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
- Baseline
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- After high pectin smoothie (HPect)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants who consumed a higher amount of dietary fiber, especially pectin smoothies first.
- 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: Fig 2
Description: Bacterial up-and down shifts after smoothie periods and recoveries of abundance after WO periods. During the intervention, group 1 consumed first pectin-enriched smoothie (HPect) followed by washout (WO HPect), and consumption of the control smoothie (LPect) with washout ()WO Lpect.
Abundance in Group 1: increased abundance in After high pectin smoothie (HPect)
NCBI | Quality Control | Links |
---|---|---|
Lachnospira |
Revision editor(s): Shulamite
Signature 2
Source: Fig 2
Description: Bacterial up-and down shifts after smoothie periods and recoveries of abundance after WO periods. During the intervention, group 1 consumed first pectin-enriched smoothie (HPect) followed by washout (WO HPect), and consumption of the control smoothie (LPect) with washout (WO Lpect).
Abundance in Group 1: decreased abundance in After high pectin smoothie (HPect)
NCBI | Quality Control | Links |
---|---|---|
Coprococcus | ||
Ruminococcus torques groupRuminococcus torques group | ||
Dorea |
Revision editor(s): Shulamite
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- High-fiber intake group (HF)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Low-fiber intake group (LF)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants who regularly consumed (<23g) less than 23g of dietary fiber per day.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 9
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
- 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
Statistical Analysis
Signature 1
Source: Fig 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: decreased abundance in Low-fiber intake group (LF)
NCBI | Quality Control | Links |
---|---|---|
Coprococcus | ||
Lactococcus | ||
Akkermansia | ||
Cloacibacillus |
Revision editor(s): Shulamite
Signature 2
Source: Fig. 4A, Supplementary Table S3 and S4
Description: Altered genera in LF intake group. 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 (*P ≤ 0.05, ** P ≤ 0.01, *** P ≤ 0.001, ns—not significant).
Abundance in Group 1: increased abundance in Low-fiber intake group (LF)
NCBI | Quality Control | Links |
---|---|---|
Lachnospira | ||
Bacteroides |
Revision editor(s): Shulamite
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Fiber intake group (Baseline LF)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- After high pectin smoothie (Low Fiber intake group (HPect))
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants who consumed a higher amount of dietary fiber, especially pectin.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 22
Lab analysis
Statistical Analysis
Signature 1
Source: 4A, 4C, Supplementary Table S3 and S4
Description: Altered genera in LF intake group. 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 After high pectin smoothie (Low Fiber intake group (HPect))
NCBI | Quality Control | Links |
---|---|---|
Coprococcus | ||
Dorea | ||
Enterococcus | ||
Evtepia | ||
Holdemania | ||
Lactococcus | ||
Streptococcus | ||
Subdoligranulum | ||
Eubacterium fissicatena groupEubacterium fissicatena group |
Revision editor(s): Shulamite
Signature 2
Source: 4B, 4C, Supplementary Table S3 and S4
Description: Altered genera in LF intake group. 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 After high pectin smoothie (Low Fiber intake group (HPect))
NCBI | Quality Control | Links |
---|---|---|
Lachnospira | ||
Bacteroides |
Revision editor(s): Shulamite
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Fiber intake (LF baseline)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Low Fiber intake (LF LPect)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants who consumed smoothies with a low amount of dietary fiber. Especially pectin.
- 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: Fig. 4B, 4C, Supplementary Table S3 and S4
Description: Altered genera in LF intake group. 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 Low Fiber intake (LF LPect)
NCBI | Quality Control | Links |
---|---|---|
Clostridium sp. CAG:352 | ||
Colidextribacter | ||
Oxalobacter |
Revision editor(s): Shulamite
Signature 2
Source: Fig. 4B, 4C, Supplementary Table S3 and S4
Description: Altered genera in LF intake group. 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 Low Fiber intake (LF LPect)
NCBI | Quality Control | Links |
---|---|---|
Holdemania | ||
Merdibacter | ||
Peptococcus | ||
Streptococcus | ||
Turicibacter | ||
Defluviitaleaceae_UCG-011Defluviitaleaceae_UCG-011 | ||
UCG-009UCG-009 |
Revision editor(s): Shulamite
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- High-fiber intake group (HF baseline)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High-fiber intake group (HF HPect)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants who consumed smoothies with high amounts of fiber, especially pectin.
