Intestinal microbiota development in preterm neonates and effect of perinatal antibiotics

Study information

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Needs review Marked as Needs review by Chloe on 2023-11-16

study design

time series / longitudinal observational

Citation

PMID PubMed identifier for scientific articles.

25444008

DOI Digital object identifier for electronic documents.

10.1016/j.jpeds.2014.09.041

URI

Authors

Arboleya S, Sánchez B, Milani C, Duranti S, Solís G, Fernández N, de los Reyes-Gavilán CG, Ventura M, Margolles A, Gueimonde M

Journal

The Journal of pediatrics

Year

2015

OBJECTIVES: To assess the establishment of the intestinal microbiota in very low birthweight preterm infants and to evaluate the impact of perinatal factors, such as delivery mode and perinatal antibiotics. STUDY DESIGN: We used 16S ribosomal RNA gene sequence-based microbiota analysis and quantitative polymerase chain reaction to evaluate the establishment of the intestinal microbiota. We also evaluated factors affecting the microbiota, during the first 3 months of life in preterm infants (n = 27) compared with full-term babies (n = 13). RESULTS: Immaturity affects the microbiota as indicated by a reduced percentage of the family Bacteroidaceae during the first months of life and by a higher initial percentage of Lactobacillaceae in preterm infants compared with full term infants. Perinatal antibiotics, including intrapartum antimicrobial prophylaxis, affects the gut microbiota, as indicated by increased Enterobacteriaceae family organisms in the infants. CONCLUSIONS: Prematurity and perinatal antibiotic administration strongly affect the initial establishment of microbiota with potential consequences for later health.

Experiment 1

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Curated date: 2021/01/10

Curator: WikiWorks

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Subjects

Location of subjects

Spain

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

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

2-day old Full-term infants(born after uncomplicated pregnancy)

Group 1 name Corresponds to the case (exposed) group for case-control studies

2-day old Pre-term infants

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

infants born at gestational ages between 24 and 32 weeks

Group 0 sample size Number of subjects in the control (unexposed) group

13

Group 1 sample size Number of subjects in the case (exposed) group

27

Lab analysis

Sequencing type

16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene

V3-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

ANOVA

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

Signature 1

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Reviewed Marked as Reviewed by ChiomaBlessing on 2023-11-19

Curated date: 2021/01/10

Curator: Mst Afroza Parvin

Revision editor(s): WikiWorks, ChiomaBlessing

Source: Results within text under the subheading "Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants" Line 7 to 15

Description: Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants

Abundance in Group 1: increased abundance in 2-day old Pre-term infants

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Bifidobacteriaceae
Comamonadaceae
Propionibacteriaceae
Streptococcaceae
unclassified Actinomycetota
unclassified Bacilli
unclassified Lactobacillales

Revision editor(s): WikiWorks, ChiomaBlessing

Signature 2

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Source: Results within text under the subheading "Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants" (Line 7 to 15)

Description: Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants

Abundance in Group 1: decreased abundance in 2-day old Pre-term infants

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Bacteroidaceae
Clostridiaceae
Micrococcaceae
Pasteurellaceae
Porphyromonadaceae

Revision editor(s): WikiWorks, ChiomaBlessing

Experiment 2

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Curator: WikiWorks

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

10-day old Full-term infants(born after uncomplicated pregnancy)

Group 1 name Corresponds to the case (exposed) group for case-control studies

10-day old Pre-term

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

born at gestational ages between 24 and 32 weeks

Lab analysis

Statistical Analysis

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Curated date: 2021/01/10

Curator: Mst Afroza Parvin

Revision editor(s): WikiWorks, ChiomaBlessing

Source: Results within text under the subheading "Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants" (line 15 to 22)

Description: Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants

Abundance in Group 1: increased abundance in 10-day old Pre-term

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Enterobacteriaceae
Gammaproteobacteria
Micrococcaceae

Revision editor(s): WikiWorks, ChiomaBlessing

Signature 2

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Curated date: 2021/01/10

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Revision editor(s): WikiWorks, Atrayees, ChiomaBlessing

Source: Results within text under the subheading "Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants" (line 15 to 22)

