Abstract
The field of genomics has expanded into subspecialties such as metagenomics over the course of the last decade and a half. The development of massively parallel sequencing capabilities has allowed for increasingly detailed study of the genome of the human microbiome, the microbial super organ that resides symbiotically within the mucosal tissues and integumentary system of the human host. The gut microbiome, and particularly the study of its origins in neonates, has become subtopics of great interest within the field of genomics. This brief review seeks to summarize recent literature regarding the origins and establishment of the neonatal gut microbiome, beginning in utero, and how it is affected by neonatal nutritional status (breastfed versus formula fed) and gestational age (term versus preterm). We also explore the role of dysbiosis, a perturbation within the fragile ecosystem of the microbiome, and its role in the origin of select pathologic states, specifically, obesity and necrotizing enterocolitis (NEC) in preterm infants. We discuss the evidence supporting enteral pre- and pro-biotic supplementation of commensal organisms such as Bifidobacterium and Lactobacillus in the neonatal period, and their role in the prevention and amelioration of NEC in premature infants. Finally, we review directions to consider for further research to promote human health within this field.
Highlights
The evolution of the field of genomics, spurred largely by the Human Genome Project, has given rise to metagenomics, or “the application of modern genomics techniques to the study of communities of microbial organisms directly in their natural environments” [1]
We explore the role of dysbiosis, a perturbation within the fragile ecosystem of the microbiome, and its role in the origin of select pathologic states, obesity and necrotizing enterocolitis (NEC) in preterm infants
We review differences in microbial colonization and immune function of the intestinal tract in healthy full-term newborns compared with their preterm very low birth weight (VLBW) counterparts and the implications for development of disease when the microbiome is disrupted
Summary
The evolution of the field of genomics, spurred largely by the Human Genome Project, has given rise to metagenomics, or “the application of modern genomics techniques to the study of communities of microbial organisms directly in their natural environments” [1]. Of particular interest is the study of the gut microbiome, its evolution beginning in utero and across the lifespan, its effect on promotion of health, and its role in the development of disease The purpose of this brief review is to introduce the reader to the concept of the human microbiome and to summarize recent literature regarding the neonatal gut microbiome, from its establishment at birth through its evolution during early infancy. Aagaard et al have recently characterized a placental microbiome profile, composed of non-pathogenic commensal microbiota from the Firmicutes, Tenericutes, Proteobacteria, Bacteroidetes, and Fusobacteria phyla which, interestingly, shares some similarities with the human oral microbiome [5] They observed that in the first week of life the fullterm neonatal gut microbiome is largely colonized by members of the Actinobacteria, Proteobacteria, Bacteroidetes, and, much less, Firmicutes phyla (Figure 1) [5, 6].
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