Nepali oral microbiomes reflect a gradient of lifestyles from traditional to industrialized
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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.
URI
Authors
Ryu EP, Gautam Y, Proctor DM, Bhandari D, Tandukar S, Gupta M, Gautam GP, Relman DA, Shibl AA, Sherchand JB, Jha AR, Davenport ER
Journal
Microbiome
Year
2024
Keywords:
Lifestyle, Nepali populations, Oral microbiome, Oral microbiota, Salivary microbiome
BACKGROUND: Lifestyle plays an important role in shaping the gut microbiome. However, its contributions to the oral microbiome remain less clear, due to the confounding effects of geography and methodology in investigations of populations studied to date. Furthermore, while the oral microbiome seems to differ between foraging and industrialized populations, we lack insight into whether transitions to and away from agrarian lifestyles shape the oral microbiota. Given the growing interest in so-called "vanishing microbiomes" potentially being a risk factor for increased disease prevalence in industrialized populations, it is important that we distinguish lifestyle from geography in the study of microbiomes across populations. RESULTS: Here, we investigate salivary microbiomes of 63 Nepali individuals representing a spectrum of lifestyles: foraging, subsistence farming (individuals that transitioned from foraging to farming within the last 50 years), agriculturalists (individuals that have transitioned to farming for at least 300 years), and industrialists (expatriates that immigrated to the USA within the last 20 years). We characterize the role of lifestyle in microbial diversity, identify microbes that differ between lifestyles, and pinpoint specific lifestyle factors that may be contributing to differences in the microbiomes across populations. Contrary to prevailing views, when geography is controlled for, oral microbiome alpha diversity does not differ significantly across lifestyles. Microbiome composition, however, follows the gradient of lifestyles from foraging through agrarianism to industrialism, supporting the notion that lifestyle indeed plays a role in the oral microbiome. Relative abundances of several individual taxa, including Streptobacillus and an unclassified Porphyromonadaceae genus, also mirror lifestyle. Finally, we identify specific lifestyle factors associated with microbiome composition across the gradient of lifestyles, including smoking and grain sources. CONCLUSION: Our findings demonstrate that by studying populations within Nepal, we can isolate an important role of lifestyle in determining oral microbiome composition. In doing so, we highlight the potential contributions of several lifestyle factors, underlining the importance of carefully examining the oral microbiome across lifestyles to improve our understanding of global microbiomes. Video Abstract. सारांश पृष्ठभूमि: मानवको आन्द्रामा ब्याक्टेरिया, भाइरस, फंगस (ढुसी), लगायत अरू विभिन्न प्रकारका सूक्ष्मजीवहरूका समुदाय