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

Study information

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/3

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

22949626

DOI Digital object identifier for electronic documents.

10.1093/jac/dks348

URI

Authors

O'Sullivan O, Coakley M, Lakshminarayanan B, Conde S, Claesson MJ, Cusack S, Fitzgerald AP, O'Toole PW, Stanton C, Ross RP

Journal

The Journal of antimicrobial chemotherapy

Year

2013

OBJECTIVES: The human intestinal microbiota composition alters naturally with age, but is unusually perturbed by antibiotic therapy. The impact of antibiotic therapy on the composition of the intestinal microbiota of a cross-section of elderly Irish subjects (n = 185, ≥ 65 years) was investigated, taking into consideration their residence location. METHODS: Forty-two of the 185 elderly subjects were treated with at least one antibiotic within 1 month prior to faecal microbiota profiling. The residence locations of the subjects varied from long-term nursing care and rehabilitation wards to day hospitals and the community. RESULTS: Culture-dependent methods indicated that faecal Bifidobacterium spp. numbers were significantly reduced following antibiotic treatment (P = 0.004, 7-fold reduction), while levels of Lactobacillus spp. and Enterobacteriaceae were unaffected. The largest decrease in Bifidobacterium spp. numbers was linked to the administration of nucleic acid synthesis inhibitors (P = 0.004, 23-fold reduction). Microbiota profiling revealed a significant compositional change across nine genera following antibiotic therapy, including a relative increase in Lactobacillus spp. (P = 0.031), as well as a decrease in the number of genera identified in the antibiotic-treated subjects (n = 58), when compared with untreated subjects (n = 79). More alterations in the intestinal microbiota were observed post-nucleic acid synthesis inhibitor therapy, most notably a decrease in relative Faecalibacterium spp. numbers (P < 0.001). CONCLUSIONS: The impact of antibiotic therapy on the intestinal microbiota in the elderly should be considered for long-term health effects, and differential susceptibility may require the development of products (e.g. prebiotics and probiotics) for at-risk subjects.

Experiment 1

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

Curated date: 2021/09/10

Curator: Mmarin

Revision editor(s): WikiWorks, LGeistlinger, Claregrieve1, Mmarin, Victoria

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

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

relative abundances

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

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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

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Bifidobacterium sp.
Acidaminococcus
Butyrivibrio
Lachnospira

Revision editor(s): Mmarin, Claregrieve1

Signature 2

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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

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Anaerococcus
Lactonifactor
Lactobacillus
Megasphaera
Penicillium
Proteus

Revision editor(s): Mmarin, Claregrieve1

Experiment 2

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

Curated date: 2021/09/16

Curator: Mmarin

Revision editor(s): WikiWorks, LGeistlinger, Claregrieve1, Mmarin, Victoria

Differences from previous experiment shown

Subjects

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

Antibiotic untreated subjects in day hospital

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

Antibiotic treated subjects in day hospital

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

subjects who were antibiotic-treated in a day hospital

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

33

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

7

Lab analysis

Statistical Analysis

Statistical test

Chi-Square

Kruskall-Wallis

Mann-Whitney (Wilcoxon)

Signature 1

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

Curated date: 2021/09/16

Curator: Mmarin

Revision editor(s): Mmarin, Claregrieve1

Source: Table 1

Description: comparison of microbiota between antibiotic-treated and untreated groups in day hospital facility

Abundance in Group 1: increased abundance in Antibiotic treated subjects in day hospital

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Lactobacillus
Mogibacterium
Moryella
Peptoniphilus
Victivallis
Weissella

Revision editor(s): Mmarin, Claregrieve1

Signature 2

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

Curated date: 2021/09/16

Curator: Mmarin

Revision editor(s): Mmarin, Claregrieve1

Source: Table 1

Description: comparison of microbiota between antibiotic-treated and untreated groups in day hospital facility

Abundance in Group 1: decreased abundance in Antibiotic treated subjects in day hospital

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Blautia
Faecalibacterium

Revision editor(s): Mmarin, Claregrieve1

Experiment 3

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

Curated date: 2021/09/16

Curator: Mmarin

Revision editor(s): WikiWorks, LGeistlinger, Claregrieve1, Mmarin, Victoria

Differences from previous experiment shown

Subjects

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

Antibiotic untreated community dwelling subjects

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

Antibiotic treated community dwelling subjects

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

community-dwelling subjects treated with antibiotics within 1 month of study

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

64

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

9

Lab analysis

Statistical Analysis

Signature 1

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

Curated date: 2021/09/16

Curator: Mmarin

Revision editor(s): Mmarin, Claregrieve1

Source: Table 1

Description: comparison of microbiota between antibiotic-treated and untreated community-dwelling subjects

Abundance in Group 1: decreased abundance in Antibiotic treated community dwelling subjects

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Bacillota
Pseudomonadota

Revision editor(s): Mmarin, Claregrieve1

Signature 2

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

Curated date: 2021/09/16

Curator: Mmarin

Revision editor(s): Mmarin, Claregrieve1

Source: Table 1

Description: comparison of microbiota between antibiotic-treated and untreated community-dwelling subjects

Abundance in Group 1: decreased abundance in Antibiotic treated community dwelling subjects

NCBI	Quality Control	Links
Bacillota
Pseudomonadota

Revision editor(s): Mmarin, Claregrieve1

Experiment 4

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

Curated date: 2021/09/16

Curator: Mmarin

Revision editor(s): WikiWorks, LGeistlinger, Claregrieve1, Mmarin, Victoria

Differences from previous experiment shown

Subjects

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

Antibiotic untreated subjects in long stay facility

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

Antibiotic treated subjects in long stay facility

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

subjects in long stay facility who have had antibiotic treatment in the past month

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

32

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

16

Lab analysis

Statistical Analysis

Signature 1

EditHistoryDelete

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

Curated date: 2021/09/16

Curator: Mmarin

Revision editor(s): Mmarin, Claregrieve1

Source: Table 1

Description: comparison of microbiota between antibiotic-treated and untreated subjects in long stay facility

Abundance in Group 1: decreased abundance in Antibiotic treated subjects in long stay facility

NCBI	Quality Control	Links
Lachnospiraceae

Revision editor(s): Mmarin, Claregrieve1