Description: Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants

Abundance in Group 1: decreased abundance in 10-day old Pre-term

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Veillonellaceae
Bacteroidaceae
Bifidobacteriaceae
Clostridiaceae
Coriobacteriaceae
Lactobacillaceae
Pasteurellaceae
Porphyromonadaceae
unclassified Actinomycetota

Revision editor(s): WikiWorks, Atrayees, ChiomaBlessing

Experiment 3

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Needs review Marked as Needs review by Lwaldron on 2023-11-16

Curated date: 2021/01/10

Curator: WikiWorks

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

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

30 and 90-day old Full-term infants

Group 1 name Corresponds to the case (exposed) group for case-control studies

30 and 90-day old Pre-term infants

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

infants born at gestational ages between 24 and 32 weeks

Lab analysis

Statistical Analysis

Signature 1

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Needs review Marked as Needs review by Lwaldron on 2023-11-16

Curated date: 2021/01/10

Curator: Mst Afroza Parvin

Revision editor(s): WikiWorks, Folakunmi

Source: Results within text under the subheading "Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants" (line 23 to 26)

Description: Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants

Abundance in Group 1: increased abundance in 30 and 90-day old Pre-term infants

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Enterobacteriaceae

Revision editor(s): WikiWorks, Folakunmi

Signature 2

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Curated date: 2021/01/10

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Revision editor(s): WikiWorks, Folakunmi

Source: Results within text under the subheading "Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants" (line 23 to 26)

Description: Establishment of Intestinal Microbiota in VLBW Preterm Neonates Compared with FTVDBF Infants

Abundance in Group 1: decreased abundance in 30 and 90-day old Pre-term infants

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Bacteroidaceae

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Experiment 4

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Curated date: 2023/11/20

Curator: Folakunmi

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Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

Delivery method DeliveryMethod,Delivery method,delivery method

Group 0 name Corresponds to the control (unexposed) group for case-control studies

10-day old cesarean-delivered pre-term neontes

Group 1 name Corresponds to the case (exposed) group for case-control studies

10-day old vaginally-delivered pre-term neonates

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

10-day old pre-term infants who were delivered vaginally.

Group 0 sample size Number of subjects in the control (unexposed) group

20

Group 1 sample size Number of subjects in the case (exposed) group

7

Lab analysis

Sequencing type

PCR

16S variable region One or more hypervariable region(s) of the bacterial 16S gene

Not specified

Statistical Analysis

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Source: Results within text under the sub-heading "Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota" (Line 6-8)

Description: Impact of Delivery method on the Intestinal Microbiota between 10-day old vaginally-delivered pre-term neonates and cesarean-delivered pre-term neonates, as observed by qPCR.

Abundance in Group 1: increased abundance in 10-day old vaginally-delivered pre-term neonates

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Bacteroides

Revision editor(s): Folakunmi

Experiment 5

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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,antimicrobial agent

Group 0 name Corresponds to the control (unexposed) group for case-control studies

2-day old full-term neonates not exposed to antibiotics (IAP/postnatal)

Group 1 name Corresponds to the case (exposed) group for case-control studies

2-day old pre-tem neonates exposed to antibiotics (IAP)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

antenatal/postnatal antibiotic exposure

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

V3-V4

Statistical Analysis

Signature 1

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Reviewed Marked as Reviewed by Atrayees on 2023-7-21

Curated date: 2021/01/10

Curator: Mst Afroza Parvin

Revision editor(s): WikiWorks, Folakunmi, ChiomaBlessing

Source: Results within text under the subheading "Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota" (2nd paragraph, from line 11)

Description: Impact of Antibiotics Use on the Intestinal Microbiota between 2-day old full-term neonates not exposed to antibiotics (IAP/postnatal) and 2-day old pre-term neonates exposed to antibiotics (IAP)

Abundance in Group 1: decreased abundance in 2-day old pre-tem neonates exposed to antibiotics (IAP)

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Lactobacillaceae

Revision editor(s): WikiWorks, Folakunmi, ChiomaBlessing

Experiment 6

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Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

10-day old full-term neonates not exposed to antibiotics (IAP/postnatal)

Group 1 name Corresponds to the case (exposed) group for case-control studies

10-day old pre-tem neonates exposed to antibiotics (IAP)