पाईन्छन्, जसलाई माइक्रोबायोम भनिन्छ। आन्द्रामा हुने माइक्रोबायोमले मानवको पाचन, प्रतिरक्षा प्रणाली, र अन्य शारीरिक प्रक्रियाहरूमा योगदान पुर्याउने हुनाले यिनले मानव स्वास्थ्य र रोगको निर्धारण गर्नमा महत्त्वपूर्ण भूमिका खेल्छन्। त्यसैगरी मानव मुखमा पनि सूक्ष्मजीवहरूका समुदायहरू हुन्छन् जसले दाँत र गिजालाई स्वस्थ राख्नमा योगदान पुर्याउँछन्। जीवनशैलीले आन्द्राको माइक्रोबायोमलाई आकार दिन महत्त्वपूर्ण भूमिका खेल्छ। साथै, जङलमा निर्भर भएर प्रकृतिक जीवनशैली जिउने र औध्योगिक्रित भएका मानव समुदायहरुको बीच मुखको माइक्रोबायोममा धेरै भिन्नता देखिन्छ। जङलमा निर्भर भएर प्रकृतिक जीवनशैली जिउने मानव समुदायहरुमा पाईने धेरै सूक्ष्मजीवहरू औद्योगिक जनसमुदायहरुमा मा पाईन छाडिसकेका छन् र यस्ता ‘विलुप्त माइक्रोबायोम’ बिभिन्न रोगहरुका जोखिमका कारक हुन सक्ने हुँदा चासोका बिषय बन्न पुगेका छन्। तथापि, अहिलेसम्मका अनुसन्धानमा जीवनशैलिको परिवर्तन सँगै मुखको माइक्रोबायोममा के कस्ता परिवर्तनहरु आउँछन् भन्ने कुरा स्पष्ट हुन सकेको छैन। विभिन्न जीवनशैली ब्यथीत गर्ने मानिसहरु बीच जीवनशैलीको साथसाथै भौगोलिक भिन्नता पनि हुने गर्दछ। तसर्थ, मनिसहरुका मुखका माईक्रोबायोममा जीवनशैली र भूगोलको असरलाई छुट्याउनु महत्त्वपूर्ण देखिएको छ। परिणामहरू: यहाँ, हामीले ६३ जना नेपाली व्यक्तिको थुक संकलन गरेर मुखका माइक्रोबायोमको अनुसन्धान गर्यौं। हाम्रो अध्ययनमा संलग्न भएका ब्यक्तिहरुले विभिन्न जीवनशैलीको प्रतिनिधित्व गर्छन्: जङलमा निर्भर भएर प्रकृतिक जीवनशैली जिउने, जङलबाट कृषितर्फ हालसालै परिवर्तन भएका (अन्तिम ५० वर्ष भित्र), कृषक (बिगतका ३०० वर्ष भन्दा बढी समयदेखि कृषिमा संलग्न भएका), र औद्योगिक (अन्तिम २० वर्ष भित्र संयुक्त राज्य अमेरिका मा आप्रवासन गरेका नेपालीहरु)। हामीले यस् अध्ययनमा जीवनशैलीले मुखका माईक्रोबायोमको विविधतामा कसरी योगदान पुर्याउँछन् भन्ने कुरको विश्लेषण गरेका छौं, जीवनशैलीहरू बीच फरक पर्ने सूक्ष्मजीवहरूको पहिचान गरेका छौं, र माइक्रोबायोममा फरक पार्ने कारकहरूको पहिचान गरेका छौं। प्रचलित दृष्टिकोणहरू विपरीत, भूगोललाई नियन्त्रण गर्दा, बिभिन्न जीवनशैलीहरू बीच मुखको माइक्रोबायोममा हुने सूक्ष्मजीवहरूको सन्ख्या (अल्फा विविधता) मा धेरै फरक देखिएन, तर मुखको माइक्रोबायोमको संरचना भने जीवनशैलीको क्रमिक चरणसँग मिल्दोजुल्दो देखियो, जसले देखाउँछ कि जीवनशैलीले मुखको माइक्रोबायोममा को संरचना निर्धारण गर्न एउटा प्रमुख भूमिका खेल्दछ। स्ट्रेप्टोबासिलस र असम्प्रेषित पोरफिरोमोनाडासिए जीनस सहितका केही सूक्ष्मजीवहरूको सापेक्ष सापेक्षिक प्रचुरता पनि जीवनशैलीसँग मेल खाने हामीले यस् अध्ययनबाट थाहा पाएका छौं। अन्ततः, हामीले जीवनशैलीको क्रमिक चरणमा माइक्रोबायोम संरचनासँग सम्बन्धित विशिष्ट जीवनशैलीसँग आबद्ध हुने धूम्रपान र अनाज जस्ता कारकहरूको पहिचान गरेका छौं। निष्कर्ष: हाम्रा निष्कर्षहरूले प्रष्ट परेका छन कि भूगोललाई नियन्त्रण गर्दा, हाम्रो जीवनशैलीले हाम्रा मुखको माइक्रोबायोमको संरचना निर्धारण गर्ने महत्त्वपूर्ण भूमिका खेल्दो रहेछ। यस् अध्ययनले मानव समुदायहरुमा मुखको माइक्रोबायोमको अध्ययन गरेमा माइक्रोबायोमबारेको हाम्रो बुझाइमा सुधार ल्याउन सकिने पनि देखाउँछ। बढ्दो शहरीकरण सँगसँगै नेपालीहरुको माइक्रोबायोममा परिवर्तन हुँदै गरेको र यस्ता परिवर्तनहरुले नेपालीहरुमा बिभिन्न दीर्घकालीन रोगहरुको व्यापकता बढाउन सक्ने हुनाले यस् सम्बन्धमा उपर्योक्त निकायहरुको ध्यानाकर्षण हुनुपर्ने आवश्यकता पनि यस् अध्ययनले प्रष्ट पारेको छ।.
