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Phylogenetic and Metabolic Tracking of Gut Microbiota during Perinatal Development.

Del Chierico F, Vernocchi P, Petrucca A, Paci P, Fuentes S, Praticò G, Capuani G, Masotti A, Reddel S, Russo A, Vallone C, Salvatori G, Buffone E, Signore F, Rigon G, Dotta A, Miccheli A, de Vos WM, Dallapiccola B, Putignani L - PLoS ONE (2015)

Bottom Line: 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.Correlations among OTUs, metabolites, and OTUs-metabolites revealed metabolic profiles associated with early microbial ecological dynamics, maturation of milk components, and host physiology.

View Article: PubMed Central - PubMed

Affiliation: Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.

ABSTRACT
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.

No MeSH data available.


Related in: MedlinePlus

Correlation heat-map between OTUs and faecal metabolites.Significant correlations (p<0.05) for Firmicutes (Panel A) and Verrucomicrobia (Panel B). 2OH3MB: 2-hydroxy-3-methylbutyrate; Isocapr: Isocaproate; Isoval: Isovalerate; Ile: Isoleucine; Leu: Leucine; EtOH: Ethanol; Fuc: Fucose; 3OH-Isoval: 3-hydroxyisovalerate; Lac: Lactate; Ala: Alanine; But: Butyrate; Ac: Acetate; N-Ac: N-Acetyl moiety; Glu: Glutamate; Suc: Succinate; DMA: Dimethylamine; Asp: Aspartate; TMA: Trimethylamine; Cr: Creatine; MA: Malonate; Cho: choline; MeOH: Methanol; Tyr: Tyrosine; Phe: Phenylalanine; For: Formate.
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pone.0137347.g007: Correlation heat-map between OTUs and faecal metabolites.Significant correlations (p<0.05) for Firmicutes (Panel A) and Verrucomicrobia (Panel B). 2OH3MB: 2-hydroxy-3-methylbutyrate; Isocapr: Isocaproate; Isoval: Isovalerate; Ile: Isoleucine; Leu: Leucine; EtOH: Ethanol; Fuc: Fucose; 3OH-Isoval: 3-hydroxyisovalerate; Lac: Lactate; Ala: Alanine; But: Butyrate; Ac: Acetate; N-Ac: N-Acetyl moiety; Glu: Glutamate; Suc: Succinate; DMA: Dimethylamine; Asp: Aspartate; TMA: Trimethylamine; Cr: Creatine; MA: Malonate; Cho: choline; MeOH: Methanol; Tyr: Tyrosine; Phe: Phenylalanine; For: Formate.

Mentions: Correlations between OTUs and acetate, AAs, NAc1, and NAc2 were also examined, with a focus on OTUs that were positively correlated with AAs and their derivatives and inversely correlated with acetate. Among Actinobacteria OTUs, Propionibacterium was positively correlated with leucine, isoleucine, isovalerate, propionate, glutamate, aspartate, and dimethylamine and negatively correlated with acetate (Fig 6, Panel A). Similarly, among Proteobacteria, Burkholderia was positively correlated with leucine, isoleucine, isovalerate, propionate, glutamate, aspartate, dimethylamine, and malonate and negatively correlated with acetate. Other bacterial OTUs were positively correlated with only AAs and their derivatives. In particular, Xanthomonadaceae (Proteobacteria) and Staphylococcus (Firmicutes) were positively correlated with isoleucine, 2-hydroxy-3-methylbutyrate, isocaproate, isovalerate, and aspartate (Fig 6, Panel C; Fig 7, Panel A). Other Proteobacteria, such as Enterobacter aerogenes, Leminorella, and Yersinia, were positively correlated with NAc1 and NAc2 and negatively correlated with butyrate (E. aerogenes only) or acetate (Leminorella only) (Fig 6, Panel C). Among Actinobacteria, Bifidobacterium was negatively correlated with leucine, isoleucine, 2-hydroxy-3-methylbutyrate, isocaproate, and isovalerate as well as with glutamate, malonate, and dimethylamine (Fig 6, Panel A). Among Firmicutes, Clostridium OTUs were positively correlated with acetate levels (Fig 7, panel A).


