dc.contributor.author	Lugli, Gabriele Andrea	en
dc.contributor.author	Mancabelli, Leonardo	en
dc.contributor.author	Milani, Christian	en
dc.contributor.author	Fontana, Federico	en
dc.contributor.author	Tarracchini, Chiara	en
dc.contributor.author	Alessandri, Giulia	en
dc.contributor.author	van Sinderen, Douwe	en
dc.contributor.author	Turroni, Francesca	en
dc.contributor.author	Ventura, Marco	en
dc.contributor.funder	Fondazione Cariparma	en
dc.contributor.funder	Science Foundation Ireland	en
dc.contributor.funder	Ministero della Salute	en
dc.date.accessioned	2023-11-09T16:14:13Z
dc.date.available	2023-11-09T16:14:13Z
dc.date.issued	2023	en
dc.description.abstract	During infancy, gut microbiota development is a crucial process involved in the establishment of microbe–host interactions which may persist throughout adulthood, and which are believed to influence host health. To fully understand the complexities of such interactions, it is essential to assess gut microbiota diversity of newborns and its associated microbial dynamics and relationships pertaining to health and disease. To explore microbial biodiversity during the first 3 years of human life, 10,935 shotgun metagenomic datasets were taxonomically and functionally classified. Microbial species distribution between infants revealed the presence of eight major Infant Community State Types (ICSTs), being dominated by 17 bacterial taxa, whose distribution was shown to correspond to the geographical origin and infant health status. In total, 2390 chromosomal sequences of the predominant taxa were reconstructed from metagenomic data and used in combination with 44,987 publicly available genomes to trace the distribution of microbial Population Subspecies (PS) within the different infant groups, revealing patterns of multistrain coexistence among ICSTs. Finally, implementation of a metagenomic- and metatranscriptomic-based metabolic profiling highlighted different enzymatic expression patterns of the gut microbiota that allowed us to acquire insights into mechanistic aspects of health-gut microbiota interplay in newborns. Comparison between metagenomic and metatranscriptomic data highlights how a complex environment like the human gut must be investigated by employing both sequencing methodologies and possibly supplemented with metabolomics approaches. While metagenomic analyses are very useful for microbial classification aimed at unveiling key players driving microbiota balances, using these data to explain functionalities of the microbiota is not always warranted.	en
dc.description.sponsorship	Fondazione Cariparma (Project “Parma Microbiota”); Italian Ministry of Health, Bando Ricerca Finalizzata (Grant Number GR-2018-12365988)	en
dc.description.status	Peer reviewed	en
dc.description.version	Published Version	en
dc.format.mimetype	application/pdf	en
dc.identifier.articleid	25	en
dc.identifier.citation	Lugli, G. A., Mancabelli, L., Milani, C., Fontana, F., Tarracchini, C., Alessandri, G., Van Sinderen, D., Turroni, F., and Ventura, M. (2023) 'Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota',Npj Biofilms and Microbiomes, 9(1), 25 (13pp). doi: 10.1038/s41522-023-00392-6	en
dc.identifier.doi	10.1038/s41522-023-00392-6	en
dc.identifier.endpage	13	en
dc.identifier.issn	2055-5008	en
dc.identifier.journaltitle	Npj Biofilms and Microbiomes	en
dc.identifier.startpage	1	en
dc.identifier.uri	https://hdl.handle.net/10468/15218
dc.identifier.volume	9	en
dc.language.iso	en	en
dc.publisher	Nature Research	en
dc.relation.ispartof	npj Biofilms and Microbiomes	en
dc.relation.project	info:eu-repo/grantAgreement/SFI/SFI Research Centres/12/RC/2273/IE/Alimentary Pharmabiotic Centre (APC) - Interfacing Food & Medicine/	en
dc.rights	© The Author(s) 2023. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use,sharing, adaptation, distribution and reproduction in any medium o rformat, 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 wil lneed to obtain permission directly from the copyright holder. To view a copy of this license,visit http:// creativecommons.org/licenses/by/4.0/.	en
dc.rights.uri	https://creativecommons.org/licenses/by/4.0/	en
dc.subject	Gut microbiota development	en
dc.subject	Infant Community State Types	en
dc.subject	ICSTs	en
dc.subject	Microbe-based biodiversity	en
dc.title	Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota	en
dc.type	Article (peer-reviewed)	en
dc.type	journal-article	en
oaire.citation.issue	1	en
oaire.citation.volume	9	en

Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota

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