The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota

Abstract

The human gut microbiota is engaged in multiple interactions affecting host health during the host's entire life span. Microbes colonize the neonatal gut immediately following birth. The establishment and interactive development of this early gut microbiota are believed to be (at least partially) driven and modulated by specific compounds present in human milk. It has been shown that certain genomes of infant gut commensals, in particular those of bifidobacterial species, are genetically adapted to utilize specific glycans of this human secretory fluid, thus representing a very intriguing example of host-microbe coevolution, where both partners are believed to benefit. In recent years, various metagenomic studies have tried to dissect the composition and functionality of the infant gut microbiome and to explore the distribution across the different ecological niches of the infant gut biogeography of the corresponding microbial consortia, including those corresponding to bacteria and viruses, in healthy and ill subjects. Such analyses have linked certain features of the microbiota/microbiome, such as reduced diversity or aberrant composition, to intestinal illnesses in infants or disease states that are manifested at later stages of life, including asthma, inflammatory bowel disease, and metabolic disorders. Thus, a growing number of studies have reported on how the early human gut microbiota composition/development may affect risk factors related to adult health conditions. This concept has fueled the development of strategies to shape the infant microbiota composition based on various functional food products. In this review, we describe the infant microbiota, the mechanisms that drive its establishment and composition, and how microbial consortia may be molded by natural or artificial interventions. Finally, we discuss the relevance of key microbial players of the infant gut microbiota, in particular bifidobacteria, with respect to their role in health and disease.

C-section and the Neonatal Gut Microbiome Acquisition: Consequences for Future Health

“…Moreover, these authors, in good agreement with Milani et al [10], indicated that the phylum Firmicutes, mainly represented by Clostridium and Lactobacillus, is more increased in CS babies in comparison with VD neonates from birth to the third month of life. Rutayisire et al [13] did not show differences in the microbiota due to the delivery mode at the age of 6 and 12 months, a fact that was indeed reported by other authors even until 7 years of life (although differences at this age between babies born by CS and VD were less pronounced than in neonates) [10,14].…”

“…Moreover, these authors, in good agreement with Milani et al [10], indicated that the phylum Firmicutes, mainly represented by Clostridium and Lactobacillus, is more increased in CS babies in comparison with VD neonates from birth to the third month of life. Rutayisire et al [13] did not show differences in the microbiota due to the delivery mode at the age of 6 and 12 months, a fact that was indeed reported by other authors even until 7 years of life (although differences at this age between babies born by CS and VD were less pronounced than in neonates) [10,14]. Discrepancies in the results obtained by different authors can be partially explained by different concurrent and confounding factors that are not always properly identified as neonatal exposures (such as the IAP), or adequately reported (such as race or geographical differences), or even due to factors related with the experimental techniques used (dependent-and independent-culture techniques, DNA extraction methods, etc.).…”

“…Several studies have confirmed different intestinal microbiota patterns between CS and VD babies; however, the source of microbial transmission is not wholly clear [9]. CS babies are not directly exposed to mother vaginal microbiota, so this first inoculum comes from other maternal localizations, such as skin or mouth, or from non-maternal sources like the surrounding delivery environment [10]. Dominguez-Bello et al [11] showed that babies born by CS harboured, just after delivery, bacterial communities at different body sites (mouth, nasopharynges or meconium) similar to the mother's skin microbiota (Staphylococcus spp.…”

Meconium‐stained amniotic fluid as a protective factor against childhood dermatitis and skin rash‐related hospitalization in the offspring – a population‐based cohort analysis

“…2 The microbiome's assembly thought by many to begin at birth is known to be influenced by mode of delivery, type of feeding and use of antibiotics. 6 Other studies have supported that notion by demonstrating that the fetal meconium is not sterile. 6 Other studies have supported that notion by demonstrating that the fetal meconium is not sterile.…”

Liquid array diagnostics: a novel method for rapid detection of microbial communities in single-tube multiplex reactions

“…The field of gut microbiota analysis has, until now, been dominated by relatively small-scale explorative studies, with several contradicting findings obscuring the truth in literature [1,2]. We are therefore at a stage where high-throughput, low-cost, targeted approaches are needed in order to generalize knowledge, and to evaluate previous findings.…”