Three-generation family gut microbiome cohort, Spain

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.

Classified as human gut / stool shotgun DNA metagenome of infant / toddler and adult and child by deterministic_prior with confidence 0.90. Assay shotgun_dna.

• host external_curation.infant_catalog · “infant triage verdict include”
• body site study.title · “of the infant gut microbiome and their”
• body site study.description · “The human gut microbiome establishes and”
• life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
• life stage study.title · “characterization of the infant gut microbiome and”
• life stage study.title · “microbiome and their maternal lineage by a”
• life stage study.description · “and their respective mothers and grandmothers, were”
• life stage study.description · “beneficial in improving childhood health outcomes.”

256 runs over 128 samples · mean 1.01 Gbp per run (median 0.57 Gbp, total 257.99 Gbp; 256 runs with a base count) · layout SINGLE 256 · platform ILLUMINA 256 · models Illumina MiSeq (256) · 45% of runs with a Sandpiper profile · first public 2024-03-24

Barker-Tejeda TC first · Zubeldia-Varela E · Macías-Camero A · Alonso L · Martín-Antoniano IA · Rey-Stolle MF · Mera-Berriatua L · Bazire R · Cabrera-Freitag P · Shanmuganathan M · Britz-McKibbin P · Ubeda C · Francino MP · Barber D · Ibáñez-Sandín MD · Barbas C · Pérez-Gordo M · Villaseñor A last · Tarracchini C first · Longhi G · Gennaioli E · Muscò A · Rizzo SM · Viappiani A · Vitale SG · Mancabelli L · Lugli GA · Angioni S · Turroni F · van Sinderen D · Milani C · Ventura M last

2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata

PRJNA991269.csv.gz (5.0 KB) · parquet (76.5 KB) — all 128 samples, every field with route and confidence · PRJNA991269_determinations.csv.gz (9.2 KB) — 1,014 evidence rows