Metagenomic analysis of the impact of nitrofurantoin treatment on the human faecal microbiota/Experiment 3

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Reviewed Marked as Reviewed by Peace Sandy on 2024-2-17

Curated date: 2022/01/14

Curator: Mmarin

Revision editor(s): Mmarin, WikiWorks, Peace Sandy

Subjects

Location of subjects
Belgium
Poland
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
Urinary tract infection INFECTION, URINARY TRACT,TRACT, INFECTION OF URINARY,urinary tract infection,urinary tract infection (disease),Urinary tract infection
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Control (day 1)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Control (day 5-15)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Did not receive nitrofurantoin treatment
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
5
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
2 months

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V3-V5
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Roche454

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
raw counts
Statistical test
Linear Regression
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

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-17

Curated date: 2022/01/14

Curator: Mmarin

Revision editor(s): Mmarin, Peace Sandy

Source: Table 1

Description: changes in mean proportions of 16S rDNA reads assigned to different phyla from baseline and between study groups. T1, day 1; T2, days 5–15; T3, days 31–43. Bold type indicates a statistically significant difference (P<0.05); generalized linear mixed model.

Abundance in Group 1: increased abundance in Control (day 5-15)

NCBI Quality ControlLinks
Bacteroidota

Revision editor(s): Mmarin, Peace Sandy