Alterations in intestinal microbiota of elderly Irish subjects post-antibiotic therapy/Experiment 1

From BugSigDB


Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27

Curated date: 2021/09/10

Curator: Mmarin

Revision editor(s): LGeistlinger, Mmarin, Claregrieve1, 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
Antibiotic untreated
Group 1 name Corresponds to the case (exposed) group for case-control studies
Antibiotic treated
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
subjects receiving antibiotics within 1 month prior to visiting an ELDERMET Clinic
Group 0 sample size Number of subjects in the control (unexposed) group
143
Group 1 sample size Number of subjects in the case (exposed) group
42

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
Kruskall-Wallis
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)?
Yes
Matched on Factors on which subjects have been matched on in a case-control study
age

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged
Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27

Curated date: 2021/09/10

Curator: Mmarin

Revision editor(s): Mmarin, Claregrieve1

Source: Figure S2, Table S4

Description: Differential microbial abundance between antibiotic-treated and -untreated elderly subjects

Abundance in Group 1: decreased abundance in Antibiotic treated

NCBI Quality ControlLinks
Bifidobacterium sp.
Acidaminococcus
Butyrivibrio
Lachnospira

Revision editor(s): Mmarin, Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27

Curated date: 2021/09/16

Curator: Mmarin

Revision editor(s): Mmarin, Claregrieve1

Source: Table S4

Description: Differential microbial abundance between antibiotic-treated and -untreated elderly subjects

Abundance in Group 1: increased abundance in Antibiotic treated

NCBI Quality ControlLinks
Anaerococcus
Lactonifactor
Lactobacillus
Megasphaera
Penicillium
Proteus

Revision editor(s): Mmarin, Claregrieve1