ArticleScientific reports2023
Effect of in vitro cultivation on human gut microbiota composition using 16S rDNA amplicon sequencing and metabolomics approach.
Article in Scientific reports, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers, 1 of them a synthesis that pooled it.
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Who cites it
31 citing papers in PubMed, 1 synthesis or guideline pooled it, 44 citations in OpenAlex.
- Meta-analysis of the Microbial Diversity Cultured in Bioreactors Simulating the Gut Microbiome.Microbial ecology · 2024Pooled it
- Gut microbiota biomarkers of chronic kidney disease progression identified by 16S rDNA sequencing and machine learning.Renal failure · 2026Article
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- Incorporation of Cryptic Plasmid Energetics Improves Genome-Scale Metabolic Predictions in Probiotic E. coli Nissle 1917.Microbial biotechnology · 2026Article
- Tools and approaches to study the human gut virome: from the bench to bioinformatics.mSystems · 2026Review
- Pooled feces reduce the inter-sample variation of microbiota in pig models.BMC microbiology · 2026Article
- Flaxseed oil and probiotics protect against induced nonalcoholic fatty liver disease (NAFLD) in male rats.Open life sciences · 2026Article
- Bacterial colonized melanoma skin models allow to study host-microbe interactionsFrontiers in microbiology · 2026Article
- Isolation and characterization of lyticFrontiers in cellular and infection microbiology · 2026Article
- Article
- Optimized Protocol for the Collection, Cryopreservation, and In Vitro Cultivation of Human Gut Microbiota for Toxicomicrobiomics Applications.Bio-protocol · 2025Article
- In Vitro Fermentation Characteristics of Purified Short-Chain Inulin and Inulin Neoseries Oligosaccharides Produced from Red Onions.Foods (Basel, Switzerland) · 2025Article
- Dual action tofacitinib-loaded PLGA nanoparticles alleviate colitis in an IBD mouse model.Drug delivery and translational research · 2025Article
- Dual Nature of Bacteriophages: Friends or Foes in Minimally Processed Food Products-A Comprehensive Review.Viruses · 2025Review
- High-throughput workflow for cultivation and characterization of gut microbiota strains with anti-inflammatory properties and metabolite signature associated with gut-brain communication.Scientific reports · 2025Article
- Metagenomic profiling of plaque microbiota in Indian subjects: identified hidden ecological tapestry.Current genetics · 2025Article
- The living medicine inside us:Gut microbes reports · 2025Article
- Differential impacts of hemin and free iron on amoxicillin susceptibility inFrontiers in microbiology · 2025Article
- Article
- Microbiome in cancer metastasis: biological insights and emerging spatial omics methods.Frontiers in cellular and infection microbiology · 2025Review
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gut microbiota (GM) plays many key functions and helps maintain the host's health. Consequently, the development of GM cultivation under in vitro stimulating physiological conditions has gained extreme interest in different fields. In this study, we evaluated the impact of four culture media: Gut Microbiota Medium (GMM), Schaedler Broth (SM), Fermentation Medium (FM), and Carbohydrate Free Basal Medium (CFBM) on preserving the biodiversity and metabolic activity of human GM in batch in vitro cultures using PMA treatment coupled with 16S rDNA sequencing (PMA-seq) and LC-HR-MS/MS untargeted metabolomics supplemented with GC-MS SCFA profiling. Before the experiments, we determined the possibility of using the pooled faecal samples (MIX) from healthy donors (n = 15) as inoculum to reduce the number of variables and ensure the reproducibility of in vitro cultivation tests. Results showed the suitability of pooling faecal samples for in vitro cultivation study. Non-cultured MIX inoculum was characterized by higher α-diversity (Shannon effective count, and Effective microbial richness) compared to inocula from individual donors. After 24 h of cultivation, a significant effect of culture media composition on GM taxonomic and metabolomic profiles was observed. The SM and GMM had the highest α-diversity (Shannon effective count). The highest number of core ASVs (125) shared with non-cultured MIX inoculum and total SCFAs production was observed in the SM. These results might contribute to the development of standardized protocols for human GM in vitro cultivation by preventing methodological bias in the data.
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