Dietary selective effects manifest in the human gut microbiota from species composition to strain genetic makeup
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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
- Germany
- 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
- Diet measurement Diet measurement,diet measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Vegan
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Omnivore
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Omnivore refers to individuals regularly consuming a mixed diet of meat and meat products of ≥170 g/day).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 33
- Group 1 sample size Number of subjects in the case (exposed) group
- 28
Lab analysis
- Sequencing type
- WMS
- 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).
- arcsine square-root
- Statistical test
- MaAsLin2
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.25
- 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, sex
Signature 1
Source: Supplementary Table 3
Description: A panel of species that were differentially abundant in one diet type compared to the other.
Abundance in Group 1: decreased abundance in Omnivore
Revision editor(s): KateRasheed
Signature 2
Source: Supplementary Table 3
Description: A panel of species that were differentially abundant in one diet type compared to the other.
Abundance in Group 1: increased abundance in Omnivore
Revision editor(s): KateRasheed
Experiment 2
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Diet Dietary,Diets,Diet,diet
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Flexitarian
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Flexitarian refers to individuals maintaining a plant-based diet with an occasional consumption of meat and meat products of ≤50 g/day
- Group 1 sample size Number of subjects in the case (exposed) group
- 31
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary Table 3
Description: A panel of species that were differentially abundant in one diet type compared to the other.
Abundance in Group 1: increased abundance in Flexitarian
Revision editor(s): KateRasheed
Signature 2
Source: Supplementary Table 3
Description: A panel of species that were differentially abundant in one diet type compared to the other.
Abundance in Group 1: decreased abundance in Flexitarian
Revision editor(s): KateRasheed
Experiment 3
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
- Flexitarian
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Omnivore
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Omnivore refers to individuals regularly consuming a mixed diet of meat and meat products of ≥170 g/day).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 31
- Group 1 sample size Number of subjects in the case (exposed) group
- 28
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary Table 3
Description: A panel of species that were differentially abundant in one diet type compared to the other.
Abundance in Group 1: increased abundance in Omnivore
Revision editor(s): KateRasheed
Signature 2
Source: Supplementary Table 3
Description: A panel of species that were differentially abundant in one diet type compared to the other.
Abundance in Group 1: decreased abundance in Omnivore
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridia bacterium | ||
| GGB9691_SGB15198GGB9691_SGB15198 | ||
| Lachnospiraceae bacterium |
Revision editor(s): KateRasheed
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Vegan merged dataset (FrancescaDF_2019 + ShettySA_2022 + this study)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Omnivore merged dataset (FrancescaDF_2019 + ShettySA_2022 + this study)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Omnivore refers to individuals regularly consuming a mixed diet of meat and meat products of ≥170 g/day). The samples was from this study and two public datasets (FrancescaDF_2019 and ShetttySA_2022)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 103
- Group 1 sample size Number of subjects in the case (exposed) group
- 103
Lab analysis
Statistical Analysis
Signature 1
Source: Figure S2C
Description: Differential abundant microbiome species across samples from this study and two public datasets (FrancescaDF_2019 and ShetttySA_2022)
Abundance in Group 1: increased abundance in Omnivore merged dataset (FrancescaDF_2019 + ShettySA_2022 + this study)
Revision editor(s): KateRasheed
Signature 2
Source: Fig. S2C
Description: Differential abundant microbiome species across samples from this study and two public datasets (FrancescaDF_2019 and ShetttySA_2022)
Abundance in Group 1: decreased abundance in Omnivore merged dataset (FrancescaDF_2019 + ShettySA_2022 + this study)
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnospiraceae bacterium | ||
| Lachnospiraceae bacterium OM04-12BH | ||
| Lachnospiraceae bacterium OF09-6 | ||
| Lachnospira hominis (ex Liu et al. 2021) | ||
| Clostridium sp. AF20-17LB |
Revision editor(s): KateRasheed
