Linking long-term dietary patterns with gut microbial enterotypes

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Needs review
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD, Lewis JD
Journal
Science (New York, N.Y.)
Year
2011
Diet strongly affects human health, partly by modulating gut microbiome composition. We used diet inventories and 16S rDNA sequencing to characterize fecal samples from 98 individuals. Fecal communities clustered into enterotypes distinguished primarily by levels of Bacteroides and Prevotella. Enterotypes were strongly associated with long-term diets, particularly protein and animal fat (Bacteroides) versus carbohydrates (Prevotella). A controlled-feeding study of 10 subjects showed that microbiome composition changed detectably within 24 hours of initiating a high-fat/low-fiber or low-fat/high-fiber diet, but that enterotype identity remained stable during the 10-day study. Thus, alternative enterotype states are associated with long-term diet.

Experiment 1


Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, 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
low animal protein
Group 1 name Corresponds to the case (exposed) group for case-control studies
High animal protein
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
high protein / low fiber
Group 0 sample size Number of subjects in the control (unexposed) group
98
Group 1 sample size Number of subjects in the case (exposed) group
98
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
V1-V2
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Roche454

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Statistical test
ANOVA
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


Signature 1

Needs review

Curated date: 2021/01/10

Curator: Lora Kasselman

Revision editor(s): WikiWorks

Source: Figure 2C and text

Description: The association of dietary components with each enterotype. The strength and direction of each association, as measured by the means of the standardized nutrient measurements, is shown by the color key at the lower right. Enterotype is shown at the right. Red indicates greater amounts, blue lesser amounts of each nutrient in each enterotype (complete lists of nutrients are in table S2). Columns were clustered by Euclidean distance.

Abundance in Group 1: increased abundance in High animal protein

NCBI Quality ControlLinks
Bacteroides

Revision editor(s): WikiWorks

Signature 2

Needs review

Curated date: 2021/01/10

Curator: Lora Kasselman

Revision editor(s): WikiWorks

Source: Figure 2C and text

Description: The association of dietary components with each enterotype. The strength and direction of each association, as measured by the means of the standardized nutrient measurements, is shown by the color key at the lower right. Enterotype is shown at the right. Red indicates greater amounts, blue lesser amounts of each nutrient in each enterotype (complete lists of nutrients are in table S2). Columns were clustered by Euclidean distance.

Abundance in Group 1: decreased abundance in High animal protein

NCBI Quality ControlLinks
Prevotellaceae

Revision editor(s): WikiWorks

Experiment 2


Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
high fiber
Group 1 name Corresponds to the case (exposed) group for case-control studies
Low fiber

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2021/01/10

Curator: Lora Kasselman

Revision editor(s): WikiWorks

Source: Figure 2C and text

Description: The association of dietary components with each enterotype. The strength and direction of each association, as measured by the means of the standardized nutrient measurements, is shown by the color key at the lower right. Enterotype is shown at the right. Red indicates greater amounts, blue lesser amounts of each nutrient in each enterotype (complete lists of nutrients are in table S2). Columns were clustered by Euclidean distance.

Abundance in Group 1: increased abundance in Low fiber

NCBI Quality ControlLinks
Bacteroidota
Actinomycetota

Revision editor(s): WikiWorks

Signature 2

Needs review

Curated date: 2021/01/10

Curator: Lora Kasselman

Revision editor(s): WikiWorks

Source: Figure 2C and text

Description: The association of dietary components with each enterotype. The strength and direction of each association, as measured by the means of the standardized nutrient measurements, is shown by the color key at the lower right. Enterotype is shown at the right. Red indicates greater amounts, blue lesser amounts of each nutrient in each enterotype (complete lists of nutrients are in table S2). Columns were clustered by Euclidean distance.

Abundance in Group 1: decreased abundance in Low fiber

NCBI Quality ControlLinks
Actinomycetota

Revision editor(s): WikiWorks