Effects of healthy low-carbohydrate diet and time-restricted eating on weight and gut microbiome in adults with overweight or obesity: Feeding RCT

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by ChiomaBlessing on 2025-4-22

Curated date: 2025/04/11

Curator: MyleeeA

Revision editor(s): MyleeeA, Daberechi

Subjects

Location of subjects: China

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: Response to diet Response to diet,response to diet

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Healthy Low Carbohydrate Diet at Baseline (HLCD)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Healthy Low Carbohydrate Diet at Endpoint (HLCD)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: The participants in the Healthy Low Carbohydrate Diet (HLCD) alone group were provided with HLCD and instructed to follow their usual eating regimens during the 12 week feeding trial. The HLCD was a relatively healthy type of LCD consisting of approximately 30%, 50%, and 20% of total energy from carbohydrates, fats, and proteins, emphasizing the consumption of unsaturated fatty acids, plant proteins, and high-quality carbohydrates including whole grains, fresh vegetables, and fruits.

Group 0 sample size Number of subjects in the control (unexposed) group: 48

Group 1 sample size Number of subjects in the case (exposed) group: 43

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: 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).: 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: 2

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2025-4-22

Curated date: 2025/04/12

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 2c and Supplementary Figure 2

Description: Significant taxonomic changes between Healthy Low Carbohydrate Diet (HLCD) at baseline and Endpoint as accessed using LefSe.

Abundance in Group 1: increased abundance in Healthy Low Carbohydrate Diet at Endpoint (HLCD)

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Bacteroidales
Bacteroidia
Bacteroidota
Betaproteobacteria
Burkholderiales
Enterobacter hormaechei
Enterobacterales
Enterobacteriaceae
Escherichia
Escherichia coli
Gammaproteobacteria
Klebsiella
Klebsiella pneumoniae
Pseudomonadota
Sutterellaceae
Weissella confusa

Revision editor(s): MyleeeA

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2025-4-22

Curated date: 2025/04/12

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 2c and Supplementary Figure 2

Description: Significant taxonomic changes between Healthy Low Carbohydrate Diet (HLCD) at baseline and Endpoint as accessed using LefSe.

Abundance in Group 1: decreased abundance in Healthy Low Carbohydrate Diet at Endpoint (HLCD)

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Bacillota
Clostridia
Dorea
Dorea longicatena
Eubacteriales
Faecalibacterium
Mediterraneibacter
Oscillospiraceae
Peptostreptococcaceae
Romboutsia
Romboutsia timonensis
Streptococcus sp. A12
Turicibacter sanguinis
[Ruminococcus] torques
unclassified Clostridia

Revision editor(s): MyleeeA

Experiment 2

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by ChiomaBlessing on 2025-4-22

Curated date: 2025/04/12

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Non-Healthy Low Carbohydrate Diet at Baseline (Non-HLCD)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Non-Healthy Low Carbohydrate Diet at Endpoint (Non-HLCD)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: The participants in the Non-Healthy Low Carbohydrate Diet (HLCD) alone group were not provided with HLCD and instructed to follow their usual eating regimens during the 12 week feeding trial.

Group 1 sample size Number of subjects in the case (exposed) group: 44

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2025-4-22

Curated date: 2025/04/12

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 2c and Supplementary Figure 2

Description: Significant taxonomic changes between Non-Healthy Low Carbohydrate Diet (Non-HLCD) at baseline and Endpoint as accessed using LefSe.

Abundance in Group 1: increased abundance in Non-Healthy Low Carbohydrate Diet at Endpoint (Non-HLCD)

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Citrobacter
Dysosmobacter
Enterobacter hormaechei
Enterobacterales
Enterobacteriaceae
Enterocloster citroniae
Escherichia
Escherichia coli
Gammaproteobacteria
Klebsiella
Klebsiella pneumoniae
Weissella confusa

Revision editor(s): MyleeeA

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2025-4-22

Curated date: 2025/04/12

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 2c and Supplementary Figure 2

Description: Significant taxonomic changes between Non-Healthy Low Carbohydrate Diet (Non-HLCD) at baseline and Endpoint as accessed using LefSe.

