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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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
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
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
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-12
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 Control | Links |
|---|---|---|
| Acidaminococcus | ||
| Megasphaera | ||
| Catenibacterium | ||
| Prevotella | ||
| Streptococcus |
Revision editor(s): Atrayees
Experiment 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-13
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
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
- 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
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
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-12
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
Revision editor(s): Atrayees
Experiment 4
Reviewed Marked as Reviewed by Atrayees on 2023-6-13
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
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
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-13
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 Control | Links |
|---|---|---|
| Cystofilobasidium | ||
| [Candida] railenensis |
Revision editor(s): Atrayees
Experiment 5
Needs review
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
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 Control | Links |
|---|---|---|
| Debaryomyces sp. |
Experiment 6
Reviewed Marked as Reviewed by Atrayees on 2023-6-13
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
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 Control | Links |
|---|---|---|
| Candida |
Revision editor(s): Atrayees
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