ReviewClinical microbiology reviews2020
State of the Art in the Culture of the Human Microbiota: New Interests and Strategies.
Review in Clinical microbiology reviews, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- Gut Microbiota as a Molecular Regulator of Mineral Homeostasis in Horses: Mechanisms and Future Perspectives.International journal of molecular sciences · 2026Review
- Translational Modeling of Gut Microbiome-Mediated Drug Metabolism: A Case Example of Sulfasalazine.CPT: pharmacometrics & systems pharmacology · 2026Article
- Infant gut microbiota coverage by different culture media.BMC microbiology · 2026Article
- Article
- Optimized Selective Media Enhance the Isolation and Characterization of Gut-Derived Probiotic Yeasts.Journal of fungi (Basel, Switzerland) · 2025Article
- Long-read metagenomics for strain tracking after faecal microbiota transplant.Nature microbiology · 2025Article
- Lignocellulose degradation capabilities and distribution of antibiotic resistance genes and virulence factors in Clostridium from the gut of giant pandas.Communications biology · 2025Article
- Prebiotic Structural Diversity Shapes Gut Microbial Diversity, Community Composition, and Metabolic Activity In Vitro.Foods (Basel, Switzerland) · 2025Article
- Enteric microbiome and obesity: a multidimensional narrative review.Microbial genomics · 2025Review
- Article
- Long read metagenomics-based precise tracking of bacterial strains and genomic changes after fecal microbiota transplantation.bioRxiv : the preprint server for biology · 2025Article
- Rapid diagnosis of urinary tract infection with miniaturised point-of-care cultivation on a dipstick.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2025Review
- Comparative analysis of three experimental methods for revealing human fecal microbial diversity.BMC microbiology · 2025Article
- Culturable Human Microorganisms and the Impact of Transportation Conditions on Cultivability.Microorganisms · 2025Article
- Fungi in the Gut Microbiota: Interactions, Homeostasis, and Host Physiology.Microorganisms · 2025Review
- Microbial insights into ruminal fiber degradation and feed efficiency of Hu sheep.Frontiers in microbiology · 2025Article
- The Gut Microbiota Impacts Gastrointestinal Cancers through Obesity, Diabetes, and Chronic Inflammation.Life (Basel, Switzerland) · 2024Review
- A streamlined culturomics case study for the human gut microbiota research.Scientific reports · 2024Article
- Multiplexing the Identification of Microorganisms via Tandem Mass Tag Labeling Augmented by Interference Removal through a Novel Modification of the Expectation Maximization Algorithm.Journal of the American Society for Mass Spectrometry · 2024Article
- An optimized culturomics strategy for isolation of human milk microbiota.Frontiers in microbiology · 2024Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The last 5 years have seen a turning point in the study of the gut microbiota with a rebirth of culture-dependent approaches to study the gut microbiota. High-throughput methods have been developed to study bacterial diversity with culture conditions aimed at mimicking the gut environment by using rich media such as YCFA (yeast extract, casein hydrolysate, fatty acids) and Gifu anaerobic medium in an anaerobic workstation, as well as media enriched with rumen and blood and coculture, to mimic the symbiosis of the gut microbiota. Other culture conditions target phenotypic and metabolic features of bacterial species to facilitate their isolation. Preexisting technologies such as next-generation sequencing and flow cytometry have also been utilized to develop innovative methods to isolate previously uncultured bacteria or explore viability in samples of interest. These techniques have been applied to isolate CPR (Candidate Phyla Radiation) among other, more classic approaches. Methanogenic archaeal and fungal cultures present different challenges than bacterial cultures. Efforts to improve the available systems to grow archaea have been successful through coculture systems. For fungi that are more easily isolated from the human microbiota, the challenge resides in the identification of the isolates, which has been approached by applying matrix-assisted laser desorption ionization-time of flight mass spectrometry technology to fungi. Bacteriotherapy represents a nonnegligible avenue in the future of medicine to correct dysbiosis and improve health or response to therapy. Although great strides have been achieved in the last 5 years, efforts in bacterial culture need to be sustained to continue deciphering the dark matter of metagenomics, particularly CPR, and extend these methods to archaea and fungi.
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