Year
2019
Keywords:
Epidemiology, Hispanic population, Microbiome, Mycobiome, Obesity
BACKGROUND: Hispanics living in the USA may have unrecognized potential birthplace and lifestyle influences on the gut microbiome. We report a cross-sectional analysis of 1674 participants from four centers of the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), aged 18 to 74 years old at recruitment. RESULTS: Amplicon sequencing of 16S rRNA gene V4 and fungal ITS1 fragments from self-collected stool samples indicate that the host microbiome is determined by sociodemographic and migration-related variables. Those who relocate from Latin America to the USA at an early age have reductions in Prevotella to Bacteroides ratios that persist across the life course. Shannon index of alpha diversity in fungi and bacteria is low in those who relocate to the USA in early life. In contrast, those who relocate to the USA during adulthood, over 45 years old, have high bacterial and fungal diversity and high Prevotella to Bacteroides ratios, compared to USA-born and childhood arrivals. Low bacterial diversity is associated in turn with obesity. Contrasting with prior studies, our study of the Latino population shows increasing Prevotella to Bacteroides ratio with greater obesity. Taxa within Acidaminococcus, Megasphaera, Ruminococcaceae, Coriobacteriaceae, Clostridiales, Christensenellaceae, YS2 (Cyanobacteria), and Victivallaceae are significantly associated with both obesity and earlier exposure to the USA, while Oscillospira and Anaerotruncus show paradoxical associations with both obesity and late-life introduction to the USA. CONCLUSIONS: Our analysis of the gut microbiome of Latinos demonstrates unique features that might be responsible for health disparities affecting Hispanics living in the USA.

Experiment 1


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

NCBI Quality ControlLinks
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

NCBI Quality ControlLinks
Acidaminococcus
Megasphaera
Catenibacterium
Prevotella
Streptococcus

Revision editor(s): Atrayees

Experiment 2


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

Curated date: 2023/03/28

Curator: Ombati

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

NCBI Quality ControlLinks
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

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

Revision editor(s): Atrayees

Experiment 4


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

Curated date: 2023/03/28

Curator: Ombati

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

NCBI Quality ControlLinks
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

NCBI Quality ControlLinks
Cystofilobasidium
[Candida] railenensis

Revision editor(s): Atrayees

Experiment 5


Needs review

Curated date: 2023/03/28

Curator: Ombati

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

NCBI Quality ControlLinks
Debaryomyces sp.

Revision editor(s): Ombati, Atrayees

Experiment 6


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

Curated date: 2023/03/28

Curator: Ombati

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

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

Curated date: 2023/06/08

Curator: Atrayees

Revision editor(s): Atrayees

Source: Table S9

Description: Association of genus level ITS1 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

NCBI Quality ControlLinks
Candida

Revision editor(s): Atrayees