Fermented foods affect the seasonal stability of gut bacteria in an Indian rural population
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- India
- 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
- Phenotype Phenotype,phenotype
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- European Individuals
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Indian Individuals
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group of individuals represents a traditional Indian agrarian population, which exhibits a Prevotella-driven gut microbiota who are long-term consumers of fermented foods.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 78
- Group 1 sample size Number of subjects in the case (exposed) group
- 78
- 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
- Not specified
- 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
- Mann-Whitney (Wilcoxon)
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, sex
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Fig. 3B
Description: The overall relative abundance distributions of Prevotella melaninogenica.
Abundance in Group 1: increased abundance in Indian Individuals
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella melaninogenica |
Revision editor(s): Joiejoie
Signature 2
Source: Fig. 3B
Description: The overall relative abundance and distributions of Bifidobacterium
Abundance in Group 1: decreased abundance in Indian Individuals
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium |
Revision editor(s): Joiejoie
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Group A ( never consumed Hawaijar and Dahi )
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Groups B (consumed both Hawaijar and Dahi), C (consumed Hawaijar, not Dahi), and D (consumed Dahi, not Hawaijar)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group consists of Individuals with a long-term dietary habit of consuming fermented foods (Dahi and/or Hawaijar) for at least 10 years, with a minimum frequency of 3 times per week.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 58
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Fig. 7A
Description: Diet alters the taxa's relative abundance on average with respect to the control diet (Group-A).
Abundance in Group 1: increased abundance in Groups B (consumed both Hawaijar and Dahi), C (consumed Hawaijar, not Dahi), and D (consumed Dahi, not Hawaijar)
| NCBI | Quality Control | Links |
|---|---|---|
| Catenibacterium mitsuokai | ||
| Parabacteroides distasonis | ||
| Tannerella | ||
| Odoribacter splanchnicus |
Revision editor(s): Joiejoie
Signature 2
Source: Fig. 7A
Description: Diet alters the taxa's relative abundance on average with respect to the control diet (Group-A).
Abundance in Group 1: decreased abundance in Groups B (consumed both Hawaijar and Dahi), C (consumed Hawaijar, not Dahi), and D (consumed Dahi, not Hawaijar)
| NCBI | Quality Control | Links |
|---|---|---|
| Alloprevotella tannerae |
Revision editor(s): Joiejoie
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Group A (never consumed Hawaijar and Dahi)
Lab analysis
Statistical Analysis
Signature 1
Source: Fig. 7B
Description: Gut bacteria with significant seasonal effects on their relative abundance, compared to autumn, after controlling for diet and subject effects.
Abundance in Group 1: increased abundance in Groups B (consumed both Hawaijar and Dahi), C (consumed Hawaijar, not Dahi), and D (consumed Dahi, not Hawaijar)
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- European Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Indian Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group consists of Indian agrarian individuals who differed in their intake of fermented milk and soybean products, with seasonal sampling during hot-humid summer, autumn, and dry winter.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 76
- Group 1 sample size Number of subjects in the case (exposed) group
- 76
Lab analysis
Statistical Analysis
Signature 1
Source: Fig. S3
Description: The abundance distribution of gut microbiota taxa significantly differing between Indian and European subjects
Abundance in Group 1: increased abundance in Indian Subjects
| NCBI | Quality Control | Links |
|---|---|---|
| Ligilactobacillus salivarius | ||
| Megamonas hypermegale | ||
| Megasphaera elsdenii | ||
| Veillonella |
Signature 2
Source: Fig. S3
Description: The abundance distribution of gut microbiota taxa significantly differing between Indian and European subjects
Abundance in Group 1: decreased abundance in Indian Subjects
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerostipes caccae | ||
| Thermoclostridium stercorarium | ||
| Anaerobutyricum hallii |
Revision editor(s): Joiejoie
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Group-A (not consumed Dahi and Hawaijar)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Group-B ( consumed Dahi and Hawaijar), Group-C ( consumed Hawaijar not Dahi), and Group-D ( consumed Dahi not Hawaijar).
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group includes Individuals in Groups B, C, and D who consumed fermented foods, with Group-B consuming both Dahi and Hawaijar, Group-C consuming only Hawaijar, and Group-D consuming only Dahi.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 58
- Group 1 sample size Number of subjects in the case (exposed) group
- 156
Signature 1
Source: Fig. S7A
Description: Long-term fermented food consumption affects Bacillus load in fecal samples across different diet groups.
Abundance in Group 1: increased abundance in Group-B ( consumed Dahi and Hawaijar), Group-C ( consumed Hawaijar not Dahi), and Group-D ( consumed Dahi not Hawaijar).
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillus |
Revision editor(s): Joiejoie
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Cluster-B/R
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cluster-P
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group includes a Prevotella-driven gut microbiota cluster characterized by a significantly higher abundance of Prevotella melaninogenica, Prevotella tannerae, Prevotella oralis and Prevotella ruminicola.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 97
- Group 1 sample size Number of subjects in the case (exposed) group
- 117
Signature 1
Source: Table S2
Description: The absolute abundance of gut bacterial taxa distinguishing Cluster-P (Prevotella-driven) and Cluster-B/R (Bifidobacterium/Ruminococcus-driven).
Abundance in Group 1: increased abundance in Cluster-P
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella melaninogenica | ||
| Alloprevotella tannerae | ||
| Hoylesella oralis | ||
| Xylanibacter ruminicola |
Revision editor(s): Joiejoie
Signature 2
Source: Table S2
Description: The absolute abundance of gut bacterial taxa distinguishing Cluster-P (Prevotella-driven) and Cluster-B/R (Bifidobacterium/Ruminococcus-driven).
Abundance in Group 1: decreased abundance in Cluster-P
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerostipes caccae | ||
| Marvinbryantia formatexigens | ||
| Ginkgoales | ||
| Blautia obeum | ||
| [Clostridium] symbiosum |
Revision editor(s): Joiejoie
