Role of dietary fiber in the recovery of the human gut microbiome and its metabolome

Study information

Reviewed Marked as Reviewed by Chloe on 2022/03/18

study design

randomized controlled trial

Citation

PMID PubMed identifier for scientific articles.

33440171

DOI Digital object identifier for electronic documents.

10.1016/j.chom.2020.12.012

URI

Authors

Tanes C, Bittinger K, Gao Y, Friedman ES, Nessel L, Paladhi UR, Chau L, Panfen E, Fischbach MA, Braun J, Xavier RJ, Clish CB, Li H, Bushman FD, Lewis JD, Wu GD

Journal

Cell host & microbe

Year

2021

Keywords:

dietary fiber, vegan, omnivore, amino acid, enteral nutrition, metabolome, microbiome

Gut microbiota metabolites may be important for host health, yet few studies investigate the correlation between human gut microbiome and production of fecal metabolites and their impact on the plasma metabolome. Since gut microbiota metabolites are influenced by diet, we performed a longitudinal analysis of the impact of three divergent diets, vegan, omnivore, and a synthetic enteral nutrition (EEN) diet lacking fiber, on the human gut microbiome and its metabolome, including after a microbiota depletion intervention. Omnivore and vegan, but not EEN, diets altered fecal amino acid levels by supporting the growth of Firmicutes capable of amino acid metabolism. This correlated with relative abundance of a sizable number of fecal amino acid metabolites, some not previously associated with the gut microbiota. The effect on the plasma metabolome, in contrast, were modest. The impact of diet, particularly fiber, on the human microbiome influences broad classes of metabolites that may modify health.

Experiment 1

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Reviewed Marked as Reviewed by Chloe on 2022/03/18

Curated date: 2021/11/11

Curator: Lorakasselman

Revision editor(s): WikiWorks, Chloe, Lorakasselman, Atrayees, Victoria

Subjects

Location of subjects: United States of America

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 Dietary,Diets,Diet,diet

Group 0 name Corresponds to the control (unexposed) group for case-control studies: regular fiber omnivore diet

Group 1 name Corresponds to the case (exposed) group for case-control studies: no fiber liquid omnivore diet

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: omnivores randomized to an enteral liquid nutrition diet devoid of any fiber (but similar in profile to regular food omnivore group)

Group 0 sample size Number of subjects in the control (unexposed) group: 10

Group 1 sample size Number of subjects in the case (exposed) group: 10

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).: raw counts

Statistical test: Linear Regression

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

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: age, body mass index

Alpha Diversity

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

Signature 1

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Reviewed Marked as Reviewed by Chloe on 2022/03/18

Curated date: 2021/11/11

Curator: Lorakasselman

Revision editor(s): Chloe, Lorakasselman

Source: Figure 2B

Description: The taxa that are significantly different in EEN diet compared with the omnivore diet during the diet phase based on linear mixed effects models (q < 0.05). The taxa that increase during the diet phase with the EEN diet are annotated in black and the taxa that decrease in abundance are annotated with white squares. Taxa are further annotated with the Clostridia clade to which they belong

Abundance in Group 1: increased abundance in no fiber liquid omnivore diet

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Mediterraneibacter gnavus
[Ruminococcus] torques

Revision editor(s): Chloe, Lorakasselman

Signature 2

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Reviewed Marked as Reviewed by Chloe on 2022/03/18

Curated date: 2021/11/11

Curator: Lorakasselman

Revision editor(s): Chloe, Lorakasselman

Source: Figure 2B

Description: The taxa that are significantly different in EEN diet compared with the omnivore diet during the diet phase based on linear mixed effects models (q < 0.05). The taxa that increase during the diet phase with the EEN diet are annotated in black and the taxa that decrease in abundance are annotated with white squares. Taxa are further annotated with the Clostridia clade to which they belong.

Abundance in Group 1: decreased abundance in no fiber liquid omnivore diet

NCBI	Quality Control	Links
Bacteroides ovatus
Faecalibacterium prausnitzii
Parabacteroides merdae
Segatella copri
Streptococcus thermophilus
Agathobacter rectalis

Revision editor(s): Chloe, Lorakasselman