Shifts in microbial diversity, composition, and functionality in the gut and genital microbiome during a natural SIV infection in vervet monkeys
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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
- South Africa
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Chlorocebus pygerythrus
- 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
- Simian immunodeficiency virus infection Simian immunodeficiency virus caused disease or disorder,Simian immunodeficiency virus disease or disorder,simian immunodeficiency virus infection,Simian immunodeficiency virus infectious disease,SIV,Simian immunodeficiency virus infection
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Simian Immunodeficiency Virus (SIV) negative
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Simian Immunodeficiency Virus (SIV) positive
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- SIV positive refers to vervet monkeys that are infected with Simian Immunodeficiency Virus (SIV)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 11
- Group 1 sample size Number of subjects in the case (exposed) group
- 33
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).
- raw counts
- Statistical test
- DESeq2
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, 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
- increased
Signature 1
Source: Fig. 3C
Description: Differential abundance of microbiota between SIV infected and uninfected in fecal samples.
Abundance in Group 1: increased abundance in Simian Immunodeficiency Virus (SIV) positive
Revision editor(s): KateRasheed
Signature 2
Source: Fig. 3C
Description: Differential abundance of microbiota between SIV infected and uninfected in fecal samples.
Abundance in Group 1: decreased abundance in Simian Immunodeficiency Virus (SIV) positive
| NCBI | Quality Control | Links |
|---|---|---|
| Succinivibrio |
Revision editor(s): KateRasheed
Experiment 2
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Rectum Intestinum rectum,Rectal sac,Terminal portion of intestine,Terminal portion of large intestine,Rectum,rectum
- Group 0 sample size Number of subjects in the control (unexposed) group
- 41
- Group 1 sample size Number of subjects in the case (exposed) group
- 62
Lab analysis
Statistical Analysis
Signature 1
Source: Fig. 3C
Description: Differential abundance of microbiota between SIV infected and uninfected in rectal samples.
Abundance in Group 1: decreased abundance in Simian Immunodeficiency Virus (SIV) positive
| NCBI | Quality Control | Links |
|---|---|---|
| Butyrivibrio | ||
| Oscillospira | ||
| Ruminococcus 2Ruminococcus 2 | ||
| Succinivibrio |
Revision editor(s): KateRasheed
Experiment 3
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Vagina Vagina,vagina,Distal oviductal region,Distal portion of oviduct,Vaginae
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 41
Lab analysis
Statistical Analysis
Signature 1
Source: Fig. 3C
Description: Differential abundance of microbiota between SIV infected and uninfected in vaginal samples.
Abundance in Group 1: increased abundance in Simian Immunodeficiency Virus (SIV) positive
| NCBI | Quality Control | Links |
|---|---|---|
| prevotellaceae UCG-003prevotellaceae UCG-003 | ||
| Prevotella sp. CAG:873 |
Revision editor(s): KateRasheed
Signature 2
Source: Fig. 3C
Description: Differential abundance of microbiota between SIV infected and uninfected in vaginal samples.
Abundance in Group 1: decreased abundance in Simian Immunodeficiency Virus (SIV) positive
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Bacteroides | ||
| Blautia | ||
| Corynebacterium | ||
| Rodentibacter | ||
| Sarcina | ||
| Streptococcus | ||
| Escherichia/shigellaEscherichia/shigella | ||
| Prevotella 9Prevotella 9 |
Revision editor(s): KateRasheed
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Alkaline
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Acidic
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Acidic refers to the vaginal-PH below 7. It is found in vagitype A of vervets monkeys.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 21
- Group 1 sample size Number of subjects in the case (exposed) group
- 16
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Supplementary Figure 4D
Description: Differentially abundant microbial genera in acidic vaginal samples vs. alkaline vaginal samples.
Abundance in Group 1: increased abundance in Acidic
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Bacteroides | ||
| Blautia | ||
| Sarcina | ||
| Ureaplasma | ||
| Streptococcus | ||
| Aerococcus | ||
| Trichococcus | ||
| Carnobacteriaceae | ||
| family XIfamily XI |
Revision editor(s): KateRasheed
Signature 2
Source: Supplementary Figure 4D
Description: Differentially abundant microbial genera in acidic vaginal samples vs. alkaline vaginal samples.
