ArticleMicrobiome2022
The bacterial density of clinical rectal swabs is highly variable, correlates with sequencing contamination, and predicts patient risk of extraintestinal infection.
Article in Microbiome, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Gut microecology in critical illness: mechanisms, biomarkers, and therapeutic strategies - a critical appraisal.Frontiers in gastroenterology (Lausanne, Switzerland) · 2026Review
- Hologenomic analysis of rectal mucus sampling for detection of adenomatous polyps and colorectal cancer.Nature communications · 2025Article
- Analyzing human gut microbiome data from global populations: challenges and resources.Trends in microbiology · 2025Review
- Anti-Anaerobic Antibiotics, Gut Microbiota, and Sepsis-associated Acute Kidney Injury.American journal of respiratory and critical care medicine · 2025Article
- Validation of rectal swabbing for total and aerobic gut microbiota study.Microbiology spectrum · 2025Article
- Towards unraveling antimicrobial resistance dynamics: a longitudinal exploration of rectal swab metagenomes.BMC microbiology · 2025Article
- A review of gut failure as a cause and consequence of critical illness.Critical care (London, England) · 2025Review
- Article
- Sampling strategies for digestive system flora studies: current research and perspectives.PeerJ · 2025Review
- Using short-read 16S rRNA sequencing of multiple variable regions to generate high-quality results to a species level.Frontiers in bioinformatics · 2025Article
- Detection ofMicroorganisms · 2024Article
- The gut microbiota composition is linked to subsequent occurrence of ventilator-associated pneumonia in critically ill patients.Microbiology spectrum · 2023Article
- The Gut Microbiome Modulates Body Temperature Both in Sepsis and Health.American journal of respiratory and critical care medicine · 2023Article
- Dysbiosis of a microbiota-immune metasystem in critical illness is associated with nosocomial infections.Nature medicine · 2023Article
- In critically ill patients, anti-anaerobic antibiotics increase risk of adverse clinical outcomes.The European respiratory journal · 2023Article
- Ciprofloxacin Alone vs. Ciprofloxacin plus an Aminoglycoside for the Prevention of Infectious Complications following a Transrectal Ultrasound-Guided Prostate Biopsy: A Retrospective Cohort Study.Antibiotics (Basel, Switzerland) · 2022Article
- Gut microbiome dysbiosis in antibiotic-treated COVID-19 patients is associated with microbial translocation and bacteremia.Nature communications · 2022Article
- Digital PCR applications for the diagnosis and management of infection in critical care medicine.Critical care (London, England) · 2022Review
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Authors and funding
6 authors.
Funding
Abstract
backgroundIn ecology, population density is a key feature of community analysis. Yet in studies of the gut microbiome, bacterial density is rarely reported. Studies of hospitalized patients commonly use rectal swabs for microbiome analysis, yet variation in their bacterial density-and the clinical and methodologic significance of this variation-remains undetermined. We used an ultra-sensitive quantification approach-droplet digital PCR (ddPCR)-to quantify bacterial density in rectal swabs from 118 hospitalized patients. We compared bacterial density with bacterial community composition (via 16S rRNA amplicon sequencing) and clinical data to determine if variation in bacterial density has methodological, clinical, and prognostic significance.
resultsBacterial density in rectal swab specimens was highly variable, spanning five orders of magnitude (1.2 × 10
conclusionsThe bacterial density of rectal swabs is highly variable, and this variability is of methodological, clinical, and prognostic significance. Microbiome studies using rectal swabs are vulnerable to sequencing contamination and should include appropriate negative sequencing controls. Among hospitalized patients, gut bacterial density is associated with clinical exposures (antibiotics, comorbidities) and independently predicts infection risk. Bacterial density is an important and under-studied feature of gut microbiome community analysis. Video abstract.
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