Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study

From BugSigDB
  • Quality control
    • Retracted paper
    • Contamination issues suspected
    • Batch effect issues suspected
    • Uncontrolled confounding suspected
    • Results are suspect (various reasons)
    • Apply tags
      Tags applied
Reviewed Marked as Reviewed by Atrayees on 2023-8-10
study design
prospective cohort
Citation
PMID PubMed identifier for scientific articles.
31006170
DOI Digital object identifier for electronic documents.
10.1111/1471-0528.15799
URI
Authors
Coker MO, Hoen AG, Dade E, Lundgren S, Li Z, Wong AD, Zens MS, Palys TJ, Morrison HG, Sogin ML, Baker ER, Karagas MR, Madan JC
Journal
BJOG : an international journal of obstetrics and gynaecology
Year
2020
Keywords:
Gut, infant, intestinal microbiota, intrapartum antibiotics, neonate
OBJECTIVE: To evaluate the potential impact of intrapartum antibiotics, and their specific classes, on the infant gut microbiota in the first year of life. DESIGN: Prospective study of infants in the New Hampshire Birth Cohort Study (NHBCS). SETTINGS: Rural New Hampshire, USA. POPULATION OR SAMPLE: Two hundred and sixty-six full-term infants from the NHBCS. METHODS: Intrapartum antibiotic use during labour and delivery was abstracted from medical records. Faecal samples collected at 6 weeks and 1 year of age were characterised by 16S rRNA sequencing, and metagenomics analysis in a subset of samples. EXPOSURES: Maternal exposure to antibiotics during labour and delivery. MAIN OUTCOME MEASURE: Taxonomic and functional profiles of faecal samples. RESULTS: Infant exposure to intrapartum antibiotics, particularly to two or more antibiotic classes, was independently associated with lower microbial diversity scores as well as a unique bacterial community at 6 weeks (GUnifrac, P = 0.02). At 1 year, infants in the penicillin-only group had significantly lower α diversity scores than infants not exposed to intrapartum antibiotics. Within the first year of life, intrapartum exposure to penicillins was related to a significantly lower increase in several taxa including Bacteroides, use of cephalosporins was associated with a significantly lower rise over time in Bifidobacterium and infants in the multi-class group experienced a significantly higher increase in Veillonella dispar. CONCLUSIONS: Our findings suggest that intrapartum antibiotics alter the developmental trajectory of the infant gut microbiome, and specific antibiotic types may impact community composition, diversity and keystone immune training taxa. TWEETABLE ABSTRACT: Class of intrapartum antibiotics administered during delivery relates to maturation of infant gut microbiota.

Experiment 1


EditHistoryDelete
Flag for review
Your review change was submittedDuplicate this ExperimentAdd a new Signature
Reviewed Marked as Reviewed by Atrayees on 2023-8-10

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Atrayees

Subjects

Location of subjects
United States of America
Host species Species from which microbiome was sampled (if applicable)
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
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
antimicrobial agent antibiotic,antibiotics,Antibiotika,Antibiotikum,antibiotique,antimicrobial,antimicrobial agents,microbicide,microbicides,antimicrobial agent
Group 0 name Corresponds to the control (unexposed) group for case-control studies
infants (6-weeks) to mothers unexposed to intrapartum antibiotic
Group 1 name Corresponds to the case (exposed) group for case-control studies
infants(6-weeks) to mothers exposed to intrapartum antibiotic
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
vaginally delivered at full-term (>37 weeks of gestation)
Group 0 sample size Number of subjects in the control (unexposed) group
179
Group 1 sample size Number of subjects in the case (exposed) group
87

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V4-V5
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).
relative abundances
Statistical test
PERMANOVA
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

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased

Signature 1

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by Atrayees on 2023-8-10

Curated date: 2021/01/10

Curator: Mst Afroza Parvin

Revision editor(s): WikiWorks, Atrayees

Source: Table S1, Figure S2 & Text

Description: MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).

Abundance in Group 1: increased abundance in infants(6-weeks) to mothers exposed to intrapartum antibiotic

NCBI Quality ControlLinks
Oscillospira   
Pseudoramibacter   
Varibaculum   
Veillonella dispar   

Revision editor(s): WikiWorks, Atrayees

Signature 2

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by Atrayees on 2023-8-10

Curated date: 2021/01/10

Curator: Mst Afroza Parvin

Revision editor(s): WikiWorks, Atrayees

Source: Table S1, Figure S2 & Text

Description: MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).

Abundance in Group 1: decreased abundance in infants(6-weeks) to mothers exposed to intrapartum antibiotic

NCBI Quality ControlLinks
Bacteroides   
Bifidobacterium   
Blautia   
Roseburia   
Ruminococcus   

Revision editor(s): WikiWorks, Atrayees

Experiment 2


EditHistoryDelete
Flag for review
Your review change was submittedDuplicate this ExperimentAdd a new Signature
Reviewed Marked as Reviewed by Atrayees on 2023-8-10

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Atrayees

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
infants (1-year) to mothers unexposed to intrapartum antibiotic
Group 1 name Corresponds to the case (exposed) group for case-control studies
infants(1-year) to mothers exposed to intrapartum antibiotic

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased

Signature 1

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by Atrayees on 2023-8-10

Curated date: 2021/01/10

Curator: Mst Afroza Parvin

Revision editor(s): WikiWorks, Atrayees

Source: Table S1

Description: MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).

