Distinct mucosal microbial communities in infants with surgical necrotizing enterocolitis correlate with age and antibiotic exposure/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/23
Subjects
- Location of subjects
- 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
- Mucosa of small intestine Mucosa of organ of small bowel,Mucosa of organ of small intestine,Mucosa of small bowel,Mucous membrane of small bowel,Mucous membrane of small intestine,Organ mucosa of small bowel,Organ mucosa of small intestine,Small bowel mucosa,Small bowel mucosa of organ,Small bowel mucous membrane,Small bowel organ mucosa,Small intestinal mucosa,Small intestine mucosa,Small intestine mucosa of organ,Small intestine mucous membrane,Small intestine organ mucosa,Tunica mucosa (intestinum tenue),Tunica mucosa intestini tenuis,Mucosa of small intestine,mucosa of small intestine
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Necrotizing enterocolitis Enterocolitis, Necrotizing,NEC,necrotizing enterocolitis,necrotizing enterocolitis in fetus or newborn,Necrotizing enterocolitis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- non-NEC
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- NEC
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- infants who underwent intestinal resection at <180 days of age with NEC
- Group 0 sample size Number of subjects in the control (unexposed) group
- 14
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V3
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
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)
- 0.1
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/23
Source: Figure 5
Description: Comparison of the abundance of tissue bacterial genera between infants with or without necrotizing enterocolitis (NEC)
Abundance in Group 1: increased abundance in NEC
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium | ||
| Staphylococcus |
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/23
Source: Figure 5
Description: Comparison of the abundance of tissue bacterial genera between infants with or without necrotizing enterocolitis (NEC)
Abundance in Group 1: decreased abundance in NEC
Revision editor(s): Claregrieve1
