Although other species support this and challenge the

Although it was commonly
believed until recently that colonization of the gut begins at birth (154), studies examining microbiota in the amniotic
fluid, placenta, and meconium suggest that colonization of the gut begins in
utero via the maternal microbiota (155-158). Various findings in other species support this and
challenge the concept of gut sterility until birth (159). Meconium, previously thought to be sterile, is
now known to host complex bacterial communities and has been used as a
surrogate for fetal gut microbiota (160, 161). Hansen et al examined the presence and composition of
bacterial populations in healthy, term, vaginally delivered neonates using
fluorescent in situ hybridization
(FISH) and identified bacteria in meconium samples (161). In a separate study examining potential mechanisms
underlying preterm birth, neonatal meconium samples were analyzed and found to contain
bacterial species previously identified in amniotic fluid (162). The authors suggested that this not only supports that colonization
of the gut begins in utero, but also provides mounting evidence that
intrauterine infections can cause spontaneous preterm birth. Another study
comparing meconium and postnatal fecal samples from preterm infants
demonstrated a distinct microbial profile in meconium that differed from the profiles
in postnatal samples (163).

 

During and after birth, rapid
colonization of the gut occurs. Numerous factors affect the composition of
neonatal gut microbiota, particularly mode of delivery (164, 165). The gut microbiota of infants delivered vaginally differs
from that of infants delivered by caesarean section, with the mother’s vaginal
and fecal microbiome being significant influences, although the importance of
this has not yet been elucidated (166). Other factors that affect colonization of the
neonatal gut include whether a cesarean section is planned and occurs before
rupture of the membranes, as a rupture during labor results in exposure to
vaginal microbes; the administration of antibiotics and, in particular, the
first exposure to a given antibiotic; and whether infants are breast- or
formula-fed (167, 168). Interestingly, one study suggested that children born via
cesarean section had increased risks for overweight and obesity (169), although whether this was associated with
altered gut microbial profiles was not determined.

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Gut bacterial translocation refers
to the passage of viable bacteria from the gut to extraintestinal sites,
including the mesenteric lymph nodes, liver, and kidney (170). Bacterial translocation, while predominantly
associated with pathogenic conditions, has also been shown to occur in healthy
individuals without significant detriment (171). Throughout pregnancy and lactation, physiologic
and anatomic alterations occur in the mother that potentially facilitate
increased bacterial translocation, and it has also been suggested that
translocation of bacteria from the maternal gut, via mononuclear cells and the
bacterial entero-mammary pathway, may be a mechanism by which maternal gut
microbiota affect the colonization of breast-fed infants (172). Furthermore, viable bacteria found in human
breast cells are also found in maternal peripheral blood mononuclear cells, supporting
that bacteria from the gut may translocate to the lactating breast (173). In a recent comparison of fetal microbiota in five primate species
(Homo sapiens, Pan troglodytes, P.
paniscus, Gorilla gorilla and G.
beringei), researchers found evidence for phylogenetically conserved
composition of the gut microbiome, suggesting vertical transmission of microbiota
from generation to generation in addition to the initial colonization from the
maternal microbiota (174). These findings also support the hypothesis that
gut microbiota and their respective hosts have evolved in tandem (175).

 

Gut microbial profiles in
infants appear to be less complex than adult profiles, but exhibit greater
interpersonal variation in terms of taxonomy and functional gene content (176, 177). Dramatic shifts in gut microbial profiles occur with
transitions to new diets, beginning with the transition from milk to baby food (178). Following the introduction of solid foods, an “adult-like”
microbial profile begins to take form. The diverse microbial profiles seen in
infants begin to converge, and adult gut microbial profiles are attained by 2-5
years of age (178). Adult microbial populations tend to remain stable unless
altered by diet, antibiotic and probiotic use, or other factors,  becoming more unstable again in elderly
populations. The strong influence of diet is illustrated by an examination of
gut microbiomes across ages and communities in Venezuelan Amerindian
populations, rural Malawian African populations and U.S. populations, which
revealed distinct differences in the gut microbiome profiles in US populations
as compared to the Venezuelan and Malawian populations at all ages (178).