Phylogenetic and Metabolic Tracking of Gut Microbiota during Perinatal Development.
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.
Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
Federica
F
Del Chierico
Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy; Interdipartimental Centre for Industrial Research-CIRI-AGRIFOOD, Alma Mater Studiorum, University of Bologna, Bologna, Italy.
Pamela
P
Vernocchi
Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy; Department of Diagnostic Science, Sant'Andrea Hospital, Rome, Italy.
Andrea
A
Petrucca
CNR, Institute of Systems Analysis and Informatics Antonio Ruberti, Rome, Italy.
Paola
P
Paci
Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
Susana
S
Fuentes
Department of Chemistry, Sapienza University, Rome, Italy.
Giulia
G
Praticò
Department of Chemistry, Sapienza University, Rome, Italy.
Giorgio
G
Capuani
Bambino Gesù Children Hospital, IRCCS, Rome, Italy.
Andrea
A
Masotti
Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
Sofia
S
Reddel
Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
Alessandra
A
Russo
Department of Obstetrics and Gyneacology, San Camillo Hospital, Rome, Italy.
Cristina
C
Vallone
Department of Neonatology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
Guglielmo
G
Salvatori
Department of Neonatology, San Camillo Hospital, Rome, Italy.
Elsa
E
Buffone
Department of Obstetrics and Gyneacology, San Camillo Hospital, Rome, Italy.
Fabrizio
F
Signore
Department of Obstetrics and Gyneacology, San Camillo Hospital, Rome, Italy.
Giuliano
G
Rigon
Department of Neonatology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
Andrea
A
Dotta
Department of Chemistry, Sapienza University, Rome, Italy.
Alfredo
A
Miccheli
Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands; Departments of Veterinary Biosciences and Bacteriology & Immunology, Helsinki University, Helsinki, Finland.
Willem M
WM
de Vos
Scientific Directorate, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
Bruno
B
Dallapiccola
Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy; Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
Lorenza
L
Putignani
D006801:Humans; D007231:Infant, Newborn; D007422:Intestines / Q000382:microbiology*; D009682:Magnetic Resonance Spectroscopy; D064307:Microbiota; D010802:Phylogeny