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

Średnicka, Paulina; Roszko, Marek; Popowski, Dominik; Kowalczyk, Monika; Wójcicki, Michał; Emanowicz, Paulina; Szczepańska, Magdalena; Kotyrba, Danuta; Juszczuk-Kubiak, Edyta

doi:10.1038/s41598-023-29637-2

Cited by 9 publications

(8 citation statements)

References 99 publications

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“…S7 , Table S4 ). These results contrast those obtained by Średnicka et al (2023), who found higher α-diversity metrics in pooled samples from healthy donors than in individual stool samples [ 34 ].…”

Section: Discussioncontrasting

confidence: 99%

Meta-analysis of the Microbial Diversity Cultured in Bioreactors Simulating the Gut Microbiome

Garcia Mendez,

Egan,

Wist

et al. 2024

Microb Ecol

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Understanding the intricate ecological interactions within the gut microbiome and unravelling its impact on human health is a challenging task. Bioreactors are valuable tools that have contributed to our understanding of gut microbial ecology. However, there is a lack of studies describing and comparing the microbial diversity cultivated in these models. This knowledge is crucial for refining current models to reflect the gastrointestinal microbiome accurately. In this study, we analysed the microbial diversity of 1512 samples from 18 studies available in public repositories that employed cultures performed in batches and various bioreactor models to cultivate faecal microbiota. Community structure comparison between samples using t-distributed stochastic neighbour embedding and the Hellinger distance revealed a high variation between projects. The main driver of these differences was the inter-individual variation between the donor faecal inocula. Moreover, there was no overlap in the structure of the microbial communities between studies using the same bioreactor platform. In addition, α-diversity analysis using Hill numbers showed that highly complex bioreactors did not exhibit higher diversities than simpler designs. However, analyses of five projects in which the samples from the faecal inoculum were also provided revealed an amplicon sequence variants enrichment in bioreactors compared to the inoculum. Finally, a comparative analysis of the taxonomy of the families detected in the projects and the GMRepo database revealed bacterial families exclusively found in the bioreactor models. These findings highlight the potential of bioreactors to enrich low-abundance microorganisms from faecal samples, contributing to uncovering the gut microbial “dark matter”.

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Section: Discussioncontrasting

confidence: 99%

Meta-analysis of the Microbial Diversity Cultured in Bioreactors Simulating the Gut Microbiome

Garcia Mendez,

Egan,

Wist

et al. 2024

Microb Ecol

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“…The presence of a group of 15 different bacterial genera known to produce short chain fatty acid also called Butycore index was further observed in both microbiotherapy products and treated responder patients ( 18 ). Finally, Średnicka and colleagues ( 60 ) also observed a reduced variability and an increase in alpha-diversity metrics in fecal pooled inoculum used for in vitro culture.…”

Section: Discussionmentioning

confidence: 94%

Reduction of product composition variability using pooled microbiome ecosystem therapy and consequence in two infectious murine models

Reygner,

Delannoy,

Barba-Goudiaby

et al. 2024

Appl Environ Microbiol

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Growing evidence demonstrates the key role of the gut microbiota in human health and disease. The recent success of microbiotherapy products to treat recurrent Clostridioides difficile infection has shed light on its potential in conditions associated with gut dysbiosis, such as acute graft-versus-host disease, intestinal bowel diseases, neurodegenerative diseases, or even cancer. However, the difficulty in defining a “good” donor as well as the intrinsic variability of donor-derived products’ taxonomic composition limits the translatability and reproducibility of these studies. Thus, the pooling of donors’ feces has been proposed to homogenize product composition and achieve higher taxonomic richness and diversity. In this study, we compared the metagenomic profile of pooled products to corresponding single donor-derived products. We demonstrated that pooled products are more homogeneous, diverse, and enriched in beneficial bacteria known to produce anti-inflammatory short chain fatty acids compared to single donor-derived products. We then evaluated pooled products’ efficacy compared to corresponding single donor-derived products in Salmonella and C. difficile infectious mouse models. We were able to demonstrate that pooled products decreased pathogenicity by inducing a structural change in the intestinal microbiota composition. Single donor-derived product efficacy was variable, with some products failing to control disease progression. We further performed in vitro growth inhibition assays of two extremely drug-resistant bacteria, Enterococcus faecium vanA and Klebsiella pneumoniae oxa48, supporting the use of pooled microbiotherapies. Altogether, these results demonstrate that the heterogeneity of donor-derived products is corrected by pooled fecal microbiotherapies in several infectious preclinical models. IMPORTANCE Growing evidence demonstrates the key role of the gut microbiota in human health and disease. Recent Food and Drug Administration approval of fecal microbiotherapy products to treat recurrent Clostridioides difficile infection has shed light on their potential to treat pathological conditions associated with gut dysbiosis. In this study, we combined metagenomic analysis with in vitro and in vivo studies to compare the efficacy of pooled microbiotherapy products to corresponding single donor-derived products. We demonstrate that pooled products are more homogeneous, diverse, and enriched in beneficial bacteria compared to single donor-derived products. We further reveal that pooled products decreased Salmonella and Clostridioides difficile pathogenicity in mice, while single donor-derived product efficacy was variable, with some products failing to control disease progression. Altogether, these findings support the development of pooled microbiotherapies to overcome donor-dependent treatment efficacy.

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“…In addition, mGAM is a commercial medium initially developed for cultivating anaerobic bacteria and has demonstrated high e cacy in recovering gut microbiota [18,33,34]. Despite being a noncommercial medium, we compared GMM to other media as it has been widely used in gut microbiome research [18, [35][36][37]. Consequently, GMM induced a high dominance of Bacillota, while BCT and mGAM maintained microbial diversity during a 30-day incubation period (Fig.…”

Section: Discussionmentioning

confidence: 99%

A streamlined culturomics approach for the human gut microbiota research

Park,

Yeo,

Ryu

et al. 2024

Preprint

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Bacterial culturomics is a set of techniques to isolate and identify live bacteria from complex microbial ecosystems. Despite its potential to revolutionize microbiome research, bacterial culturomics has significant challenges when applied to human gut microbiome studies due to its labor-intensive nature. Therefore, we established a streamlined culturomics approach with minimal culture conditions for stool sample preincubation. We evaluated the suitability of non-selective medium candidates for maintaining microbial diversity during a 30-day incubation period based on 16S rRNA amplicon analysis. Subsequently, we applied four culture conditions (two preincubation media under an aerobic/anaerobic atmosphere) to isolate gut bacteria on a large scale from eight stool samples of healthy humans. We identified 8,141 isolates, classified into 263 bacterial species, including 12 novel species candidates. Our analysis of cultivation efficiency revealed that seven days of aerobic and ten days of anaerobic incubation captured approximately 91% and 95% of the identified species within each condition, respectively, with a synergistic effect confirmed when selected preincubation media were combined. Moreover, our culturomics findings expanded the coverage of gut microbial diversity compared to 16S rRNA amplicon sequencing results. In conclusion, this study demonstrated the potential of a streamlined culturomics approach for the efficient isolation of gut bacteria from human stool samples. This approach might pave the way for the broader adoption of culturomics in human gut microbiome studies, ultimately leading to a more comprehensive understanding of this complex microbial ecosystem.

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

Cited by 9 publications

References 99 publications

Meta-analysis of the Microbial Diversity Cultured in Bioreactors Simulating the Gut Microbiome

Meta-analysis of the Microbial Diversity Cultured in Bioreactors Simulating the Gut Microbiome

Reduction of product composition variability using pooled microbiome ecosystem therapy and consequence in two infectious murine models

A streamlined culturomics approach for the human gut microbiota research

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