Abundance in Group 1: increased abundance in infants(1-year) to mothers exposed to intrapartum antibiotic

NCBI Quality ControlLinks
Oscillospira   
Pseudoramibacter   
Varibaculum   
Veillonella dispar   

Revision editor(s): WikiWorks, Atrayees

Signature 2

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by Atrayees on 2023-8-10

Curated date: 2021/01/10

Curator: Mst Afroza Parvin

Revision editor(s): WikiWorks, Atrayees

Source: Table S1

Description: MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).

Abundance in Group 1: decreased abundance in infants(1-year) to mothers exposed to intrapartum antibiotic

NCBI Quality ControlLinks
Bacteroides   
Bifidobacterium   
Blautia   
Roseburia   

Revision editor(s): WikiWorks, Atrayees

Experiment 3


EditHistoryDelete
Flag for review
Your review change was submittedDuplicate this ExperimentAdd a new Signature
Reviewed Marked as Reviewed by Atrayees on 2023-8-10

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Atrayees

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
infants (6-weeks) to mothers unexposed to antibiotic
Group 1 name Corresponds to the case (exposed) group for case-control studies
infants(6-weeks) to mothers exposed to antibiotic penicillin
Group 1 sample size Number of subjects in the case (exposed) group
55

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged

Signature 1

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by Atrayees on 2023-8-10

Curated date: 2021/01/10

Curator: Mst Afroza Parvin

Revision editor(s): WikiWorks, Atrayees

Source: text, Figure 3

Description: MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).

Abundance in Group 1: decreased abundance in infants(6-weeks) to mothers exposed to antibiotic penicillin

NCBI Quality ControlLinks
Bacteroides   
Bacteroides ovatus   
Bifidobacterium   

Revision editor(s): WikiWorks, Atrayees

Experiment 5


EditHistoryDelete
Flag for review
Your review change was submittedDuplicate this ExperimentAdd a new Signature
Reviewed Marked as Reviewed by Atrayees on 2023-8-10

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Atrayees

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
infants(6-weeks) to mothers exposed to multi-class antibiotics
Group 1 sample size Number of subjects in the case (exposed) group
12

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
increased
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged

Signature 1

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by Atrayees on 2023-8-10

Curated date: 2021/01/10

Curator: Mst Afroza Parvin

Revision editor(s): WikiWorks, Atrayees

Source: Text, Figure 3

Description: MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).

Abundance in Group 1: increased abundance in infants(6-weeks) to mothers exposed to multi-class antibiotics

NCBI Quality ControlLinks
Veillonella dispar   

Revision editor(s): WikiWorks, Atrayees

Experiment 6


EditHistoryDelete
Flag for review
Your review change was submittedDuplicate this ExperimentAdd a new Signature
Reviewed Marked as Reviewed by Atrayees on 2023-8-10

Curated date: 2023/08/10

Curator: Atrayees

Revision editor(s): Atrayees

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
antimicrobial agent antibiotic,antibiotics,Antibiotika,Antibiotikum,antibiotique,antimicrobial,antimicrobial agents,microbicide,microbicides,antimicrobial agent
Group 0 name Corresponds to the control (unexposed) group for case-control studies
infants to mothers unexposed to intrapartum antibiotic
Group 1 name Corresponds to the case (exposed) group for case-control studies
infants to mothers exposed to cephalosporins
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Not specified
Group 1 sample size Number of subjects in the case (exposed) group
14

Lab analysis

Statistical Analysis

Signature 1

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by Atrayees on 2023-8-10

Curated date: 2023/08/10

Curator: Atrayees

Revision editor(s): Atrayees

Source: text, figure 3

Description: Taxa that are significantly associated with maternal antibiotic exposure (unexposed infants as the reference group).

Abundance in Group 1: decreased abundance in infants to mothers exposed to cephalosporins

NCBI Quality ControlLinks
Bifidobacterium   

Revision editor(s): Atrayees

Signature 2

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by Atrayees on 2023-8-10

Curated date: 2023/08/10

Curator: Atrayees

Revision editor(s): Atrayees

Source: Text, Figure 3

Description: Taxa that are significantly associated with maternal antibiotic exposure (unexposed infants as the reference group).

Abundance in Group 1: increased abundance in infants to mothers exposed to cephalosporins

NCBI Quality ControlLinks
Bacteroides fragilis   

Revision editor(s): Atrayees

Retrieved from "https://bugsigdb.org/w/index.php?title=Study_320&oldid=82279"
The City University of New York
Bioconductor - Open Source Software for Bioinformatics
WikiWorks
Powered by MediaWiki
Powered by Semantic MediaWiki