Effect of in vitro cultivation on human gut microbiota composition using 16S rDNA amplicon sequencing and metabolomics approach

• Published in: Scientific reports Vol. 13; no. 1; pp. 3026 - 25
• Main Authors: Średnicka, Paulina, Roszko, Marek Łukasz, Popowski, Dominik, Kowalczyk, Monika, Wójcicki, Michał, Emanowicz, Paulina, Szczepańska, Magdalena, Kotyrba, Danuta, Juszczuk-Kubiak, Edyta
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 21.02.2023; Nature Publishing Group; Nature Portfolio
• Subjects: 631/1647/1513; 631/1647/2217; 631/1647/2234; 631/1647/320; 631/1647/48; 631/1647/514; 631/208/325; 631/326/2565/2134; Biodiversity; Cultivation; Culture media; Culture Media - pharmacology; DNA, Ribosomal; Feces; Fermentation; Gastrointestinal Microbiome; Humanities and Social Sciences; Humans; Inoculum; Intestinal microflora; Metabolomics; Microbiota; Microorganisms; multidisciplinary; Reproducibility of Results; RNA, Ribosomal, 16S - genetics; rRNA 16S; Science; Science (multidisciplinary); Tandem Mass Spectrometry
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-023-29637-2

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.