Meconium microbiome analysis identifies bacteria correlated with premature birth

From BugSigDB
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
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

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks

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 ControlLinks
Leuconostoc
Negativicoccus
Vagococcus
Butyrivibrio

Revision editor(s): WikiWorks

Experiment 2


Reviewed Marked as Reviewed by Fatima on 2021/07/16

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Rimsha, WikiWorks, Folakunmi, Victoria

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

Statistical test
Spearman Correlation

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

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks

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

NCBI Quality ControlLinks
Bacillota
Bacillaceae
Staphylococcaceae
Enterococcaceae
Lactobacillaceae
Lactobacillaceae
Clostridiaceae
Peptostreptococcaceae
Veillonellaceae
Erysipelotrichaceae
Bifidobacteriaceae
Enterobacteriaceae
Bacillus
Staphylococcus
Enterococcus
Vagococcus
Lactobacillus
Leuconostoc
Clostridium
Veillonella
Negativicoccus
Bifidobacterium
Enterobacter
Citrobacter
Erwinia
Klebsiella
Raoultella
Pantoea
Photorhabdus
Tannerella
Actinomycetota

Revision editor(s): WikiWorks

Signature 2

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks

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 ControlLinks
Oxalicibacterium

Revision editor(s): WikiWorks