Phylogenetic and Metabolic Tracking of Gut Microbiota during Perinatal Development.

Del Chierico F, Vernocchi P, Petrucca A, Paci P, Fuentes S, Praticò G, Capuani G, Masotti A, Reddel S, Russo A, Vallone C, Salvatori G, Buffone E, Signore F, Rigon G, Dotta A, Miccheli A, de Vos WM, Dallapiccola B, Putignani L - PLoS ONE (2015)

Correlation heat-map between OTUs and faecal metabolites.Significant correlations (p<0.05) for Firmicutes (Panel A) and Verrucomicrobia (Panel B). 2OH3MB: 2-hydroxy-3-methylbutyrate; Isocapr: Isocaproate; Isoval: Isovalerate; Ile: Isoleucine; Leu: Leucine; EtOH: Ethanol; Fuc: Fucose; 3OH-Isoval: 3-hydroxyisovalerate; Lac: Lactate; Ala: Alanine; But: Butyrate; Ac: Acetate; N-Ac: N-Acetyl moiety; Glu: Glutamate; Suc: Succinate; DMA: Dimethylamine; Asp: Aspartate; TMA: Trimethylamine; Cr: Creatine; MA: Malonate; Cho: choline; MeOH: Methanol; Tyr: Tyrosine; Phe: Phenylalanine; For: Formate.
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Related In: Results  -  Collection

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pone.0137347.g007: Correlation heat-map between OTUs and faecal metabolites.Significant correlations (p<0.05) for Firmicutes (Panel A) and Verrucomicrobia (Panel B). 2OH3MB: 2-hydroxy-3-methylbutyrate; Isocapr: Isocaproate; Isoval: Isovalerate; Ile: Isoleucine; Leu: Leucine; EtOH: Ethanol; Fuc: Fucose; 3OH-Isoval: 3-hydroxyisovalerate; Lac: Lactate; Ala: Alanine; But: Butyrate; Ac: Acetate; N-Ac: N-Acetyl moiety; Glu: Glutamate; Suc: Succinate; DMA: Dimethylamine; Asp: Aspartate; TMA: Trimethylamine; Cr: Creatine; MA: Malonate; Cho: choline; MeOH: Methanol; Tyr: Tyrosine; Phe: Phenylalanine; For: Formate.
Mentions: Correlations between OTUs and acetate, AAs, NAc1, and NAc2 were also examined, with a focus on OTUs that were positively correlated with AAs and their derivatives and inversely correlated with acetate. Among Actinobacteria OTUs, Propionibacterium was positively correlated with leucine, isoleucine, isovalerate, propionate, glutamate, aspartate, and dimethylamine and negatively correlated with acetate (Fig 6, Panel A). Similarly, among Proteobacteria, Burkholderia was positively correlated with leucine, isoleucine, isovalerate, propionate, glutamate, aspartate, dimethylamine, and malonate and negatively correlated with acetate. Other bacterial OTUs were positively correlated with only AAs and their derivatives. In particular, Xanthomonadaceae (Proteobacteria) and Staphylococcus (Firmicutes) were positively correlated with isoleucine, 2-hydroxy-3-methylbutyrate, isocaproate, isovalerate, and aspartate (Fig 6, Panel C; Fig 7, Panel A). Other Proteobacteria, such as Enterobacter aerogenes, Leminorella, and Yersinia, were positively correlated with NAc1 and NAc2 and negatively correlated with butyrate (E. aerogenes only) or acetate (Leminorella only) (Fig 6, Panel C). Among Actinobacteria, Bifidobacterium was negatively correlated with leucine, isoleucine, 2-hydroxy-3-methylbutyrate, isocaproate, and isovalerate as well as with glutamate, malonate, and dimethylamine (Fig 6, Panel A). Among Firmicutes, Clostridium OTUs were positively correlated with acetate levels (Fig 7, panel A).

Bottom Line: 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.Correlations among OTUs, metabolites, and OTUs-metabolites revealed metabolic profiles associated with early microbial ecological dynamics, maturation of milk components, and host physiology.

View Article: PubMed Central - PubMed

Affiliation: Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.

ABSTRACT
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.

No MeSH data available.


Related in: MedlinePlus