Lab analysis

Statistical Analysis

Signature 1

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Reviewed Marked as Reviewed by Atrayees on 2023-7-21

Curated date: 2021/01/10

Curator: Mst Afroza Parvin

Revision editor(s): WikiWorks, ChiomaBlessing

Source: Results within text under the subheading "Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota" (2nd paragraph, from line 11)

Description: Impact of Antibiotics Use on the Intestinal Microbiota between 10-day old full-term neonates not exposed to antibiotics (IAP/postnatal) and 10-day old pre-tem neonates exposed to antibiotics (IAP)

Abundance in Group 1: decreased abundance in 10-day old pre-tem neonates exposed to antibiotics (IAP)

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Micrococcaceae
Propionibacteriaceae

Revision editor(s): WikiWorks, ChiomaBlessing

Experiment 7

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Curator: WikiWorks

Revision editor(s): WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

30-day old full-term neonates not exposed to antibiotics (IAP/postnatal)

Group 1 name Corresponds to the case (exposed) group for case-control studies

30-day old pre-tem neonates exposed to antibiotics (IAP)

Lab analysis

Statistical Analysis

Signature 1

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Reviewed Marked as Reviewed by Atrayees on 2023-7-21

Curated date: 2021/01/10

Curator: Mst Afroza Parvin

Revision editor(s): WikiWorks, Atrayees, ChiomaBlessing

Source: Results within text under the subheading "Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota" (2nd paragraph, from line 18)

Description: Impact of Antibiotics Use on the Intestinal Microbiota between 30-day old full-term neonates not exposed to antibiotics (IAP/postnatal) and 30-day old pre-term neonates exposed to antibiotics (IAP)

Abundance in Group 1: decreased abundance in 30-day old pre-tem neonates exposed to antibiotics (IAP)

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Comamonadaceae
Staphylococcaceae
unclassified Bacilli

Revision editor(s): WikiWorks, Atrayees, ChiomaBlessing

Experiment 8

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Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Folakunmi, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

90-day old full-term neonates not exposed to antibiotics (IAP/postnatal)

Group 1 name Corresponds to the case (exposed) group for case-control studies

90-day old pre-term neonates with mothers exposed to antibiotics (IAP)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

90-day old pre-term neonates whose mothers received antibiotics (IAP) independently on whether or not the infant received antibiotics.

Lab analysis

Statistical Analysis

Signature 1

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Source: Results within text under the subheading "Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota" (2nd paragraph, from line 31)

Description: Impact of Antibiotics Use on the Intestinal Microbiota between 90-day old full-term neonates not exposed to antibiotics (IAP/postnatal) and 90-day old pre-term neonates with mothers exposed to antibiotics (IAP)

Abundance in Group 1: decreased abundance in 90-day old pre-term neonates with mothers exposed to antibiotics (IAP)

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Oscillospiraceae

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Experiment 9

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Curator: WikiWorks

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

30-day old full-term neonates not exposed to antibiotics (IAP/postnatal)

Group 1 name Corresponds to the case (exposed) group for case-control studies

30-day old pre-tem neonates with mothers exposed to antibiotics (IAP)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

30-day old pre-term neonates whose mothers received antibiotics (IAP) independently on whether or not the infant received antibiotics.

Group 0 sample size Number of subjects in the control (unexposed) group

5

Group 1 sample size Number of subjects in the case (exposed) group

14

Lab analysis

Statistical Analysis

Signature 1

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Curator: Mst Afroza Parvin

Revision editor(s): WikiWorks, ChiomaBlessing

Source: Results within text under the subheading "Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota" (2nd paragraph, from line 24)

Description: Impact of Antibiotics Use on the Intestinal Microbiota between 30-day old full-term neonates not exposed to antibiotics (IAP/postnatal) and 30-day old pre-term neonates with mothers exposed to antibiotics (IAP)

Abundance in Group 1: increased abundance in 30-day old pre-tem neonates with mothers exposed to antibiotics (IAP)

NCBI	Quality Control	Links
Enterobacteriaceae

Revision editor(s): WikiWorks, ChiomaBlessing

Signature 2

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Reviewed Marked as Reviewed by ChiomaBlessing on 2023-11-20