Experiment 1
Subjects
- Location of subjects
- Nepal
- 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
- Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Lifestyle measurement Lifestyle measurement,lifestyle measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Combination of Foragers, recently settled, agriculturalists, expats.
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- American Industrial
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Expatriates that immigrated to the USA within the last 20 years.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 85
- Group 1 sample size Number of subjects in the case (exposed) group
- 6
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Current antibiotic use
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).
- relative abundances
- 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
- sex
Signature 1
Source: Figure 4
Description: Abundances of genera significantly following the lifestyle gradient ordered from most traditional (foragers) to most industrialized (American industrialists), left to right.
Abundance in Group 1: increased abundance in American Industrial
| NCBI | Quality Control | Links |
|---|---|---|
| Atopobium |
Revision editor(s): Tosin
Signature 2
Source: Figure 4
Description: Abundances of genera significantly following the lifestyle gradient ordered from most traditional (foragers) to most industrialized (American industrialists), left to right.
Abundance in Group 1: decreased abundance in American Industrial
| NCBI | Quality Control | Links |
|---|---|---|
| Granulicatella | ||
| Moraxella | ||
| Neisseria | ||
| Simonsiella | ||
| Streptobacillus | ||
| unclassified Bacteroidota | ||
| unclassified Porphyromonadaceae |
Revision editor(s): Tosin
Experiment 2
Differences from previous experiment shown
Subjects
- Location of subjects
- Nepal
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Wheat/Rice
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Barley/Maize
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Barley/Maize a grain type considered as a lifestyle factor associated with the oral microbiome of individuals.
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex
Signature 1
Source: Figure 5B, 5C
Description: Grain, a lifestyle factor associated with significant individual oral genera.
Abundance in Group 1: increased abundance in Barley/Maize
| NCBI | Quality Control | Links |
|---|---|---|
| Brachymonas |
Revision editor(s): Tosin
Experiment 3
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-smokers
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Smokers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals engaged in smoking
Signature 1
Source: S11A
Description: Differentially abundant taxa between smokers and Non-smokers group
Abundance in Group 1: increased abundance in Smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Atopobium |
Revision editor(s): Tosin
Signature 2
Source: Figure S11A
Description: Differentially abundant taxa between smokers and Non-smokers group.
Abundance in Group 1: decreased abundance in Smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Granulicatella | ||
| unclassified Porphyromonadaceae | ||
| Neisseria |
Revision editor(s): Tosin
Experiment 4
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-sinsu consumers
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Sinsu comsumers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals that consume sinsu.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure S11B
Description: Differentially abundant taxa between non-sinsu consumers and sinsu consumers.
Abundance in Group 1: increased abundance in Sinsu comsumers
| NCBI | Quality Control | Links |
|---|---|---|
| Brachymonas | ||
| Moraxella | ||
| unclassified Porphyromonadaceae |
Revision editor(s): Tosin
Experiment 5
Differences from previous experiment shown
Subjects
- Location of subjects
- Nepal
- United States of America
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Traditional populations
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Industrialized populations
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- American industrialists and Expats were categorized as Industralized populations.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 73
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
Lab analysis
Statistical Analysis
- Statistical test
- Kruskall-Wallis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- sex
Signature 1
Source: Figure S16B
Description: Abundance of Fusobacterium contributing to platinum resistance significantly differs between the traditional and industrialized populations.
Abundance in Group 1: decreased abundance in Industrialized populations
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacterium |
Revision editor(s): Tosin
Experiment 6
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Combination of Foragers, recently settled, agriculturalists, expats.
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- American Industrial
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Expatriates that immigrated to the USA within the last 20 years.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 85
- Group 1 sample size Number of subjects in the case (exposed) group
- 6
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4
Description: Abundances of genera significantly following the lifestyle gradient ordered from most traditional (foragers) to most industrialized (American industrialists), left to right.
Abundance in Group 1: decreased abundance in American Industrial
| NCBI | Quality Control | Links |
|---|---|---|
| Streptobacillus | ||
| unclassified Porphyromonadaceae |
Revision editor(s): Tosin
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