ReviewThe journal of pathology. Clinical research2020
Microbiome applications for pathology: challenges of low microbial biomass samples during diagnostic testing.
Review in The journal of pathology. Clinical research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
What it found
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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.
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Who cites it
40 citing papers in PubMed, 58 citations in OpenAlex.
- Systematic quantification and removal of host DNA contamination in 16S rRNA gene sequencing.Quantitative biology (Beijing, China) · 2026Article
- Harnessing microfluidics for microbiology: from bacteria-host interactions to emerging cancer therapies.Communications biology · 2026Review
- Microbiome analysis and epigenetic patterns revealed distinct differences between two elm species with contrasting Dutch elm disease resistance.Microbiome · 2026Article
- Assessing the female urogenital-rectal axis microbiome: focus on endometriosis and recurrent implantation failure.Reproductive biology and endocrinology : RB&E · 2026Article
- The Equine Reproductive Microbiota: Composition, Dynamics, Dysbiosis, and Implications for Fertility in Mares and Stallions.Animals : an open access journal from MDPI · 2026Review
- Evaluating Sequencing Strategies for Endometrial Microbiome Profiling in Endometrial Cancer: A Comparative Study of Short- and Long-Read 16S rRNA Approaches.Cancer reports (Hoboken, N.J.) · 2026Article
- Miscarriage and the Microbiome: Host Genetics, Immunity, and the Reproductive Tract Ecosystem.Genes · 2026Review
- Planning and Analyzing a Low-Biomass Microbiome Study: A Data Analysis Perspective.The Journal of infectious diseases · 2026Review
- Enhancing infection diagnostics in advanced chronic liver disease: harnessing clinical metagenomics for rapid pathogen and antimicrobial resistance detection.npj antimicrobials and resistance · 2026Review
- Microbial dysbiosis in cholangiocarcinoma.Frontiers in microbiology · 2026Review
- Methodological bias shapes the interpretation of the urinary microbiome in low-biomass systems.Frontiers in microbiology · 2026Review
- Contamination-controlled upper gastrointestinal microbiota profiling reveals salivary-duodenal community types linked to opportunistic pathogen carriage and inflammation.Gut microbes · 2025Article
- From Identification to Insight: Making Full Use of the Diagnostic Potential of MS/MS Proteotyping in Clinical Microbiology Using Efficient Bioinformatics.Journal of proteome research · 2025Review
- Advancing metagenomic classification with NABAS+: a novel alignment-based approach.NAR genomics and bioinformatics · 2025Article
- Bioinformatic approaches to blood and tissue microbiome analyses: challenges and perspectives.Briefings in bioinformatics · 2025Review
- Randomized Trial Demonstrating No Translocation of Intact Intestinal Bacteria During Hemodialysis or Hemodiafiltration.Kidney international reports · 2025Article
- Blood microbiome signatures in systemic diseases: current insights, methodological pitfalls, and future horizons.Frontiers in cellular and infection microbiology · 2025Review
- Common microbial signatures in blood and their amplification in clinical disorders.Gut microbes reports · 2025Review
- Sequencing the ocular surface microbiome: a review of methodological practices and considerations.Frontiers in ophthalmology · 2025Review
- Microbiota and urinary tumor immunity: Mechanisms, therapeutic implications, and future perspectives.Chinese journal of cancer research = Chung-kuo yen cheng yen chiu · 2024Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The human microbiome can play key roles in disease, and diagnostic testing will soon have the ability to examine these roles in the context of clinical applications. Currently, most diagnostic testing in pathology applications focuses on a small number of disease-causing microbes and dismisses the whole microbial community that causes or is modulated by disease. Microbiome modifications have already provided clinically relevant insights in gut and oral diseases, such as irritable bowel disease, but there are currently limitations when clinically examining microbiomes outside of these body sites. This is critical, as the majority of microbial samples used in pathology originate from body sites that contain low concentrations of microbial DNA, including skin, tissue, blood, and urine. These samples, also known as low microbial biomass samples, are difficult to examine without careful consideration and precautions to mitigate contamination and biases. Here, we present the limitations when analysing low microbial biomass samples using current protocols and techniques and highlight the advantages that microbiome testing can offer diagnostics in the future, if the proper precautions are implemented. Specifically, we discuss the sources of contamination and biases that may result in false assessments for these sample types. Finally, we provide recommendations to mitigate contamination and biases from low microbial biomass samples during diagnostic testing, which will be especially important to effectively diagnose and treat patients using microbiome analyses.
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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.