ArticleClinical microbiology reviews2015
The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota.
Article in Clinical microbiology reviews, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 435 papers, 3 of them syntheses that pooled it.
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.
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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
435 citing papers in PubMed, 3 syntheses or guidelines pooled it, 733 citations in OpenAlex.
- Gut and Vaginal Microbiota in the Endometriosis: Systematic Review and Meta-Analysis.BioMed research international · 2023Pooled it
- Gut microbiota is a potential goalkeeper of dyslipidemia.Frontiers in endocrinology · 2022Pooled it
- Antimicrobial De-Escalation in the ICU: From Recommendations to Level of Evidence.Advances in therapy · 2020Pooled it
- Dereplication-assisted culturomics enables strain-level ecological analysis of the human gut microbiome.Gut microbes · 2026Article
- Liangfu Pill Alleviates Constipation-Predominant Irritable Bowel Syndrome through Modulation of 5-HT Signaling Pathway and Gut Microbiota.Chinese journal of integrative medicine · 2026Article
- From diet to function: using synthetic microbial communities to map gut microbial interactions.NPJ biofilms and microbiomes · 2026Review
- Beyond metagenomics: culturomics uncovers aerobic and facultative anaerobic bacterial diversity in the camel gut.Animal microbiome · 2026Article
- Article
- The gut-tumor connection: the role of microbiota in cancer progression and treatment strategies.Journal of advanced research · 2026Review
- Live tissue microbiota and bacterial translocation: mechanisms and translational perspectives in cardiometabolic diseases.Reviews in endocrine & metabolic disorders · 2026Review
- High-throughput single-cell isolation ofMicrobiology spectrum · 2026Article
- Multi-omics insights into dietary zinc-mediated reprogramming of the gut-nasal ecosystem in allergic rhinitis.Frontiers in allergy · 2026Article
- Low-Grade Inflammation: Pathophysiological Mechanisms and Drug Targets in Irritable Bowel Syndrome with Diarrhea.Journal of inflammation research · 2026Review
- From dysbiosis to tumorigenesis: microbiome-derived metabolites as emerging cancer biomarkers.Frontiers in microbiology · 2026Review
- Assessing endometrial microbiota in endometriosis: culturomics and sequencing analysis of receptive-phase tissue.Current research in microbial sciences · 2026Article
- Extensive cultivation of human gut phages revealing undescribedGut microbes · 2025Article
- Current concepts of Helicobacter pylori infection.European journal of medical research · 2025Review
- Article
- Lignocellulose degradation capabilities and distribution of antibiotic resistance genes and virulence factors in Clostridium from the gut of giant pandas.Communications biology · 2025Article
- Tunable lysis of functionalized nanocultures for efficient microbial and nucleic acid recovery.Chemical engineering journal (Lausanne, Switzerland : 1996) · 2025Article
375 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bacterial culture was the first method used to describe the human microbiota, but this method is considered outdated by many researchers. Metagenomics studies have since been applied to clinical microbiology; however, a "dark matter" of prokaryotes, which corresponds to a hole in our knowledge and includes minority bacterial populations, is not elucidated by these studies. By replicating the natural environment, environmental microbiologists were the first to reduce the "great plate count anomaly," which corresponds to the difference between microscopic and culture counts. The revolution in bacterial identification also allowed rapid progress. 16S rRNA bacterial identification allowed the accurate identification of new species. Mass spectrometry allowed the high-throughput identification of rare species and the detection of new species. By using these methods and by increasing the number of culture conditions, culturomics allowed the extension of the known human gut repertoire to levels equivalent to those of pyrosequencing. Finally, taxonogenomics strategies became an emerging method for describing new species, associating the genome sequence of the bacteria systematically. We provide a comprehensive review on these topics, demonstrating that both empirical and hypothesis-driven approaches will enable a rapid increase in the identification of the human prokaryote repertoire.
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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.