Exploring species-level infant gut bacterial biodiversity by meta-analysis and formulation of an optimized cultivation medium

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Date
2022-10
Authors
Alessandri, Giulia
Fontana, Federico
Mancabelli, Leonardo
Lugli, Gabriele Andrea
Tarracchini, Chiara
Argentini, Chiara
Longhi, Giulia
Viappiani, Alice
Milani, Christian
Turroni, Francesca
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Nature Research
Published Version
10.1038/s41522-022-00349-1
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Abstract
In vitro gut cultivation models provide host-uncoupled, fast, and cost-efficient solutions to investigate the effects of intrinsic and extrinsic factors impacting on both composition and functionality of the intestinal microbial ecosystem. However, to ensure the maintenance and survival of gut microbial players and preserve their functions, these systems require close monitoring of several variables, including oxygen concentration, pH, and temperature, as well as the use of a culture medium satisfying the microbial nutritional requirements. In this context, in order to identify the macro- and micro-nutrients necessary for in vitro cultivation of the infant gut microbiota, a meta-analysis based on 1669 publicly available shotgun metagenomic samples corresponding to fecal samples of healthy, full-term infants aged from a few days to three years was performed to define the predominant species characterizing the "infant-like" gut microbial ecosystem. A subsequent comparison of growth performances was made using infant fecal samples that contained the most abundant bacterial taxa of the infant gut microbiota, when cultivated on 18 different culture media. This growth analysis was performed by means of flow cytometry-based bacterial cell enumeration and shallow shotgun sequencing, which allowed the formulation of an optimized growth medium, i.e., Infant Gut Super Medium (IGSM), which maintains and sustains the infant gut microbial biodiversity under in vitro growth conditions. Furthermore, this formulation was used to evaluate the in vitro effect of two drugs commonly used in pediatrics, i.e., acetaminophen and simethicone, on the taxonomic composition of the infant gut microbiota.
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Microbiome , Bifidobacterium , Mucin , Strategies , Stability , Health impact
Citation
Alessandri, G., Fontana, F., Mancabelli, L., Lugli, G.A., Tarracchini, C., Argentini, C., Longhi, G., Viappiani, A., Milani, C., Turroni, F., Van Sinderen, D. and Ventura, M. (2022) ‘Exploring species-level infant gut bacterial biodiversity by meta-analysis and formulation of an optimized cultivation medium’, npj Biofilms and Microbiomes, 8, 88 (12pp). doi: 10.1038/s41522-022-00349-1
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https://hdl.handle.net/10468/15177
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APC Microbiome Ireland - Journal Articles
Microbiology - Journal Articles
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© The Author(s) 2022. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.