Microbiome Responses to an Uncontrolled Short-Term Diet Intervention in the Frame of the Citizen Science Project/Experiment 2

From BugSigDB


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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

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
before dietary intervention
Group 1 name Corresponds to the case (exposed) group for case-control studies
two weeks after a dietry intervention
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

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

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
Verrucomicrobiae
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