- 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
Statistical Analysis
Signature 1
Source: 5A, 5C, Supplementary Table S3 and S4
Description: Altered genera in the HF intake group. 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 High-fiber intake group (HF HPect)
NCBI | Quality Control | Links |
---|---|---|
Lachnoclostridium | ||
Lachnospiraceae_NK4A136_groupLachnospiraceae_NK4A136_group | ||
Parasutterella |
Revision editor(s): Shulamite
Signature 2
Source: Fig. 5A, 5C, Supplementary Table S3 and S4
Description: Altered genera in the HF intake group. 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 High-fiber intake group (HF HPect)
NCBI | Quality Control | Links |
---|---|---|
Anaerostipes | ||
Ruminococcus |
Revision editor(s): Shulamite
Experiment 6
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High-fiber intake group (HF LPect)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participant who consumes a high amount of dietary with low pectin.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 9
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
- 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
Statistical Analysis
Signature 1
Source: Fig. 5A, 5C, Supplementary Table S3 and S4
Description: Altered genera in the HF intake group. 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 High-fiber intake group (HF LPect)
NCBI | Quality Control | Links |
---|---|---|
Bilophila |
Revision editor(s): Shulamite
Signature 2
Source: Fig. 5B, 5C, Supplementary Table S3 and S4
Description: Altered genera in the HF intake group. 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 High-fiber intake group (HF LPect)
NCBI | Quality Control | Links |
---|---|---|
Agathobacter | ||
Ruminococcus |
Revision editor(s): Shulamite
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low fiber intake (Baseline)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Low fiber intake After (LPect)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants who consumed smoothies with a low amount of fiber, especially pectin.
- 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: Fig. 6, Supplementary Table S3 and S4
Description: Altered genera in both groups. 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 Low fiber intake After (LPect)
NCBI | Quality Control | Links |
---|---|---|
Oscillibacter | ||
Paraprevotella |
Revision editor(s): Shulamite
Signature 2
Source: Fig. 6, Supplementary Table S3 and S4
Description: Altered genera in both groups. 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 Low fiber intake After (LPect)
NCBI | Quality Control | Links |
---|---|---|
Erysipelotrichaceae_UCG-003Erysipelotrichaceae_UCG-003 | ||
Eubacterium ventriosum groupEubacterium ventriosum group |
Revision editor(s): Shulamite
Experiment 8
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- High-fiber intake group (HF baseline)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High-fiber intake group after HPect(HF HPect)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants who consumed a high amount of dietary fiber, especially pectin.
- 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: Fig. 6, Supplementary Table S3 and S4
Description: Altered genera in both groups. 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 High-fiber intake group after HPect(HF HPect)
NCBI | Quality Control | Links |
---|---|---|
Erysipelotrichaceae_UCG-003Erysipelotrichaceae_UCG-003 | ||
Ruminococcus torques groupRuminococcus torques group |
Revision editor(s): Shulamite
Experiment 9
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Washout (WO-HPect)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- LPect
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants who consumed a low amount of dietary fiber, especially pectin smoothies first.
- 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: Fig. 2
Description: Bacterial up- and down-shifts after smoothie periods and recoveries of abundances after WO periods. Box plots are arranged in period order. Base period characterizes microbiota before the intervention. During the intervention, group 1 consumed first pectin-enriched smoothie (HPect), followed by washout (WO HPect), and consumption of control smoothie (LPect) with washout (WO LPect).
Abundance in Group 1: decreased abundance in LPect
NCBI | Quality Control | Links |
---|---|---|
Coprococcus |
Revision editor(s): Shulamite
Experiment 10
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Washout WO-Hpect
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HPect
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants who consumed a high amount of dietary fiber, especially pectin.
- 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
Statistical Analysis
Signature 1
Source: Fig. 2
Description: Bacterial up- and down-shifts after smoothie periods and recoveries of abundances after WO periods. Box plots are arranged in period order. Base period characterizes microbiota before the intervention. During the intervention, group 1 consumed first pectin-enriched smoothie (HPect), followed by washout (WO HPect),
Abundance in Group 1: increased abundance in HPect
NCBI | Quality Control | Links |
---|---|---|
Lachnospira |
Revision editor(s): Shulamite