Predictability and persistence of prebiotic dietary supplementation in a healthy human cohort

Study information

Needs review

study design

randomized controlled trial

Citation

PMID PubMed identifier for scientific articles.

30139999

DOI Digital object identifier for electronic documents.

10.1038/s41598-018-30783-1

URI

Authors

Gurry T, Gibbons SM, Nguyen LTT, Kearney SM, Ananthakrishnan A, Jiang X, Duvallet C, Kassam Z, Alm EJ

Journal

Scientific reports

Year

2018

Dietary interventions to manipulate the human gut microbiome for improved health have received increasing attention. However, their design has been limited by a lack of understanding of the quantitative impact of diet on a host's microbiota. We present a highly controlled diet perturbation experiment in a healthy, human cohort in which individual micronutrients are spiked in against a standardized background. We identify strong and predictable responses of specific microbes across participants consuming prebiotic spike-ins, at the level of both strains and functional genes, suggesting fine-scale resource partitioning in the human gut. No predictable responses to non-prebiotic micronutrients were found. Surprisingly, we did not observe decreases in day-to-day variability of the microbiota compared to a complex, varying diet, and instead found evidence of diet-induced stress and an associated loss of biodiversity. Our data offer insights into the effect of a low complexity diet on the gut microbiome, and suggest that effective personalized dietary interventions will rely on functional, strain-level characterization of a patient's microbiota.

Experiment 1

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Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Fatima, 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

Group 0 name Corresponds to the control (unexposed) group for case-control studies: day 6 of PECTIN spike-in

Group 1 name Corresponds to the case (exposed) group for case-control studies: day 3 of PECTIN spike-in

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: before pectin spike-in

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): 6 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).: raw counts

Statistical test: DESeq2

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.1

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

Signature 1

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Curated date: 2021/01/10

Curator: Lora Kasselman

Revision editor(s): WikiWorks

Source: Figure 1b and text

Description: OTUs that showed statistically significant (DESeq. 2, FDR < 0.1) differential abundance on day 6 compared to day 3 in response to particular spike-ins. Mean relative abundances are computed across all participants and then converted to Z-scores across timepoints, to illustrate relative changes through time. - PECTIN

Abundance in Group 1: decreased abundance in day 3 of PECTIN spike-in

NCBI	Quality Control	Links
Lachnospiraceae
Roseburia
Bacteroides
Sporobacter
Oscillospiraceae
Faecalibacterium prausnitzii

Revision editor(s): WikiWorks

Experiment 2

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Your review change was submittedDuplicate this Experiment Add a new Signature

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Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Lwaldron, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: day 6 of INULIN spike-in

Group 1 name Corresponds to the case (exposed) group for case-control studies: day 3 of INULIN spike-in

Lab analysis

Statistical Analysis

Signature 1

Edit History Delete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2021/01/10

Curator: Lora Kasselman

Revision editor(s): WikiWorks

Source: Figure 1b and text

Description: OTUs that showed statistically significant (DESeq. 2, FDR < 0.1) differential abundance on day 6 compared to day 3 in response to particular spike-ins. Mean relative abundances are computed across all participants and then converted to Z-scores across timepoints, to illustrate relative changes through time. - INULIN

Abundance in Group 1: decreased abundance in day 3 of INULIN spike-in

NCBI	Quality Control	Links
Lachnospiraceae
Bacteroides uniformis
Faecalibacterium prausnitzii

Revision editor(s): WikiWorks