Alterations in the Gut Microbiota and Metabolomics of Seafarers after a Six-Month Sea Voyage/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-4-5
Subjects
- Location of subjects
- Thailand
- 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
- Seasonal gut microbiome measurement Seasonal gut microbiome measurement,seasonal gut microbiome measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Day 0
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Day 180
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Seafarers at the end (day 180) of the 6-month voyage
- Group 0 sample size Number of subjects in the control (unexposed) group
- 30
- Group 1 sample size Number of subjects in the case (exposed) group
- 30
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- None
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-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
- Mann-Whitney (Wilcoxon)
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-4-5
Source: Fig. 1c, Fig. 1d
Description: Differential relative abundances of bacterial genera between day 0 and day 180 of the voyage. *, P , 0.05; **, P , 0.01. (Wilcoxon rank sum test and LeFse)
Abundance in Group 1: increased abundance in Day 180
Revision editor(s): Scholastica, Welile
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-4-5
Source: Fig. 1c, Fig. 1d
Description: Differential relative abundances of bacterial genera between day 0 and day 180 of the voyage. *, P , 0.05; **, P , 0.01. (Wilcoxon rank sum test and LeFse)
Abundance in Group 1: decreased abundance in Day 180
Revision editor(s): Scholastica, Welile
