Short-term pectin-enriched smoothie consumption has beneficial effects on the gut microbiota of low-fiber consumers
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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
- Estonia
- 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
- Base (Pre-intervention point of diet) (Group 1)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HPect (High Pectin smoothie) (Group 1)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants in group 1 who consumed a higher amount of dietary fiber, especially high pectin smoothies first before a washout period and a low pectin smoothies consumption period
- Group 0 sample size Number of subjects in the control (unexposed) group
- 17
- Group 1 sample size Number of subjects in the case (exposed) group
- 17
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
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
- Mann-Whitney (Wilcoxon)
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
Signature 1
Source: Figure 2
Description: Bacterial up and down shifts after smoothie periods and recoveries of abundance after WO periods.
Abundance in Group 1: increased abundance in HPect (High Pectin smoothie) (Group 1)
NCBI | Quality Control | Links |
---|---|---|
Lachnospira |
Revision editor(s): Shulamite, Anne-mariesharp
Signature 2
Source: Figure 2
Description: Bacterial up and down shifts after smoothie periods and recoveries of abundance after washout periods.
Abundance in Group 1: decreased abundance in HPect (High Pectin smoothie) (Group 1)
NCBI | Quality Control | Links |
---|---|---|
Coprococcus | ||
Dorea | ||
[Ruminococcus] torques |
Revision editor(s): Shulamite, Anne-mariesharp
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- LF-intake (Low-fiber intake)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HF-intake (High fiber-intake)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants who regularly consumed >23 g of dietary fiber per day
- Group 0 sample size Number of subjects in the control (unexposed) group
- 22
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 3B
Description: At lower levels of abundance, four genera show the difference between LF and HF intake groups in the base period.
Abundance in Group 1: increased abundance in HF-intake (High fiber-intake)
NCBI | Quality Control | Links |
---|---|---|
Akkermansia | ||
Cloacibacillus | ||
Coprococcus | ||
Lactococcus |
Revision editor(s): Shulamite, Anne-mariesharp
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Base (LF intake group)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HPect (LF intake group)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants consuming a low-fiber diet (<23 g/day, LF intake group), who received the high-pectin (HPect) smoothie during the intervention period.
- 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
- 22
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4A, 6A, Table S3
Description: Altered genera in LF intake group (Base vs HPect). The pairwise comparison was performed using the Wilcoxon signed-rank test for statistical analysis to compare LPect and HPect effects on base period microbiota at the genus level
Abundance in Group 1: increased abundance in HPect (LF intake group)
NCBI | Quality Control | Links |
---|---|---|
Bacteroides | ||
Lachnospira | ||
Paraprevotella |
Revision editor(s): Shulamite, Anne-mariesharp
Signature 2
Source: Figure 4A, 4C, 6A, Table S3
Description: Altered genera in LF intake group (Base vs HPect). The pairwise comparison was performed using the Wilcoxon signed-rank test for statistical analysis to compare LPect and HPect effects on base period microbiota at the genus level.
Abundance in Group 1: decreased abundance in HPect (LF intake group)
NCBI | Quality Control | Links |
---|---|---|
Coprococcus | ||
Dorea | ||
Enterococcus | ||
Eubacterium ventriosum | ||
Faecalicatena fissicatena | ||
Holdemanella | ||
Streptococcus | ||
Subdoligranulum | ||
[Ruminococcus] torques | ||
Lactococcus | ||
Evtepia |
Revision editor(s): Shulamite, Anne-mariesharp
Experiment 4
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- LPect (Low pectin smoothie) (LF intake group)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants in the low-fiber intake group (<23 g/day) who received the low-pectin (LPect) smoothie as part of the intervention.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4B, 6A, Table S3
Description: Altered genera in LF intake group (Base vs LPect). The pairwise comparison was performed using the Wilcoxon signed-rank test for statistical analysis to compare LPect and HPect effects on base period microbiota at the genus level.
Abundance in Group 1: increased abundance in LPect (Low pectin smoothie) (LF intake group)
NCBI | Quality Control | Links |
---|---|---|
Clostridium sp. CAG:352 | ||
Colidextribacter | ||
Oscillibacter | ||
Oxalobacter | ||
Paraprevotella |
Revision editor(s): Shulamite, Anne-mariesharp
Signature 2
Source: Figure 4B, 4C, 6A, Table S3
Description: Altered genera in LF intake group (Base vs LPect). The pairwise comparison was performed using the Wilcoxon signed-rank test for statistical analysis to compare LPect and HPect effects on base period microbiota at the genus level
Abundance in Group 1: decreased abundance in LPect (Low pectin smoothie) (LF intake group)
Revision editor(s): Shulamite, Anne-mariesharp
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Base (HF intake group)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HPect (HF intake group)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants in the high-fiber intake group (>23 g/day) during the high-pectin (HPect) smoothie intervention period.
