Dynamics of Gut Microbiota Recovery after Antibiotic Exposure in Young and Old Mice (A Pilot Study)

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/27

Curated date: 2021/09/27

Curator: Gina

Revision editor(s): WikiWorks, LGeistlinger, Claregrieve1, Gina, Peace Sandy

Subjects

Location of subjects: United States of America

Host species Species from which microbiome was sampled. Contact us to have more species added.: Mus musculus

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: 7 week old (young) mice before antibiotic treatment

Group 1 name Corresponds to the case (exposed) group for case-control studies: 7 week old (young) mice 10 days after antibiotic treatments

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: 7-week old mice (young mice) administered treated with broad-spectrum antibiotics metronidazole (500 mg/L) and ciprofloxacin (200 mg/L) for 10 days.

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): Mice were not previously given antibiotics before the study

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: Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances

Statistical test: LEfSe

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

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: sex

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

Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/27

Curated date: 2021/09/27

Curator: Gina

Revision editor(s): Gina

Source: Figure 5

Description: Linear discriminant analysis (LDA) effect size (LEfSe) of differentially abundant bacterial taxa between young mice after 10 days of antibiotic treatment

Abundance in Group 1: increased abundance in 7 week old (young) mice 10 days after antibiotic treatments

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Enterococcaceae
Lactobacillales
Enterococcus

Revision editor(s): Gina

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/27

Curated date: 2021/09/28

Curator: Gina

Revision editor(s): Gina

Source: Figure 5

Description: Linear discriminant analysis (LDA) effect size (LEfSe) of differentially abundant bacterial taxa between young after 10 days of Abx treatment

Abundance in Group 1: decreased abundance in 7 week old (young) mice 10 days after antibiotic treatments

NCBI	Quality Control	Links
Candidatus Stoquefichus
Clostridiales Family XIII bacterium
Erysipelotrichaceae
Erysipelotrichales
Faecalibaculum
Peptostreptococcaceae
Romboutsia
Clostridiales bacterium

Revision editor(s): Gina

Experiment 2

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/27

Curated date: 2021/09/29

Curator: Gina

Revision editor(s): LGeistlinger, Gina, Claregrieve1, WikiWorks

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies: 7 week old (young) mice 6 months after antibiotic treatments

Lab analysis

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: Not specified

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

Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/27

Curated date: 2021/09/29

Curator: Gina

Revision editor(s): Gina

Source: Figure 5

Description: Linear discriminant analysis (LDA) effect size (LEfSe) of differentially abundant bacterial taxa between young after 6 months of recovery

Abundance in Group 1: increased abundance in 7 week old (young) mice 6 months after antibiotic treatments

NCBI	Quality Control	Links
Romboutsia
Peptostreptococcaceae
Dubosiella

Revision editor(s): Gina

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/27

Curated date: 2021/09/29

Curator: Gina

Revision editor(s): Gina

Source: Figure 5

Description: Linear discriminant analysis (LDA) effect size (LEfSe) of differentially abundant bacterial taxa between young after 6 months of recovery (lower panels)

Abundance in Group 1: decreased abundance in 7 week old (young) mice 6 months after antibiotic treatments

NCBI	Quality Control	Links
Clostridiales Family XIII bacterium
Candidatus Stoquefichus

Revision editor(s): Gina

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/27

Curated date: 2021/09/29

Curator: Gina

Revision editor(s): LGeistlinger, Gina, Claregrieve1, WikiWorks

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: 40 week old (old) mice before antibiotic treatment

Group 1 name Corresponds to the case (exposed) group for case-control studies: 40 week old (old) mice 10 days after antibiotic treatments

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: 40-week old mice (old) administered treated with broad-spectrum antibiotics metronidazole (500 mg/L) and ciprofloxacin (200 mg/L) for 10 days.

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

Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/27

Curated date: 2021/09/29

Curator: Gina

Revision editor(s): Gina

Source: Figure 5

Description: Linear discriminant analysis (LDA) effect size (LEfSe) of differentially abundant bacterial taxa between older mice (right panels) after 10 days of Abx treatment

Abundance in Group 1: increased abundance in 40 week old (old) mice 10 days after antibiotic treatments

NCBI	Quality Control	Links
Bacteroidales

Revision editor(s): Gina

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/27

Curated date: 2021/09/29

Curator: Gina

Revision editor(s): Gina

Source: Figure 5

Description: Linear discriminant analysis (LDA) effect size (LEfSe) of differentially abundant bacterial taxa between older mice (right panels) after 10 days of Abx treatment.

Abundance in Group 1: decreased abundance in 40 week old (old) mice 10 days after antibiotic treatments

NCBI	Quality Control	Links
Romboutsia
Peptostreptococcaceae
Faecalibaculum
Erysipelotrichaceae
Erysipelotrichales

Revision editor(s): Gina

Experiment 4

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/27

Curated date: 2021/09/29

Curator: Gina

Revision editor(s): LGeistlinger, Gina, Claregrieve1, WikiWorks

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies: 40 week old (old) mice 6 months after antibiotic treatments

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

Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/27

Curated date: 2021/09/29

Curator: Gina

Revision editor(s): Gina

Source: Figure 5

Description: Linear discriminant analysis (LDA) effect size (LEfSe) of differentially abundant bacterial taxa between older mice (right panels) after 6 months of recovery (lower panels).

Abundance in Group 1: decreased abundance in 40 week old (old) mice 6 months after antibiotic treatments

NCBI	Quality Control	Links
Bacteroidales
Faecalibaculum
Muribaculaceae
Muribaculum
Peptostreptococcaceae
Romboutsia
Clostridiales bacterium

Revision editor(s): Gina

Signature 2