Comparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach

Tomás Clive Barker-Tejeda, Elisa Zubeldia-Varela, Andrea Macías-Camero, Lola Alonso, Isabel Adoración Martín-Antoniano, María Fernanda Rey-Stolle, Leticia Mera-Berriatua, Raphaëlle Bazire, Paula Cabrera-Freitag, Meera Shanmuganathan, Philip Britz-McKibbin, Carles Ubeda, M. Pilar Francino, Domingo Barber, María Dolores Ibáñez-Sandín, Coral Barbas, Marina Pérez-Gordo () and Alma Villaseñor ()
Additional contact information
Tomás Clive Barker-Tejeda: Universidad San Pablo-CEU, CEU Universities
Elisa Zubeldia-Varela: Universidad San Pablo-CEU, CEU Universities
Andrea Macías-Camero: Universidad San Pablo-CEU, CEU Universities
Lola Alonso: Spanish National Cancer Research Centre (CNIO)
Isabel Adoración Martín-Antoniano: Universidad San Pablo-CEU, CEU Universities
María Fernanda Rey-Stolle: Universidad San Pablo-CEU, CEU Universities
Leticia Mera-Berriatua: Universidad San Pablo-CEU, CEU Universities
Raphaëlle Bazire: Hospital Infantil Niño Jesús, Fib-HNJ
Paula Cabrera-Freitag: Hospital General Universitario Gregorio Marañón, and Gregorio Marañón Health Research Institute
Meera Shanmuganathan: McMaster University
Philip Britz-McKibbin: McMaster University
Carles Ubeda: Fundació per al Foment de la Investigació Sanitària i Biomèdica de la Comunitat Valenciana (FISABIO)
M. Pilar Francino: CIBER en Epidemiología y Salud Pública
Domingo Barber: Universidad San Pablo-CEU, CEU Universities
María Dolores Ibáñez-Sandín: Hospital Infantil Niño Jesús, Fib-HNJ
Coral Barbas: Universidad San Pablo-CEU, CEU Universities
Marina Pérez-Gordo: Universidad San Pablo-CEU, CEU Universities
Alma Villaseñor: Universidad San Pablo-CEU, CEU Universities

Nature Communications, 2024, vol. 15, issue 1, 1-21

Abstract: Abstract The human gut microbiome establishes and matures during infancy, and dysregulation at this stage may lead to pathologies later in life. We conducted a multi-omics study comprising three generations of family members to investigate the early development of the gut microbiota. Fecal samples from 200 individuals, including infants (0-12 months old; 55% females, 45% males) and their respective mothers and grandmothers, were analyzed using two independent metabolomics platforms and metagenomics. For metabolomics, gas chromatography and capillary electrophoresis coupled to mass spectrometry were applied. For metagenomics, both 16S rRNA gene and shotgun sequencing were performed. Here we show that infants greatly vary from their elders in fecal microbiota populations, function, and metabolome. Infants have a less diverse microbiota than adults and present differences in several metabolite classes, such as short- and branched-chain fatty acids, which are associated with shifts in bacterial populations. These findings provide innovative biochemical insights into the shaping of the gut microbiome within the same generational line that could be beneficial in improving childhood health outcomes.

Date: 2024
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DOI: 10.1038/s41467-024-47182-y

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