Phylogenetic and metabolic tracking of gut microbiota during perinatal development

Federica Del Chierico, Pamela Vernocchi, Andrea Petrucca, Paola Paci, Susana Fuentes, Giulia Praticò, Giorgio Capuani, Andrea Masotti, Sofia Reddel, Alessandra Russo, Cristina Vallone, Guglielmo Salvatori, Elsa Buffone, Fabrizio Signore, Giuliano Rigon, Andrea Dotta, Alfredo Miccheli, Willem M. De Vos, Bruno Dallapiccola, Lorenza Putignani

Research output: Contribution to journalArticlepeer-review


The colonization and development of gut microbiota immediately after birth is highly variable and depends on several factors, such as delivery mode and modality of feeding during the first months of life. A cohort of 31 mother and neonate pairs, including 25 at-term caesarean (CS) and 6 vaginally (V) delivered neonates (DNs), were included in this study and 121 meconium/faecal samples were collected at days 1 through 30 following birth. Operational taxonomic units (OTUs) were assessed in 69 stool samples by phylogenetic microarray HITChip and inter- and intra-individual distributions were established by inter-OTUs correlation matrices and OTUs co-occurrence or co-exclusion networks. 1H-NMR metabolites were determined in 70 stool samples, PCA analysis was performed on 55 CS DNs samples, and metabolome/OTUs co-correlations were assessed in 45 CS samples, providing an integrated map of the early microbiota OTUs-metabolome. A microbiota "core" of OTUs was identified that was independent of delivery mode and lactation stage, suggesting highly specialized communities that act as seminal colonizers of microbial networks. Correlations among OTUs, metabolites, and OTUs-metabolites revealed metabolic profiles associated with early microbial ecological dynamics, maturation of milk components, and host physiology.

Original languageEnglish
Article numbere0137347
JournalPLoS One
Issue number9
Publication statusPublished - Sep 2 2015

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)


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