Comparative study of gut microbiota reveals the adaptive strategies of gibbons living in suboptimal habitats
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Nomascus hainanus
- 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 measurement Diet measurement,diet measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low + Middle feeding group - Nomascus hainanus
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High feeding group - Nomascus hainanus
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- These refers to gibbon species living in high-quality (Nomascus hainanus) habitats with stable fruit production; who consumed high proportion of leaf per month.
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
Source: Fig. 5, Supplementary Table 6
Description: Linear Discriminant Analysis Effect Size (LEfSe) analyses revealed significant contributions to the differences in abundance across various bacteria taxonomic levels, from phylum to genus, among different gibbon species with varying proportions of leaf consumption.
Abundance in Group 1: increased abundance in High feeding group - Nomascus hainanus
Revision editor(s): KateRasheed
Experiment 2
Subjects
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Nomascus concolor
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- High + Middle feeding group - Nomascus concolor
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Low feeding group - Nomascus concolor
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- These refers to gibbon species living in suboptimal habitats with lower and more variable fruit availability, relying more on leaves. They consumed low proportion of leaf per month.
Lab analysis
Statistical Analysis
Signature 1
Source: Fig. 5, Supplementary Table 6
Description: Linear Discriminant Analysis Effect Size (LEfSe) analyses revealed significant contributions to the differences in abundance across various bacteria taxonomic levels, from phylum to genus, among different gibbon species with varying proportions of leaf consumption.
Abundance in Group 1: increased abundance in Low feeding group - Nomascus concolor
Revision editor(s): KateRasheed
Experiment 3
Subjects
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Hoolock tianxing
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low + Middle feeding group - Hoolock tianxing
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High feeding group - Hoolock tianxing
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- These refers to gibbon species living in suboptimal habitats with lower and more variable fruit availability, relying more on leaves. They had the lowest monthly fruit intake. This group consumed high proportion of leaf per month.
Lab analysis
Statistical Analysis
Signature 1
Source: Fig. 5, Supplementary Table 6
Description: Linear Discriminant Analysis Effect Size (LEfSe) analyses revealed significant contributions to the differences in abundance across various bacteria taxonomic levels, from phylum to genus, among different gibbon species with varying proportions of leaf consumption.
Abundance in Group 1: increased abundance in High feeding group - Hoolock tianxing
Revision editor(s): KateRasheed
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low + High feeding group - Hoolock tianxing
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Middle feeding group - Hoolock tianxing
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- These refers to gibbon species living in suboptimal habitats with lower and more variable fruit availability, relying more on leaves. They had the lowest monthly fruit intake. This group consumed middle (not high or low) proportion of leaf per month.
Lab analysis
Statistical Analysis
Signature 1
Source: Fig. 5, Supplementary Table 6
Description: Linear Discriminant Analysis Effect Size (LEfSe) analyses revealed significant contributions to the differences in abundance across various bacteria taxonomic levels, from phylum to genus, among different gibbon species with varying proportions of leaf consumption.
Abundance in Group 1: increased abundance in Middle feeding group - Hoolock tianxing
Revision editor(s): KateRasheed
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- High + Middle feeding group - Hoolock tianxing
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Low feeding group - Hoolock tianxing
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- These refers to gibbon species living in suboptimal habitats with lower and more variable fruit availability, relying more on leaves. They had the lowest monthly fruit intake. This group consumed low proportion of leaf per month.
Lab analysis
Statistical Analysis
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
Signature 1
Source: Fig. 5, Supplementary Table 6
Description: Linear Discriminant Analysis Effect Size (LEfSe) analyses revealed significant contributions to the differences in abundance across various bacteria taxonomic levels, from phylum to genus, among different gibbon species with varying proportions of leaf consumption.
Abundance in Group 1: increased abundance in Low feeding group - Hoolock tianxing
Revision editor(s): KateRasheed
Experiment 6
Subjects
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Nomascus hainanus
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- High + Middle feeding group - Nomascus hainanus
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Low feeding group - Nomascus hainanus
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- These refers to gibbon species living in high-quality (Nomascus hainanus) habitats with stable fruit production; who consumed low proportion of leaf per month.
Lab analysis
Statistical Analysis
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Signature 1
Source: Fig. 5, Supplementary Table 6
Description: Linear Discriminant Analysis Effect Size (LEfSe) analyses revealed significant contributions to the differences in abundance across various bacteria taxonomic levels, from phylum to genus, among different gibbon species with varying proportions of leaf consumption.
Abundance in Group 1: increased abundance in Low feeding group - Nomascus hainanus
Revision editor(s): KateRasheed
Experiment 7
Subjects
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Nomascus concolor
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low + Middle feeding group - Nomascus concolor
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High feeding group - Nomascus concolor
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- These refers to gibbon species living in suboptimal habitats with lower and more variable fruit availability, relying more on leaves. They consumed high proportion of leaf per month.
Lab analysis
Statistical Analysis
Signature 1
Source: Fig. 5, Supplementary Table 6
Description: Linear Discriminant Analysis Effect Size (LEfSe) analyses revealed significant contributions to the differences in abundance across various bacteria taxonomic levels, from phylum to genus, among different gibbon species with varying proportions of leaf consumption.
Abundance in Group 1: increased abundance in High feeding group - Nomascus concolor
Revision editor(s): KateRasheed
Experiment 8
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low + High feeding group - Nomascus concolor
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Middle feeding group - Nomascus concolor
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- These refers to gibbon species living in suboptimal habitats with lower and more variable fruit availability, relying more on leaves. They consumed middle (not high or low) proportion of leaf per month.
Lab analysis
Statistical Analysis
Signature 1
Source: Fig. 5, Supplementary Table 6
Description: Linear Discriminant Analysis Effect Size (LEfSe) analyses revealed significant contributions to the differences in abundance across various bacteria taxonomic levels, from phylum to genus, among different gibbon species with varying proportions of leaf consumption.
Abundance in Group 1: increased abundance in Middle feeding group - Nomascus concolor
| NCBI | Quality Control | Links |
|---|---|---|
| uncultured Anaeroplasmataceaeuncultured Anaeroplasmataceae |
Revision editor(s): KateRasheed
Experiment 9
Subjects
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Nomascus hainanus
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- High + Low feeding group - Nomascus hainanus
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Middle feeding group - Nomascus hainanus
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- These refers to gibbon species living in high-quality (Nomascus hainanus) habitats with stable fruit production; who consumed middle (not high or low) proportion of leaf per month.
Lab analysis
Statistical Analysis
Signature 1
Source: Fig. 5, Supplementary Table 6
Description: Linear Discriminant Analysis Effect Size (LEfSe) analyses revealed significant contributions to the differences in abundance across various bacteria taxonomic levels, from phylum to genus, among different gibbon species with varying proportions of leaf consumption.
Abundance in Group 1: increased abundance in Middle feeding group - Nomascus hainanus
Revision editor(s): KateRasheed
