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

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dc.contributor.authorAlessandri, Giulia
dc.contributor.authorFontana, Federico
dc.contributor.authorMancabelli, Leonardo
dc.contributor.authorLugli, Gabriele Andrea
dc.contributor.authorTarracchini, Chiara
dc.contributor.authorArgentini, Chiara
dc.contributor.authorLonghi, Giulia
dc.contributor.authorViappiani, Alice
dc.contributor.authorMilani, Christian
dc.contributor.authorTurroni, Francesca
dc.contributor.authorvan Sinderen, Douwe
dc.contributor.authorVentura, Marco
dc.contributor.funderGenProbio srl
dc.contributor.funderUniversità degli Studi di Parma
dc.contributor.funderScience Foundation Ireland
dc.contributor.funderFondazione Cariparma
dc.contributor.funderMinistero della Salute
dc.date.accessioned2023-11-01T15:59:15Z
dc.date.available2023-11-01T15:12:32Zen
dc.date.available2023-11-01T15:59:15Z
dc.date.issued2022-10en
dc.date.updated2023-11-01T15:12:35Zen
dc.description.abstractIn 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.en
dc.description.statusPeer revieweden
dc.description.versionPublished Version
dc.format.mimetypeapplication/pdfen
dc.identifier.articleid88
dc.identifier.citationAlessandri, 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
dc.identifier.doi10.1038/s41522-022-00349-1en
dc.identifier.eissn2055-5008
dc.identifier.endpage12
dc.identifier.journaltitlenpj Biofilms and Microbiomes
dc.identifier.startpage1
dc.identifier.urihttps://hdl.handle.net/10468/15177
dc.identifier.volume8
dc.language.isoenen
dc.publisherNature Research
dc.relation.projectinfo:eu-repo/grantAgreement/SFI/SFI Research Centres/12/RC/2273/IE/Alimentary Pharmabiotic Centre (APC) - Interfacing Food & Medicine/
dc.rights© 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/.
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectMicrobiome
dc.subjectBifidobacterium
dc.subjectMucin
dc.subjectStrategies
dc.subjectStability
dc.subjectHealth impact
dc.titleExploring species-level infant gut bacterial biodiversity by meta-analysis and formulation of an optimized cultivation mediumen
dc.typeArticle (peer-reviewed)
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