Meconium microbiome analysis identifies bacteria correlated with premature birth
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Ardissone AN, de la Cruz DM, Davis-Richardson AG, Rechcigl KT, Li N, Drew JC, Murgas-Torrazza R, Sharma R, Hudak ML, Triplett EW, Neu J
Journal
PloS one
Year
2014
BACKGROUND: Preterm birth is the second leading cause of death in children under the age of five years worldwide, but the etiology of many cases remains enigmatic. The dogma that the fetus resides in a sterile environment is being challenged by recent findings and the question has arisen whether microbes that colonize the fetus may be related to preterm birth. It has been posited that meconium reflects the in-utero microbial environment. In this study, correlations between fetal intestinal bacteria from meconium and gestational age were examined in order to suggest underlying mechanisms that may contribute to preterm birth. METHODS: Meconium from 52 infants ranging in gestational age from 23 to 41 weeks was collected, the DNA extracted, and 16S rRNA analysis performed. Resulting taxa of microbes were correlated to clinical variables and also compared to previous studies of amniotic fluid and other human microbiome niches. FINDINGS: Increased detection of bacterial 16S rRNA in meconium of infants of <33 weeks gestational age was observed. Approximately 61·1% of reads sequenced were classified to genera that have been reported in amniotic fluid. Gestational age had the largest influence on microbial community structure (R = 0·161; p = 0·029), while mode of delivery (C-section versus vaginal delivery) had an effect as well (R = 0·100; p = 0·044). Enterobacter, Enterococcus, Lactobacillus, Photorhabdus, and Tannerella, were negatively correlated with gestational age and have been reported to incite inflammatory responses, suggesting a causative role in premature birth. INTERPRETATION: This provides the first evidence to support the hypothesis that the fetal intestinal microbiome derived from swallowed amniotic fluid may be involved in the inflammatory response that leads to premature birth.
Experiment 1
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): Shaimaa, WikiWorks, Folakunmi, ChiomaBlessing
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
- Meconium Meconium,meconium
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Cesarean section caesarean section,Cesarean section,cesarean section
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- vaginal delivery
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- C-section
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- the study groups are devided into two groups acc to the gestational age. 1) gestational age < 33 weeks. 2) gestational age >/= 33 weeks
- Group 0 sample size Number of subjects in the control (unexposed) group
- 19
- 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
- Ion Torrent
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- 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)?
- No
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- birth weight, chorioamnionitis, feeding practices, sex, Confounders controlled for: "infant antibiotic" 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.infant antibiotic, Confounders controlled for: "maternal antibiotic" 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.maternal antibiotic, Confounders controlled for: "insurance" 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.insurance, Confounders controlled for: "ROM>18 h" 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.ROM>18 h
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Source: Table S6 in File S1
Description: Meconium microbiome related to mode of delivery in premature infants
Abundance in Group 1: increased abundance in C-section
| NCBI | Quality Control | Links |
|---|---|---|
| Leuconostoc | ||
| Negativicoccus | ||
| Vagococcus | ||
| Butyrivibrio |
Revision editor(s): WikiWorks
Experiment 2
Reviewed Marked as Reviewed by Fatima on 2021/07/16
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Premature birth Birth, Premature,Birth, Preterm,Births, Premature,Births, Preterm,Premature Births,Preterm Birth,Preterm Births,Premature birth,premature birth
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- >/=33 weeks
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- infants <33 weeks gestational age
- Group 0 sample size Number of subjects in the control (unexposed) group
- 17
- Group 1 sample size Number of subjects in the case (exposed) group
- 35
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
- Statistical test
- Spearman Correlation
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- birth weight, chorioamnionitis, sex, Confounders controlled for: "infant antibiotic" 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.infant antibiotic, Confounders controlled for: "maternal antibiotic" 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.maternal antibiotic, Confounders controlled for: "insurance" 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.insurance, Confounders controlled for: "ROM>18 h" 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.ROM>18 h, feeding practices
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Source: Table 1
Description: Phyla, family, and genera taxonomy significantly correlated with gestational age
Abundance in Group 1: increased abundance in infants <33 weeks gestational age
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Source: Table 1
Description: Phyla, family, and genera taxonomy significantly correlated with gestational age
Abundance in Group 1: decreased abundance in infants <33 weeks gestational age
| NCBI | Quality Control | Links |
|---|---|---|
| Oxalicibacterium |
Revision editor(s): WikiWorks
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