Curated date: 2021/01/10

Curator: Mst Afroza Parvin

Revision editor(s): WikiWorks, ChiomaBlessing

Source: Results within text under the subheading "Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota" (2nd paragraph, from line 20)

Description: Impact of Antibiotics Use on the Intestinal Microbiota between 30-day old full-term neonates not exposed to antibiotics (IAP/postnatal) and 30-day old pre-term neonates with mothers exposed to antibiotics (IAP)

Abundance in Group 1: decreased abundance in 30-day old pre-tem neonates with mothers exposed to antibiotics (IAP)

NCBI	Quality Control	Links
Bifidobacteriaceae
Streptococcaceae
unclassified Lactobacillales
unclassified Actinomycetota

Revision editor(s): WikiWorks, ChiomaBlessing

Experiment 10

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Reviewed Marked as Reviewed by Atrayees on 2023-7-21

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Curator: WikiWorks

Revision editor(s): WikiWorks, ChiomaBlessing, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

30-day old pre-term neonates not exposed to antibiotics (IAP/postnatal)

Group 1 name Corresponds to the case (exposed) group for case-control studies

30-day old pre-tem neonates exposed to antibiotics (IAP/postnatal)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

pre-term infants and mothers exposed to antibiotics

Group 1 sample size Number of subjects in the case (exposed) group

9

Lab analysis

Sequencing type

PCR

16S variable region One or more hypervariable region(s) of the bacterial 16S gene

Not specified

Statistical Analysis

Signature 1

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Reviewed Marked as Reviewed by ChiomaBlessing on 2023-11-20

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Curator: Mst Afroza Parvin

Revision editor(s): WikiWorks, Atrayees, ChiomaBlessing

Source: Results for qtPCR within text under the subheading "Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota", 5th paragraph)

Description: Impact of Antibiotics Use on the Intestinal Microbiota between 30-day old pre-term neonates not exposed to antibiotics (IAP/postnatal) and 30-day old pre-term neonates exposed to antibiotics (IAP/postnatal)

Abundance in Group 1: decreased abundance in 30-day old pre-tem neonates exposed to antibiotics (IAP/postnatal)

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Staphylococcaceae

Revision editor(s): WikiWorks, Atrayees, ChiomaBlessing

Signature 2

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Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Source: Results for qtPCR within text under the subheading "Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota", 5th paragraph)

Description: Impact of Antibiotics Use on the Intestinal Microbiota between 30-day old pre-term neonates not exposed to antibiotics (IAP/postnatal) and 30-day old pre-term neonates exposed to antibiotics (IAP/postnatal)

Abundance in Group 1: increased abundance in 30-day old pre-tem neonates exposed to antibiotics (IAP/postnatal)

NCBI	Quality Control	Links
Enterobacteriaceae

Revision editor(s): ChiomaBlessing

Experiment 11

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Reviewed Marked as Reviewed by Atrayees on 2023-7-21

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, ChiomaBlessing, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

90-day old pre-term neonates not exposed to antibiotics (IAP/postnatal)

Group 1 name Corresponds to the case (exposed) group for case-control studies

90-day old pre-tem neonates exposed to antibiotics (IAP/postnatal)

Lab analysis

Statistical Analysis

Signature 1

EditHistoryDelete

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Reviewed Marked as Reviewed by ChiomaBlessing on 2023-11-20

Curated date: 2021/01/10

Curator: Mst Afroza Parvin

Revision editor(s): WikiWorks, ChiomaBlessing

Source: Results for qtPCR within text under the subheading "Impact of Delivery Mode and Antibiotics Use on the Establishment of Intestinal Microbiota" (5th paragraph)

Description: Impact of Antibiotics Use on the Intestinal Microbiota between 90-day old pre-term neonates not exposed to antibiotics (IAP/postnatal) and 90-day old pre-term neonates exposed to antibiotics (IAP/postnatal)

Abundance in Group 1: decreased abundance in 90-day old pre-tem neonates exposed to antibiotics (IAP/postnatal)

NCBI	Quality Control	Links
Bifidobacterium

Revision editor(s): WikiWorks, ChiomaBlessing