Cited by 440Gut microbiota and healthOral microbiology and periodontitis researchMicrobial Community Ecology and Physiology

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Antibiotic perturbations to the gut microbiome

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Fishbein, Skye R. S., Mahmud, Bejan, Dantas, Gautam·2023·Nature Reviews Microbiology

DOI 10.1038/s41579-023-00933-yPMC PMC12087466

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Abstract

Antibiotic-mediated perturbation of the gut microbiome is associated with numerous infectious and autoimmune diseases of the gastrointestinal tract. Yet, as the gut microbiome is a complex ecological network of microorganisms, the effects of antibiotics can be highly variable. With the advent of multi-omic approaches for systems-level profiling of microbial communities, we are beginning to identify microbiome-intrinsic and microbiome-extrinsic factors that affect microbiome dynamics during antibiotic exposure and subsequent recovery. In this Review, we discuss factors that influence restructuring of the gut microbiome on antibiotic exposure. We present an overview of the currently complex picture of treatment-induced changes to the microbial community and highlight essential considerations for future investigations of antibiotic-specific outcomes. Finally, we provide a synopsis of available strategies to minimize antibiotic-induced damage or to restore the pretreatment architectures of the gut microbial community.

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“Rather than signaling a harmful shift, the presence of these genes might re ﬂ ect a microbiome that ’ s been shaped by past antibiotic exposure but remains functionally resilient (Bhattarai et al., 2024; Fishbein et al., 2023).”
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Gut bacterial dysbiosis in pediatric severe malaria associates with post-discharge mortality
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Background
Gut microbiota: a potential influencer of insomnia occurring after COVID-19 infection
Fang, J., Wang, S., Liu, L., Zhang, X., Liu, R., Pang, X., Cui, J., Han, J., & Zhu, X. (2024) · Frontiers in Psychiatry · doi:10.3389/fpsyt.2024.1423715 · Cited by 4
“Antibiotics eliminate pathogenic bacteria in the gut while destroying bene ﬁ cial ﬂ ora, thus affecting the ecological niches of microorganisms responsible for metabolic transformation in the gut wall (74).”

Authors: Fishbein, S. R. S., Mahmud, B., & Dantas, G.
Affiliations: Washington University in St. Louis (US)
Corresponding author: Dantas, Gautam
ORCID: Fishbein, Skye R. S.
Mahmud, Bejan
Dantas, Gautam
Venue: Nature Reviews Microbiology
Publisher: Springer Science and Business Media LLC
Published: 2023-07-25
Volume: 21
Issue: 12
Pages: 772-788
ISSN: 1740-1526 (ISSN-L)
1740-1534
DOI: 10.1038/s41579-023-00933-y
PMC: PMC12087466
OpenAlex: W4385240643
Cited by: 440
References: 229
Citations by year: 2026: 152 · 2025: 165 · 2024: 115 · 2023: 7
FWCI: 11.59
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.springernature.com/gp/researchers/text-and-data-mining (tdm)
www.springernature.com/gp/researchers/text-and-data-mining (vor)
Locations: Nature Reviews Microbiology (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
Funders: U.S. Department of Health and Human Services
National Institutes of Health
Centers for Disease Control and Prevention (R01OH011578)
Agency for Healthcare Research and Quality (R01 HS027621)
National Institute of Allergy and Infectious Diseases (U01AI123394, R01AI155893)
National Institute of Diabetes and Digestive and Kidney Diseases (T32DK077653)
National Institute for Occupational Safety and Health (R01 OH011578)
National Center for Complementary and Integrative Health (R01AT009741)
Eunice Kennedy Shriver National Institute of Child Health and Human Development (R01HD092414)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Keywords: gut microbiota, antibiotics, microbiome perturbation, microbiome recovery, gastrointestinal diseases, autoimmune disease, multi-omics profiling
MeSH terms: Gastrointestinal Microbiome, Anti-Bacterial Agents, Gastrointestinal Tract, Microbiota

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