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5A, Table S3
Description: Altered genera in the HF intake group (Base vs HPect). The pairwise comparison was performed using the Wilcoxon signed-rank test for statistical analysis to compare LPect and HPect effects on base period microbiota at the genus level.
Abundance in Group 1: increased abundance in HPect (HF intake group)
NCBI | Quality Control | Links |
---|---|---|
Anaerostipes | ||
Lachnoclostridium | ||
Lachnospiraceae bacterium NK4A136 | ||
Parasutterella |
Revision editor(s): Shulamite, Anne-mariesharp
Signature 2
Source: Figure 5A, 5C, 6B, Table S3
Description: Altered genera in the HF intake group (Base vs HPect). The pairwise comparison was performed using the Wilcoxon signed-rank test for statistical analysis to compare LPect and HPect effects on base period microbiota at the genus level.
Abundance in Group 1: decreased abundance in HPect (HF intake group)
NCBI | Quality Control | Links |
---|---|---|
Ruminococcus | ||
[Ruminococcus] torques | ||
Erysipelotrichaceae UCG 003Erysipelotrichaceae UCG 003 | ||
Anaerostipes |
Revision editor(s): Shulamite, Anne-mariesharp
Experiment 6
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- LPect (HF intake group)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants in the high-fiber intake group (>23 g/day) during the low-pectin (LPect) smoothie intervention period.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5B, 6B, Table S3
Description: Altered genera in the HF intake group (Base vs LPect). The pairwise comparison was performed using the Wilcoxon signed-rank test for statistical analysis to compare LPect and HPect effects on base period microbiota at the genus level.
Abundance in Group 1: increased abundance in LPect (HF intake group)
NCBI | Quality Control | Links |
---|---|---|
Bilophila | ||
Oscillibacter | ||
Paraprevotella |
Revision editor(s): Shulamite, Anne-mariesharp
Signature 2
Source: Figure 5B, 5C, 6B, Table S3
Description: Altered genera in the HF intake group (Base vs LPect). The pairwise comparison was performed using the Wilcoxon signed-rank test for statistical analysis to compare LPect and HPect effects on base period microbiota at the genus level.
Abundance in Group 1: decreased abundance in LPect (HF intake group)
NCBI | Quality Control | Links |
---|---|---|
Agathobacter | ||
Eubacterium ventriosum | ||
Ruminococcus |
Revision editor(s): Shulamite, Anne-mariesharp
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- WO LPect (Wash out low pectin smoothie) (Group 2)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HPect (Group 2)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants in group 2 who consumed the high-pectin smoothie during their second intervention period, following the low-pectin smoothie consumption period and a washout period.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 14
- Group 1 sample size Number of subjects in the case (exposed) group
- 14
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 2
Description: Bacterial up- and down-shifts after smoothie periods and recoveries of abundances after WO periods.
Abundance in Group 1: decreased abundance in HPect (Group 2)
NCBI | Quality Control | Links |
---|---|---|
Coprococcus | ||
[Ruminococcus] torques |
Revision editor(s): Shulamite, Anne-mariesharp
Experiment 8
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HPect (Group 2)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- WO HPect (Wash out high pectin smoothie) (Group 2)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants in group 2 during the washout period after completing the high-pectin smoothie intervention.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 2
Description: Bacterial up- and down-shifts after smoothie periods and recoveries of abundances after WO periods.
Abundance in Group 1: decreased abundance in WO HPect (Wash out high pectin smoothie) (Group 2)
NCBI | Quality Control | Links |
---|---|---|
Lachnospira |
Revision editor(s): Shulamite, Anne-mariesharp
Experiment 9
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- WO-HPect (Washout - high pectin smoothie) (Group 1)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- LPect (Group 1)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants in group 1 who consumed the low-pectin smoothie during their second intervention period, following the high-pectin smoothie consumption period and wash-out period
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 2
Description: Bacterial up- and down-shifts after smoothie periods and recoveries of abundances after WO periods.
Abundance in Group 1: decreased abundance in LPect (Group 1)
NCBI | Quality Control | Links |
---|---|---|
Coprococcus |
Revision editor(s): Shulamite, Anne-mariesharp
Experiment 10
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HPect (Group 1)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- WO HPect (Group 1)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants in group 1 during the washout period after completing the high-pectin smoothie intervention.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 17
- Group 1 sample size Number of subjects in the case (exposed) group
- 17
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 2
Description: Bacterial up- and down-shifts after smoothie periods and recoveries of abundances after WO periods.
Abundance in Group 1: decreased abundance in WO HPect (Group 1)
NCBI | Quality Control | Links |
---|---|---|
Lachnospira |
Revision editor(s): Shulamite, Anne-mariesharp