Gut microbiome and serum metabolome alterations associated with lactose intolerance (LI): a case‒control study and paired-sample study based on the American Gut Project (AGP)/Experiment 1
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Reviewed Marked as Reviewed by Svetlana up on 2024-11-27
Subjects
- Location of subjects
- Canada
- United Kingdom
- 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
- Lactose intolerance lactase persistence,lactose intolerance,lactose intolerance (disease),LM - lactose malabsorption,Lactose intolerance
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Participants without Lactose Intolerance(Non-LI)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Participants with Lactose Intolerance(LI)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with condition, Lactose intolerance (LI) which is a prevalent condition characterized by gastrointestinal symptoms that arise following lactose consumption.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 562
- Group 1 sample size Number of subjects in the case (exposed) group
- 562
- 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).
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
- Matched on Factors on which subjects have been matched on in a case-control study
- age, alcohol consumption measurement, body mass index, diet, geographic area, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-11-27
Source: Fig 1c
Description: Gut microbiota alterations between LI cohort and non-LI cohort assessed using the linear discriminative analysis (LDA) effect size (LEfSe).
Abundance in Group 1: increased abundance in Participants with Lactose Intolerance(LI)
Revision editor(s): Nathcynthia, Rahila, Tosin
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-11-27
Source: Fig 1c
Description: Gut microbiota alterations between LI cohort and non-LI cohort assessed using the linear discriminative analysis (LDA) effect size (LEfSe)'.
Abundance in Group 1: decreased abundance in Participants with Lactose Intolerance(LI)
Revision editor(s): Nathcynthia, Rahila, Tosin
