Microbiome Responses to an Uncontrolled Short-Term Diet Intervention in the Frame of the Citizen Science Project

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Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Klimenko NS, Tyakht AV, Popenko AS, Vasiliev AS, Altukhov IA, Ischenko DS, Shashkova TI, Efimova DA, Nikogosov DA, Osipenko DA, Musienko SV, Selezneva KS, Baranova A, Kurilshikov AM, Toshchakov SM, Korzhenkov AA, Samarov NI, Shevchenko MA, Tepliuk AV, Alexeev DG
Journal
Nutrients
Year
2018
Keywords:
16S rRNA metagenomics, citizen science, gut microbiota, intervention, microbiome stability, personalized diet, responders
Personalized nutrition is of increasing interest to individuals actively monitoring their health. The relations between the duration of diet intervention and the effects on gut microbiota have yet to be elucidated. Here we examined the associations of short-term dietary changes, long-term dietary habits and lifestyle with gut microbiota. Stool samples from 248 citizen-science volunteers were collected before and after a self-reported 2-week personalized diet intervention, then analyzed using 16S rRNA sequencing. Considerable correlations between long-term dietary habits and gut community structure were detected. A higher intake of vegetables and fruits was associated with increased levels of butyrate-producing Clostridiales and higher community richness. A paired comparison of the metagenomes before and after the 2-week intervention showed that even a brief, uncontrolled intervention produced profound changes in community structure: resulting in decreased levels of Bacteroidaceae, Porphyromonadaceae and Rikenellaceae families and decreased alpha-diversity coupled with an increase of Methanobrevibacter, Bifidobacterium, Clostridium and butyrate-producing Lachnospiraceae- as well as the prevalence of a permatype (a bootstrapping-based variation of enterotype) associated with a higher diversity of diet. The response of microbiota to the intervention was dependent on the initial microbiota state. These findings pave the way for the development of an individualized diet.

Experiment 1


Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Victoria

Subjects

Location of subjects
Russian Federation
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
high vegetable, fruit, grain
Group 1 name Corresponds to the case (exposed) group for case-control studies
Low vegetable, fruit, grains,
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
low fiber
Group 0 sample size Number of subjects in the control (unexposed) group
215
Group 1 sample size Number of subjects in the case (exposed) group
215

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


Signature 1

Needs review

Curated date: 2021/01/10

Curator: Lora Kasselman

Revision editor(s): WikiWorks

Source: Figure 1 and Figure 2

Description: Figure 1. Associations of the microbial taxa with long-term dietary habits and other factors from the questionnaire (n = 207 subjects). Analysis was performed for the baseline samples at taxonomic levels from species to phyla. Rows are sorted in alphabetic order. Cell color denotes the value of the linear model coefficient from the MaAsLin analysis. All significant associations (FDR adjusted p < 0.1) are marked with one of the symbols (&, #, @): “&”. Figure 2. Major changes in the gut community structure of the volunteers after following the dietary recommendations. Red branches of the cladogram denote the taxa that were increased in abundance, while the blue ones—decreased. Significance criterion: p < 0.05 in metagenomeSeq model and log10 of the effect size >2 in LEfSe method (n = 430 paired samples).

Abundance in Group 1: increased abundance in Low vegetable, fruit, grains,

NCBI Quality ControlLinks
Bacteroidaceae
Porphyromonadaceae
Prevotellaceae
Rikenellaceae
Oscillospiraceae
Acidaminococcaceae
Veillonellaceae
Sutterellaceae
Desulfovibrionaceae
Lactobacillaceae

Revision editor(s): WikiWorks

Signature 2

Needs review

Curated date: 2021/01/10

Curator: Lora Kasselman

Revision editor(s): WikiWorks

Source: Figure 1 and Figure 2

Description: Figure 1. Associations of the microbial taxa with long-term dietary habits and other factors from the questionnaire (n = 207 subjects). Analysis was performed for the baseline samples at taxonomic levels from species to phyla. Rows are sorted in alphabetic order. Cell color denotes the value of the linear model coefficient from the MaAsLin analysis. All significant associations (FDR adjusted p < 0.1) are marked with one of the symbols (&, #, @): “&”. Figure 2. Major changes in the gut community structure of the volunteers after following the dietary recommendations. Red branches of the cladogram denote the taxa that were increased in abundance, while the blue ones—decreased. Significance criterion: p < 0.05 in metagenomeSeq model and log10 of the effect size >2 in LEfSe method (n = 430 paired samples).

Abundance in Group 1: decreased abundance in Low vegetable, fruit, grains,

NCBI Quality ControlLinks
Clostridium
Eubacterium
Lachnospiraceae
Oscillibacter
Methanobacteriaceae
Bifidobacteriaceae
Coriobacteriaceae
Staphylococcaceae
Enterococcaceae
Streptococcaceae
Christensenellaceae
Clostridiaceae
Erysipelotrichaceae
Bacillota
Sphingomonadaceae
Enterobacteriaceae
Verrucomicrobiaceae

Revision editor(s): WikiWorks

Experiment 2


Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

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
before dietary intervention
Group 1 name Corresponds to the case (exposed) group for case-control studies
two weeks after a dietry intervention
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Not specified

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: Shaimaa Elsafoury

Revision editor(s): WikiWorks

Source: Figure S8

Description: Сhanges in relative abundance of microbial taxa after dietary intervention. The analysis was performed using metagenomeSeq. For each taxon, the columns “Beta” and “Eff. size” contain the values of linear model coefficient and effect size calculated using LEfSe.

Abundance in Group 1: increased abundance in two weeks after a dietry intervention

NCBI Quality ControlLinks
Eggerthella lenta
Howardella ureilytica
Eggerthella
Lactococcus lactis
Bifidobacterium longum subsp. longum
Lactococcus
Streptococcus
Verrucomicrobiaceae
Enterococcus
Streptococcaceae
Enterococcaceae
Verrucomicrobiia
Verrucomicrobiales
Dorea longicatena
Verrucomicrobiota
Alphaproteobacteria
Eubacterium
Bacilli
Bifidobacterium adolescentis
Collinsella aerofaciens
Collinsella
Clostridium
Clostridiaceae
Eubacteriales
Clostridia
Bifidobacterium
Bifidobacteriaceae
Blautia

Revision editor(s): WikiWorks

Signature 2

Reviewed Marked as Reviewed by Fatima on 2021/08/11

Curated date: 2021/01/10

Curator: Shaimaa Elsafoury

Revision editor(s): Fatima, WikiWorks

Source: Figure S8

Description: Сhanges in relative abundance of microbial taxa after dietary intervention. The analysis was performed using metagenomeSeq. For each taxon, the columns “Beta” and “Eff. size” contain the values of linear model coefficient and effect size calculated using LEfSe.

Abundance in Group 1: decreased abundance in two weeks after a dietry intervention

NCBI Quality ControlLinks
Bacteroides clarus
Bacteroides eggerthii
Deltaproteobacteria
Desulfovibrio
Desulfovibrionales
Dialister
Faecalibacterium
Lachnospira eligens
Lactobacillaceae
Phascolarctobacterium succinatutens
Phocaeicola plebeius
Roseburia hominis
Ruminococcus
Slackia
Slackia isoflavoniconvertens
Veillonella
Veillonellaceae
[Ruminococcus] lactaris
[Eubacterium] siraeum

Revision editor(s): Fatima, WikiWorks