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

dc.contributor.authorLugli, Gabriele Andreaen
dc.contributor.authorMancabelli, Leonardoen
dc.contributor.authorMilani, Christianen
dc.contributor.authorFontana, Federicoen
dc.contributor.authorTarracchini, Chiaraen
dc.contributor.authorAlessandri, Giuliaen
dc.contributor.authorvan Sinderen, Douween
dc.contributor.authorTurroni, Francescaen
dc.contributor.authorVentura, Marcoen
dc.contributor.funderFondazione Cariparmaen
dc.contributor.funderScience Foundation Irelanden
dc.contributor.funderMinistero della Saluteen
dc.date.accessioned2023-11-09T16:14:13Z
dc.date.available2023-11-09T16:14:13Z
dc.date.issued2023en
dc.description.abstractDuring 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.sponsorshipFondazione Cariparma (Project “Parma Microbiota”); Italian Ministry of Health, Bando Ricerca Finalizzata (Grant Number GR-2018-12365988)en
dc.description.statusPeer revieweden
dc.description.versionPublished Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.articleid25en
dc.identifier.citationLugli, 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/s41522-023-00392-6en
dc.identifier.doi10.1038/s41522-023-00392-6en
dc.identifier.endpage13en
dc.identifier.issn2055-5008en
dc.identifier.journaltitleNpj Biofilms and Microbiomesen
dc.identifier.startpage1en
dc.identifier.urihttps://hdl.handle.net/10468/15218
dc.identifier.volume9en
dc.language.isoenen
dc.publisherNature Researchen
dc.relation.ispartofnpj Biofilms and Microbiomesen
dc.relation.projectinfo: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.urihttps://creativecommons.org/licenses/by/4.0/en
dc.subjectGut microbiota developmenten
dc.subjectInfant Community State Typesen
dc.subjectICSTsen
dc.subjectMicrobe-based biodiversityen
dc.titleComprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiotaen
dc.typeArticle (peer-reviewed)en
dc.typejournal-articleen
oaire.citation.issue1en
oaire.citation.volume9en
Files
Original bundle
Now showing 1 - 3 of 3
Loading...
Thumbnail Image
Name:
s41522-023-00392-6.pdf
Size:
2.89 MB
Format:
Adobe Portable Document Format
Description:
Published Version
Loading...
Thumbnail Image
Name:
41522_2023_392_MOESM1_ESM.xlsx
Size:
6.04 MB
Format:
Microsoft Excel XML
Description:
Supplementary Tables
Loading...
Thumbnail Image
Name:
41522_2023_392_MOESM2_ESM.pdf
Size:
111.99 KB
Format:
Adobe Portable Document Format
Description:
Supplementary Figure 1
License bundle
Now showing 1 - 1 of 1
Loading...
Thumbnail Image
Name:
license.txt
Size:
2.71 KB
Format:
Item-specific license agreed upon to submission
Description: