ArticleCell host & microbe2019
Recovery of the Gut Microbiota after Antibiotics Depends on Host Diet, Community Context, and Environmental Reservoirs.
Article in Cell host & microbe, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 158 papers, 2 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
158 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Bioregulatory periodontal medicine: could the molecular networks, inflammation and system biology modify the auto-regulatory capacity of the patients?Frontiers in physiology · 2026Pooled it
- AGA Technical Review on the Role of Probiotics in the Management of Gastrointestinal Disorders.Gastroenterology · 2020Guideline
- Remote Stewardship for Medically Underserved Nurseries: A Stepped-Wedge, Cluster Randomized Study.Pediatrics · 2022Trial
- Effects of Irrational Use of Antibiotics on Intestinal Health of Children with Extraintestinal Infectious Diseases.Contrast media & molecular imaging · 2022Trial
- From gut dysbiosis to eubiosis: understanding microbiome recovery as an ecological process.Gut microbes · 2026Review
- Intra-species competition combats vancomycin-resistant enterococci.Gut microbes · 2026Article
- Article
- Article
- The Cost of the Cure: Antibiotic Exposure as a Risk Factor for Irritable Bowel Syndrome.Antibiotics (Basel, Switzerland) · 2026Review
- Evaluating the impact of immunization with the "pan-fungal" vaccine, NXT-2, on the gut mycobiome and microbiome in non-human primates (NHPs).Microbiology spectrum · 2026Article
- Antibiotic Class-Specific Effects on Inflammatory Bowel Disease: Microbiome Disruption, Risk, and Recovery.International journal of molecular sciences · 2026Review
- Antibiotic-Driven Gut Microbiome Dysbiosis: Resistome Dynamics, Metabolic Disruption, and Paths to Restoration.Antibiotics (Basel, Switzerland) · 2026Review
- High early-life gut Bacteroides links to microbiome stability, resilience, and risk for childhood infections.NPJ biofilms and microbiomes · 2026Article
- A Nutrient-Dense Diet with Optimal Protein Level Restores Goblet Cells and Alleviates Microbial Dysbiosis in a Mouse Model of Colitis.The Journal of nutrition · 2026Article
- Antibiotic-induced gut microbiome dysbiosis: risks and strategies for mitigation.The EMBO journal · 2026Review
- Host genetics shapes the recovery of the gut microbiome after antibiotic treatment: the role of the blood group relatedmSystems · 2026Article
- Plant-based enteral nutrition outperforms ultra-processed formulas in mitigating consequences of antibiotic-induced dysbiosis.JCI insight · 2026Article
- Social microbiome transmission predicts microbial specialization and host lifespan in a wild primate.bioRxiv : the preprint server for biology · 2026Article
- Metabiosis underlies a microbiota permissive to Pseudomonadota and increases the risk of gut-borne bloodstream infection.bioRxiv : the preprint server for biology · 2026Article
- Damage and recovery of artificial diet rearing silkworms (Bombyx mori L.) exposed to high-concentration florfenicol as well as the dynamic changes of midgut flora after functional bacterium supplementation.BMC microbiology · 2026Article
98 more citing papers are in PubMed but not listed here.
Corrections and comments
- Commented on by
- Erratum issued
Authors and funding
16 authors.
Funding
Abstract
Antibiotics alter microbiota composition and increase infection susceptibility. However, the generalizable effects of antibiotics on and the contribution of environmental variables to gut commensals remain unclear. To address this, we tracked microbiota dynamics with high temporal and taxonomic resolution during antibiotic treatment in a controlled murine system by isolating variables such as diet, treatment history, and housing co-inhabitants. Human microbiotas were remarkably resilient and recovered during antibiotic treatment, with transient dominance of resistant Bacteroides and taxa-asymmetric diversity reduction. In certain cases, in vitro sensitivities were not predictive of in vivo responses, underscoring the significance of host and community context. A fiber-deficient diet exacerbated microbiota collapse and delayed recovery. Species replacement through cross housing after ciprofloxacin treatment established resilience to a second treatment. Single housing drastically disrupted recovery, highlighting the importance of environmental reservoirs. Our findings highlight deterministic microbiota adaptations to perturbations and the translational potential for modulating diet, sanitation, and microbiota composition during antibiotics.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.