Abundance in Group 1: decreased abundance in Acidic
Revision editor(s): KateRasheed
Experiment 5
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Rectum Intestinum rectum,Rectal sac,Terminal portion of intestine,Terminal portion of large intestine,Rectum,rectum
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Free_State
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- KwaZulu-Natal
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- KwaZulu-Natal refers to vervet monkeys representing the Indian Ocean Coastal Belt (N = 33) and Savanna (N = 12) biomes from the KwaZulu-Natal Province (KZN)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 57
- Group 1 sample size Number of subjects in the case (exposed) group
- 45
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex, Confounders controlled for: "SIV infection status" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.SIV infection status
Signature 1
Source: Supplementary Figure 5E
Description: Differentially abundant taxa between KZN and FS in rectal microbiome
Abundance in Group 1: increased abundance in KwaZulu-Natal
Revision editor(s): KateRasheed
Signature 2
Source: Supplementary Figure 5E
Description: Differentially abundant taxa between KZN and FS in rectal microbiome
Abundance in Group 1: decreased abundance in KwaZulu-Natal
Revision editor(s): KateRasheed
Experiment 6
Subjects
- 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
- Group 0 sample size Number of subjects in the control (unexposed) group
- 27
- Group 1 sample size Number of subjects in the case (exposed) group
- 16
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary Figure 5F
Description: Differentially abundant taxa between KZN and FS in fecal microbiome
Abundance in Group 1: increased abundance in KwaZulu-Natal
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella 1Prevotella 1 | ||
| Fibrobacter | ||
| Solobacterium | ||
| Alloprevotella |
Revision editor(s): KateRasheed
Signature 2
Source: Supplementary Figure 5F
Description: Differentially abundant taxa between KZN and FS in fecal microbiome
Abundance in Group 1: decreased abundance in KwaZulu-Natal
Revision editor(s): KateRasheed
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Female
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Male
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Male refers to the masculine gender of the vervet monkeys.
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Not specified
Signature 1
Source: Supplementary Figure 10A
Description: Differentially abundant taxa in males compared to females in feces
Abundance in Group 1: decreased abundance in Male
| NCBI | Quality Control | Links |
|---|---|---|
| Candidatus Paracaedibacteraceae | ||
| Delftia |
Revision editor(s): KateRasheed
Experiment 8
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Rectum Intestinum rectum,Rectal sac,Terminal portion of intestine,Terminal portion of large intestine,Rectum,rectum
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary Figure 10B
Description: Differentially abundant taxa in males compared to females in rectum
Abundance in Group 1: increased abundance in Male
| NCBI | Quality Control | Links |
|---|---|---|
| Dehalobacterium | ||
| Selenomonas | ||
| Spirochaetes bacterium GWE2_31_10 | ||
| Clostridium sp. CAG:352 |
Revision editor(s): KateRasheed
Signature 2
Source: Supplementary Figure 10B
Description: Differentially abundant taxa in males compared to females in rectum
Abundance in Group 1: decreased abundance in Male
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella | ||
| Parvimonas | ||
| Aerococcus | ||
| Rodentibacter | ||
| Mobiluncus |
Revision editor(s): KateRasheed
Experiment 9
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Adult
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Infant
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Infant refers to vervet monkeys in their early years of life.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 76
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- sex, Confounders controlled for: "province" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.province, Confounders controlled for: "SIV status" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.SIV status
Signature 1
Source: Supplementary Figure 11B
Description: Differentially abundant genera between the rectal microbiome in infants and adults.
Abundance in Group 1: increased abundance in Infant
Revision editor(s): KateRasheed
Signature 2
Source: Supplementary Figure 11B
Description: Differentially abundant genera between the rectal microbiome in infants and adults.
Abundance in Group 1: decreased abundance in Infant
| NCBI | Quality Control | Links |
|---|---|---|
| Dialister | ||
| Sutterella | ||
| Corynebacterium | ||
| Thomasclavelia | ||
| Herbinix |
Revision editor(s): KateRasheed
Experiment 10
Subjects
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Acute
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Chronic
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Chronic refers to the severity of the SIV infection in vervet monkeys.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 4
- Group 1 sample size Number of subjects in the case (exposed) group
- 23
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, 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
- unchanged
Signature 1
Source: Supplementary Figure 14
Description: Differentially abundant fecal microbiome in chronic vs. acute SIV infection
Abundance in Group 1: increased abundance in Chronic
| NCBI | Quality Control | Links |
|---|---|---|
| Herbinix | ||
| Ruminococcaceae UCG-009Ruminococcaceae UCG-009 | ||
| Burkholderiaceae |
Revision editor(s): KateRasheed
Signature 2
Source: Supplementary Figure 14
Description: Differentially abundant fecal microbiome in chronic vs. acute SIV infection
Abundance in Group 1: decreased abundance in Chronic
| NCBI | Quality Control | Links |
|---|---|---|
| Acetitomaculum |
Revision editor(s): KateRasheed
Experiment 11
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Rectum Intestinum rectum,Rectal sac,Terminal portion of intestine,Terminal portion of large intestine,Rectum,rectum
- Group 0 sample size Number of subjects in the control (unexposed) group
- 11
- Group 1 sample size Number of subjects in the case (exposed) group
- 43
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Supplementary Figure 14
Description: Differentially abundant rectal microbiome in chronic vs. acute SIV infection
Abundance in Group 1: increased abundance in Chronic
| NCBI | Quality Control | Links |
|---|---|---|
| Actinotignum | ||
| Facklamia | ||
| Butyricicoccus |
Revision editor(s): KateRasheed
Experiment 12
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Vagina Vagina,vagina,Distal oviductal region,Distal portion of oviduct,Vaginae
- Group 0 sample size Number of subjects in the control (unexposed) group
- 6
- Group 1 sample size Number of subjects in the case (exposed) group
- 30
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Supplementary Figure 14
Description: Differentially abundant vaginal microbiome in chronic vs. acute SIV infection
Abundance in Group 1: increased abundance in Chronic
Revision editor(s): KateRasheed
