Changes in social environment impact primate gut microbiota composition
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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
Pearce CS, Bukovsky D, Douchant K, Katoch A, Greenlaw J, Gale DJ, Nashed JY, Brien D, Kuhlmeier VA, Sabbagh MA, Blohm G, De Felice FG, Pare M, Cook DJ, Scott SH, Munoz DP, Sjaarda CP, Tusche A, Sheth PM, Winterborn A, Boehnke S, Gallivan JP
Journal
Animal microbiome
Year
2024
Keywords:
Gut microbiota, Metagenomics, Monkeys, Primates, Social environment, Social living
BACKGROUND: The gut microbiota (GM) has proven to be essential for both physical health and mental wellbeing, yet the forces that ultimately shape its composition remain opaque. One critical force known to affect the GM is the social environment. Prior work in humans and free-ranging non-human primates has shown that cohabitation and frequent social interaction can lead to changes in GM composition. However, it is difficult to assess the direction of causation in these studies, and interpretations are complicated by the influence of uncontrolled but correlated factors, such as shared diet. RESULTS: We performed a 15-month longitudinal investigation wherein we disentangled the impacts of diet and social living conditions on GM composition in a captive cohort of 13 male cynomolgus macaques. The animals were in single housing for the first 3 months of the study initially with a variable diet. After baseline data collection they were placed on a controlled diet for the remainder of the study. Following this diet shift the animals were moved to paired housing for 6 months, enabling enhanced social interaction, and then subsequently returned to single housing at the end of our study. This structured sequencing of diet and housing changes allowed us to assess their distinct impacts on GM composition. We found that the early dietary adjustments led to GM changes in both alpha and beta diversity, whereas changes in social living conditions only altered beta diversity. With respect to the latter, we found that two particular bacterial families - Lactobacillaceae and Clostridiaceae - demonstrated significant shifts in abundance during the transition from single housing to paired housing, which was distinct from the shifts we observed based on a change in diet. Conversely, we found that other bacteria previously associated with sociality were not altered based on changes in social living conditions but rather only by changes in diet. CONCLUSIONS: Together, these findings decouple the influences that diet and social living have on GM composition and reconcile previous observations in the human and animal literatures. Moreover, the results indicate biological alterations of the gut that may, in part, mediate the relationship between sociality and wellbeing.
Experiment 1
Needs review
Subjects
- Location of subjects
- Canada
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Macaca fascicularis
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Uncontrolled diet (T1 single)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Controlled diet (T2 single)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Following T1Single data collection, at the beginning of the Single Living phase, the enrichment elements of NHP’s diet for the remainder of the study (referred to as “controlled” diet) was strictly controlled. This controlled diet approach directly help to investigate how diet alterations impact GM composition during a period of stable single living, i.e., comparing the transition from uncontrolled (T1Single) to controlled diet (T2Single) during the Single Living phase.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 13
- Group 1 sample size Number of subjects in the case (exposed) group
- 13
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-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
- LEfSe
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Figure 2C and Figure S7A
Description: Differential relative abundance of bacterial families and genus exhibiting the diet effect. LEfSe analysis identified significantly different taxa between diet-uncontrolled (red, T1Single) and diet-controlled (light blue, T2Single) conditions.
Abundance in Group 1: increased abundance in Controlled diet (T2 single)
Signature 2
Source: Figure 2C and Figure S7A
Description: Differential relative abundance of bacterial families and genus exhibiting the diet effect. LEfSe analysis identified significantly different taxa between diet-uncontrolled (red, T1Single) and diet-controlled (light blue, T2Single) conditions.
Abundance in Group 1: decreased abundance in Controlled diet (T2 single)
Experiment 3
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Diet measurement Diet measurement,diet measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- T1 Single (Effect of Diet)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- T2 Single (Effect of Diet)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Group with controlled diet (T2Single) during the Single Living phase.
- 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
- Statistical test
- Mann-Whitney (Wilcoxon)
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Experiment 4
Needs review
Curated date: 2024/11/28
Curator:
Revision editor(s):
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Social environment measurement Social environment measurement,social environment measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- T2Single (effect of moving from single to pairwise living)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- T3Social(effect of moving from single to pairwise living)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The Protected Pairwise Social Living phase was implemented and lasted for 6 months, during which T3Social and T4Social data were collected.
Lab analysis
Statistical Analysis
Experiment 5
Needs review
Curated date: 2024/11/28
Curator:
Revision editor(s):
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Social interaction measurement Social interaction measurement,social interaction measurement
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- T4Social(effect of moving from single to pairwise living)
Lab analysis
Statistical Analysis
Experiment 6
Needs review
Curated date: 2024/11/28
Curator:
Revision editor(s):
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Diet Effect Timepoint 2 (Decreasing)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Diet Effect Timepoint 2 (Increasing)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Diet alterations impact (Controlled diet/Timepoint 2) during the Single Living phase
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- log transformation
- Statistical test
- ANCOM-BC
Signature 2
Source: Supplementary Table 6 and 7
Description: Significant taxa associated with Diet Effect in Timepoint 2
Abundance in Group 1: decreased abundance in
Experiment 7
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Social interaction measurement Social interaction measurement,social interaction measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Social Living Effect Timepoint 2 (Decreasing)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Social Living Effect Timepoint 2 (Increasing)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Social living effect of moving from single living (Timepoint 2) to pairwise living (Timepoint 3).
Lab analysis
Statistical Analysis
Experiment 8
Needs review
Curated date: 2025/01/20
Curator:
Revision editor(s):
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Social Living Effect Timepoint 3 (Decreasing)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Social Living Effect Timepoint 3 (Increasing)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Social living effect in the protected pairwise living phase (Timepoint 3)
Lab analysis
Statistical Analysis
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