High-throughput sequencing reveals the incomplete, short-term recovery of infant gut microbiota following parenteral antibiotic treatment with ampicillin and gentamicin/Experiment 3

From BugSigDB


Reviewed Marked as Reviewed by Chloe on 2021/11/18

Curated date: 2021/10/07

Curator: Mmarin

Revision editor(s): LGeistlinger, Mmarin, WikiWorks

Subjects

Location of subjects
Ireland
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
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
Week 4 (treated)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Week 8 (treated)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Had received parenteral antibiotic treatment with a combination of ampicillin and gentamicin within 48 hours of birth
Group 0 sample size Number of subjects in the control (unexposed) group
9
Group 1 sample size Number of subjects in the case (exposed) group
9
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
excluded if they required oral antibiotics (no time frame given)

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
Roche454

Statistical Analysis

Statistical test
Mann-Whitney (Wilcoxon)
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.05

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 Chloe on 2021/11/18

Curated date: 2021/10/07

Curator: Mmarin

Revision editor(s): Mmarin

Source: Figure 1, Figure 2, Figure 3

Description: Figure 1: Microbial distributions at the phylum level in the samples from treated and control infants at week 4 and week 8. Figure 2: Microbial distributions at the family level in the samples from treated and control infants at week 4 and week 8. Figure 3: Microbial distributions at the genus level in the samples from treated and control infants at week 4 and week 8.

A statistically significant difference between treated infants at week 4 and week 8 (i.e., the recovery of the treated infants) is indicated by a diamond. Percentages are based on proportions of assignable tags.

Abundance in Group 1: increased abundance in Week 8 (treated)

NCBI Quality ControlLinks
Actinomycetota
Bifidobacteriaceae
Bifidobacterium

Revision editor(s): Mmarin

Signature 2

Reviewed Marked as Reviewed by Chloe on 2021/11/18

Curated date: 2021/10/07

Curator: Mmarin

Revision editor(s): Mmarin

Source: Figure 1, Figure 2, Figure 3

Description: Figure 1: Microbial distributions at the phylum level in the samples from treated and control infants at week 4 and week 8. Figure 2: Microbial distributions at the family level in the samples from treated and control infants at week 4 and week 8. Figure 3: Microbial distributions at the genus level in the samples from treated and control infants at week 4 and week 8.

A statistically significant difference between treated infants at week 4 and week 8 (i.e., the recovery of the treated infants) is indicated by a diamond. Percentages are based on proportions of assignable tags.

Abundance in Group 1: decreased abundance in Week 8 (treated)

NCBI Quality ControlLinks
Enterobacteriaceae
Peptostreptococcaceae
Pseudomonadota
unclassified Enterobacteriaceae

Revision editor(s): Mmarin