Abundance in Group 1: decreased abundance in Non-Healthy Low Carbohydrate Diet at Endpoint (Non-HLCD)

NCBI	Quality Control	Links
Dorea
Dorea longicatena
Mediterraneibacter
Peptostreptococcaceae
Romboutsia
Romboutsia timonensis
Streptococcus rubneri

Revision editor(s): MyleeeA

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by ChiomaBlessing on 2025-4-22

Curated date: 2025/04/12

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Fasting Fast,Fasting,fasting

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Time-Restricted eating (TRE) at Baseline

Group 1 name Corresponds to the case (exposed) group for case-control studies: Time-Restricted eating (TRE) at Endpoint

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: The participants in the Time Restricted eating (TRE) alone group were provided with control diets and instructed to follow the 10-h TRE during the 12 week feeding trial. The 10-h TRE required participants to consume the provided meals within a 10-h window each day.

Group 1 sample size Number of subjects in the case (exposed) group: 43

Statistical Analysis

Statistical test: Mann-Whitney (Wilcoxon); T-Test

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: Not specified

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2025-4-22

Curated date: 2025/04/12

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Figure 4A

Description: Significant taxonomic changes between Time-Restricted eating (TRE) at baseline and Endpoint.

Abundance in Group 1: increased abundance in Time-Restricted eating (TRE) at Endpoint

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Parabacteroides distasonis
Eubacteriaceae bacterium
Bacteroides intestinalis
Escherichia coli
Barnesiella intestinihominis

Revision editor(s): MyleeeA

Experiment 6

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by ChiomaBlessing on 2025-4-22

Curated date: 2025/04/14

Curator: Daberechi

Revision editor(s): Daberechi

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Time Restricted Eating at Baseline (TRE)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Time Restricted Eating at Endpoint (TRE)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: The participants in the Time Restricted Eating (TRE) alone group were provided with control diets and instructed to follow the 10-h TRE. The control diet was the traditional Chinese diet designed according to Dietary Guidelines for Chinese Resident characterized by approximately 50%, 34%, and 16% of energy from carbohydrates, fat, and protein. The 10-h TRE required participants to consume the provided meals within a 10-h window each day.

Statistical Analysis

Statistical test: LEfSe

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 2

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2025-4-22

Curated date: 2025/04/14

Curator: Daberechi

Revision editor(s): Daberechi

Source: Figure 2D and Supplementary Figure 2

Description: Significant taxonomic changes between Time Restricted Eating (TRE) at baseline and Endpoint as accessed using LefSe.

Abundance in Group 1: increased abundance in Time Restricted Eating at Endpoint (TRE)

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Citrobacter
Enterobacter hormaechei
Enterobacterales
Enterobacteriaceae
Escherichia
Escherichia coli
Gammaproteobacteria
Klebsiella
Klebsiella pneumoniae
Parabacteroides
Parabacteroides distasonis
Tannerellaceae
Weissella confusa
Pseudomonadota

Revision editor(s): Daberechi

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2025-4-22

Curated date: 2025/04/14

Curator: Daberechi

Revision editor(s): Daberechi

Source: Figure 2D and Supplementary Figure 2

Description: Significant taxonomic changes between Time Restricted Eating (TRE) at baseline and Endpoint as accessed using LefSe.

Abundance in Group 1: decreased abundance in Time Restricted Eating at Endpoint (TRE)

NCBI	Quality Control	Links
Clostridia
Coprococcus comes
Dorea
Dorea longicatena
Eubacterium ramulus
Faecalibacterium
Faecalibacterium prausnitzii
Mediterraneibacter
Peptostreptococcaceae
Romboutsia
Romboutsia timonensis
Streptococcus rubneri
Oscillospiraceae

Revision editor(s): Daberechi

Experiment 7

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by ChiomaBlessing on 2025-4-22

Curated date: 2025/04/14

Curator: Daberechi

Revision editor(s): Daberechi

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Binge eating binge eating,binge eating disorder,Binge eating

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Non-Time Restricted Eating at Baseline (Non-TRE)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Non-Time Restricted Eating at Endpoint (Non-TRE)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: The participants in the Non-Time Restricted Eating (TRE) alone group were provided with control diets and not instructed to follow the 10-h TRE. The 10-h TRE required participants to consume the provided meals within a 10-h window each day.

