Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism
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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
Curated date: 2025/01/20
Curator:
Revision editor(s):
Subjects
- Location of subjects
- Finland
- 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
- Postpartum Postpartum,postpartum
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Gestational week 27
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mothers at delivery
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Women at the time of childbirth
- Group 0 sample size Number of subjects in the control (unexposed) group
- 69
- Group 1 sample size Number of subjects in the case (exposed) group
- 63
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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).
- arcsine square-root
- Statistical test
- MaAsLin2
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.25
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Signature 2
Source: Figure 2A
Description: Differences in species at delivery compared to gestational week 27
Abundance in Group 1: decreased abundance in
Experiment 2
Curated date: 2025/01/23
Curator:
Revision editor(s):
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Women at gestational week 27
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Women at 3 months postpartum
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mothers at their third month after childbirth.
- Group 1 sample size Number of subjects in the case (exposed) group
- 64
Lab analysis
Statistical Analysis
Signature 2
Source: Figure 2A
Description: Differences in species at 3months postpartum compared to gestational week 27
Abundance in Group 1: decreased abundance in
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Women at 3 months postpartum
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Infants
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples collected from infants up to 3 months old
- Group 0 sample size Number of subjects in the control (unexposed) group
- 64
- Group 1 sample size Number of subjects in the case (exposed) group
- 74
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Linear Regression
Signature 1
Source: Figure S3C
Description: Association of maternal B. cellulosilyticus with infant abundances of microbial glycoside hydrolases
Abundance in Group 1: increased abundance in Infants
Revision editor(s): Miss Lulu, Aleru Divine, WikiWorks
Signature 2
Source: Figure S3C
Description: Association of maternal B. cellulosilyticus with infant abundances of microbial glycoside hydrolases
Abundance in Group 1: decreased abundance in Infants
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides cellulosilyticus |
Revision editor(s): Aleru Divine, WikiWorks
Experiment 4
Subjects
Lab analysis
Statistical Analysis
Signature 1
Source: Figure S3E
Description: Associations of maternal B. cellulosilyticus with species in infants up to 3 months old.
Abundance in Group 1: increased abundance in Infants
Revision editor(s): Miss Lulu, Aleru Divine, WikiWorks
Experiment 5
Curated date: 2025/02/07
Curator:
Revision editor(s):
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Hydrolyzed Formula
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Regular Formula
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Standard infant formula (with the intention to treat).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 107
- Group 1 sample size Number of subjects in the case (exposed) group
- 111
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- age, antibiotic exposure, breast feeding, delivery procedure, sex
Signature 1
Source: Figure 5A
Description: Species difference between infants who received regular versus hydrolyzed formula (with intention to treat).
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Actinotignum timonense | ||
| Cutibacterium avidum | ||
| Schaalia radingae | ||
| Streptococcus thermophilus | ||
| Varibaculum cambriense |
Revision editor(s): Miss Lulu, Aleru Divine, WikiWorks
Signature 2
Source: Figure 5A
Description: Species difference between infants who received regular versus hydrolyzed formula (with intention to treat).
Abundance in Group 1: decreased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Mediterraneibacter gnavus | ||
| Rothia mucilaginosa | ||
| Staphylococcus hominis | ||
| Thomasclavelia ramosa | ||
| [Clostridium] innocuum |
Revision editor(s): Miss Lulu, Aleru Divine, WikiWorks
Experiment 6
Curated date: 2025/02/07
Curator:
Revision editor(s):
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Standard infant formula (Real use)
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5A
Description: Species difference between infants who received regular versus hydrolyzed formula.
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Atopobium deltae | ||
| Enterococcus faecalis | ||
| Schaalia radingae | ||
| Streptococcus thermophilus | ||
| Varibaculum cambriense |
Revision editor(s): Miss Lulu, Aleru Divine, WikiWorks
Signature 2
Source: Figure 5A
Description: Species difference between infants who received regular versus hydrolyzed formula.
Abundance in Group 1: decreased abundance in
Revision editor(s): Miss Lulu, Aleru Divine, WikiWorks
