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

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Date
2023
Authors
Lugli, Gabriele Andrea
Mancabelli, Leonardo
Milani, Christian
Fontana, Federico
Tarracchini, Chiara
Alessandri, Giulia
van Sinderen, Douwe
Turroni, Francesca
Ventura, Marco
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Nature Research
Published Version
10.1038/s41522-023-00392-6
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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.
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Keywords
Gut microbiota development , Infant Community State Types , ICSTs , Microbe-based biodiversity
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
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https://hdl.handle.net/10468/15218
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APC Microbiome Ireland - Journal Articles
Microbiology - Journal Articles
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© 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/.