Group 1 sample size Number of subjects in the case (exposed) group: 44

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2025-4-22

Curated date: 2025/04/14

Curator: Daberechi

Revision editor(s): Daberechi

Source: Figure 2D and Supplementary Figure 2

Description: Significant taxonomic changes between Non-Time Restricted Eating (Non-TRE) at baseline and Endpoint as accessed using LefSe.

Abundance in Group 1: increased abundance in Non-Time Restricted Eating at Endpoint (Non-TRE)

NCBI	Quality Control	Links
Klebsiella pneumoniae
Escherichia coli
Enterobacter hormaechei
Clostridium sp. AF34-10BH
Weissella confusa
Citrobacter
Enterobacter
Escherichia
Klebsiella
Enterobacterales
Enterobacteriaceae

Revision editor(s): Daberechi

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2025-4-22

Curated date: 2025/04/14

Curator: Daberechi

Revision editor(s): Daberechi

Source: Figure 2D and Supplementary Figure 2

Description: Significant taxonomic changes between Non-Time Restricted Eating (Non-TRE) at baseline and Endpoint as accessed using LefSe.

Abundance in Group 1: decreased abundance in Non-Time Restricted Eating at Endpoint (Non-TRE)

NCBI	Quality Control	Links
Dorea longicatena
Dorea
Mediterraneibacter

Revision editor(s): Daberechi

Experiment 8

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by ChiomaBlessing on 2025-4-22

Curated date: 2025/04/14

Curator: Daberechi

Revision editor(s): Daberechi

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Response to diet Response to diet,response to diet

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Healthy Low Carbohydrate Diet at Baseline (HLCD)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Healthy Low Carbohydrate Diet at Endpoint (HLCD)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: The participants in the Healthy Low Carbohydrate Diet (HLCD) alone group were provided with HLCD and instructed to follow their usual eating regimens during the 12 week feeding trial. The HLCD was a relatively healthy type of LCD consisting of approximately 30%, 50%, and 20% of total energy from carbohydrates, fats, and proteins, emphasizing the consumption of unsaturated fatty acids, plant proteins, and high-quality carbohydrates including whole grains, fresh vegetables, and fruits.

Group 1 sample size Number of subjects in the case (exposed) group: 43

Statistical Analysis

Statistical test: Mann-Whitney (Wilcoxon); T-Test

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: Not specified

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2025-4-22

Curated date: 2025/04/14

Curator: Daberechi

Revision editor(s): Daberechi

Source: Supplementary Figure 3A

Description: Significant taxonomic changes between Healthy Low Carbohydrate Diet (HLCD) at baseline and Endpoint as accessed.

Abundance in Group 1: decreased abundance in Healthy Low Carbohydrate Diet at Endpoint (HLCD)

NCBI	Quality Control	Links
Phocaeicola dorei
Ruminococcus callidus

Revision editor(s): Daberechi

Experiment 9

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by ChiomaBlessing on 2025-4-22

Curated date: 2025/04/14

Curator: Daberechi

Revision editor(s): Daberechi

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Non-Healthy Low Carbohydrate Diet at Baseline (Non-HLCD)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Non-Healthy Low Carbohydrate Diet at Endpoint (Non-HLCD)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: The participants in the Non-Healthy Low Carbohydrate Diet (HLCD) alone group were not provided with HLCD and instructed to follow their usual eating regimens during the 12 week feeding trial.

Group 1 sample size Number of subjects in the case (exposed) group: 44

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2025-4-22

Curated date: 2025/04/14

Curator: Daberechi

Revision editor(s): Daberechi

Source: Supplementary Figure 3B

Description: Significant taxonomic changes between Non-Healthy Low Carbohydrate Diet (Non-HLCD) at baseline and Endpoint as accessed.

Abundance in Group 1: increased abundance in Non-Healthy Low Carbohydrate Diet at Endpoint (Non-HLCD)

NCBI	Quality Control	Links
Dysosmobacter hominis

Revision editor(s): Daberechi

Signature 2