ArticleFrontiers in microbiology2019
Optimization of Culturomics Strategy in Human Fecal Samples.
Article in Frontiers in microbiology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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33 citing papers in PubMed.
- Exploring the predominant factors associated with shaping the cultivable swine gut microbiota of Wuzhishan piglets under in vitro cultivation conditions.BMC microbiology · 2026Article
- Enhancing the fiber degradation efficiency in dairy cattle rumen through engineered bacterial communities.Microbiome · 2026Article
- Lignocellulose degradation capabilities and distribution of antibiotic resistance genes and virulence factors in Clostridium from the gut of giant pandas.Communications biology · 2025Article
- Isolation, culture, and in vitro functional validation of intratumor bacteria from lung cancer patients.BMC microbiology · 2025Article
- New insights into the cultivability of human milk bacteria from ingestion to digestion and implications for their Immunomodulatory properties.Scientific reports · 2025Article
- Integrating the milk microbiome signatures in mastitis: milk-omics and functional implications.World journal of microbiology & biotechnology · 2025Review
- Impact of Ex Vivo Bisphenol A Exposure on Gut Microbiota Dysbiosis and Its Association with Childhood Obesity.Journal of xenobiotics · 2025Article
- The mycobiome in human cancer: analytical challenges, molecular mechanisms, and therapeutic implications.Molecular cancer · 2025Review
- Culture-based characterization of gut microbiota in inflammatory bowel disease.Frontiers in microbiology · 2025Article
- The living medicine inside us:Gut microbes reports · 2025Article
- Multi-Omics Analysis Unravels the Impact of Stool Sample Logistics on Metabolites and Microbial Composition.Microorganisms · 2024Article
- Identification and Characterization of Human Breast Milk and Infant Fecal Cultivable Lactobacilli Isolated in Bulgaria: A Pilot Study.Microorganisms · 2024Article
- A streamlined culturomics case study for the human gut microbiota research.Scientific reports · 2024Article
- Advances in the isolation, cultivation, and identification of gut microbes.Military Medical Research · 2024Review
- Advances in Culturomics Research on the Human Gut Microbiome: Optimizing Medium Composition and Culture Techniques for Enhanced Microbial Discovery.Journal of microbiology and biotechnology · 2024Review
- An optimized culturomics strategy for isolation of human milk microbiota.Frontiers in microbiology · 2024Article
- Article
- Gut microbiome-derived hydrolases-an underrated target of natural product metabolism.Frontiers in cellular and infection microbiology · 2024Review
- Uncultured Microorganisms and Their Functions in the Fermentation Systems of Traditional Chinese Fermented Foods.Foods (Basel, Switzerland) · 2023Review
- Characterization of Lung and Oral Microbiomes in Lung Cancer Patients Using Culturomics and 16S rRNA Gene Sequencing.Microbiology spectrum · 2023Article
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Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Most bacteria in the human gut are difficult to culture, and culturomics has been designed to overcome this issue. Culturomics makes it possible to obtain living bacteria for further experiments, unlike metagenomics. However, culturomics is work-intensive, which prevents its wide application. In this study, we performed a 30-day continuous enrichment in blood culture bottles and cultured bacterial isolates from pre-cultures removed at different time points. We compared the bacteria isolated from the enriched culture with or without adding fresh medium after each pre-culture was removed. We also compared "experienced" colony picking (i.e., picking two to three colonies for each recognized colony type) and picking all the colonies from each plate. In total, from five fecal samples, 106 species were isolated, including three novel species and six that have not previously been isolated from the human body. Adding fresh medium to the culture increased the rate of bacterial species isolation by 22% compared with the non-supplemented culture. Picking all colonies increased the rate of bacterial isolation by only 8.5% compared with experienced colony picking. After optimization through statistical analysis and simulation, sampling aerobic and anaerobic enrichment cultures at six and seven time-points, respectively, is likely to isolate >90% of bacterial species, reducing the workload by 40%. In conclusion, an extended enrichment step ensures isolation of different bacterial species at different time-points, while adding the same quantity of fresh medium after sampling, the experienced picking and the optimized time-points favor the chance of isolating more bacterial species with less work.
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