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

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Reviewed Marked as Reviewed by Chloe on 2022/03/18
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
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


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

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

NCBI Quality ControlLinks
Mediterraneibacter gnavus
[Ruminococcus] torques

Revision editor(s): Chloe, Lorakasselman

Signature 2

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 ControlLinks
Bacteroides ovatus
Faecalibacterium prausnitzii
Parabacteroides merdae
Segatella copri
Streptococcus thermophilus
Agathobacter rectalis

Revision editor(s): Chloe, Lorakasselman