Microbiota assembly, structure, and dynamics among Tsimane horticulturalists of the Bolivian Amazon
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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
Sprockett DD, Martin M, Costello EK, Burns AR, Holmes SP, Gurven MD, Relman DA
Journal
Nature communications
Year
2020
Selective and neutral forces shape human microbiota assembly in early life. The Tsimane are an indigenous Bolivian population with infant care-associated behaviors predicted to increase mother-infant microbial dispersal. Here, we characterize microbial community assembly in 47 infant-mother pairs from six Tsimane villages, using 16S rRNA gene amplicon sequencing of longitudinal stool and tongue swab samples. We find that infant consumption of dairy products, vegetables, and chicha (a fermented drink inoculated with oral microbes) is associated with stool microbiota composition. In stool and tongue samples, microbes shared between mothers and infants are more abundant than non-shared microbes. Using a neutral model of community assembly, we find that neutral processes alone explain the prevalence of 79% of infant-colonizing microbes, but explain microbial prevalence less well in adults from river villages with more regular access to markets. Our results underscore the importance of neutral forces during microbiota assembly. Changing lifestyle factors may alter traditional modes of microbiota assembly by decreasing the role of neutral processes.
Experiment 1
Subjects
- Location of subjects
- Bolivia
- 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
- Restricted to specific location localized,Restricted to specific location,restricted to specific location
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Proximal River Village
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Distal River Village
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Tsimane adults (>14 years old) that live in a village along the Maniqui river, that is more than 20 km away from the regional market and have access to the market via 6-12 hour trips by foot or boat.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 19
- Group 1 sample size Number of subjects in the case (exposed) group
- 77
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).
- log transformation
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
Signature 1
Source: Figure 5C and Sprockett_Tsimane_ps.rds
Description: Discriminatory ASVs for proximal and distal river villages identified using a tree-based LDA algorithm.
Abundance in Group 1: increased abundance in Distal River Village
Revision editor(s): YokoC
Signature 2
Source: Figure 5C and Sprockett_Tsimane_ps.rds
Description: Discriminatory ASVs for proximal and distal river villages identified using a tree-based LDA algorithm.
Abundance in Group 1: decreased abundance in Distal River Village
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae UCG-003Prevotellaceae UCG-003 |
Revision editor(s): YokoC
Experiment 2
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- River Village
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Forest Village
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Tsimane adults that live in a village from the forest ecotype, distant by 40 km or more from the regional market. Samples were collected in the dry season of 2009.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 96
- Group 1 sample size Number of subjects in the case (exposed) group
- 73
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5C and Sprockett_Tsimane_ps.rds
Description: Discriminatory ASVs for forest or river villages identified using a tree-based LDA algorithm.
Abundance in Group 1: increased abundance in Forest Village
Revision editor(s): YokoC
Signature 2
Source: Figure 5C and Sprockett_Tsimane_ps.rds
Description: Discriminatory ASVs for forest or river villages identified using a tree-based LDA algorithm.
Abundance in Group 1: decreased abundance in Forest Village
Revision editor(s): YokoC
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