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Page 8 of 22 Borrego-Ruiz et al. Microbiome Res Rep. 2025;4:20 https://dx.doi.org/10.20517/mrr.2024.78

[75]
disruption of the GM balance and the sustained impacts on immune system disorders . This cross-talk
occurs through host-microbial interactions in the initial days of life, or via microbial acquisition in
gestation, indicating that the risk of disease may be established early in life, including during the prenatal
[60]
period .

Allergic diseases
Among the immune pathologies associated with the establishment of a specific microbiota, allergies,
especially in the form of atopic dermatitis (AD) and subsequently asthma, are probably the result of
inadequate GM development and the consequent disturbance of immune homeostasis in the initial year of
existence [76,77] . In the case of AD or eczema, several classic studies have provided evidence of early shifts in
the microbiota of infants who later developed this skin disease [20,78,79] . These investigations revealed
differences in the microbial composition of infant GM, with an increased abundance of clostridia and
Escherichia coli, and diminished levels of bifidobacteria and Faecalibacterium for the later development of

allergic disease [80,81] . Further research has shown that a decreased microbial α- and β-diversity of the early-life
microbiota and depletion of Bacteroides and Clostridium sensu stricto 1 directly correlate with later
development of eczema at one year of age [82-84] , and a reduction in eczema severity during the three-month
follow-up interval was directly associated with an enhancement in butyrate-producing bacteria, such as
Coprococcus eutactus [85,86] .

Although the development of asthma has been associated with genetic, epigenetic, and environmental
factors [87,88] , there is a growing recognition of the critical role that the GM plays in the perinatal
programming of this condition [89,90] . The concept of the “gut-lung axis” illustrates the influence of the GM
on lung immune function, both through direct activation of the innate immune response and indirectly via
the metabolites generated by gut microbes. The colonization of the intestinal microbes in newborns is
pivotal for their overall health, with dysbiosis occurring in the first 100 days and being particularly impactful
[91]
for the development of hypersensitivity disorders . Infants at risk for asthma have significantly reduced
relative abundances of the genera Rothia, Faecalibacterium, Lachnospira, and Veillonella, and these
dissimilarities in bacterial taxa abundance were also associated with distinct amounts of microbial
metabolites in feces . Additionally, lower gut microbiota diversity in the first month of life has been
[92]
[93]
associated with an increased incidence of asthma in children by age seven . Moreover, reduced levels of
Lachnospira combined with elevated levels of Clostridium spp., especially Clostridioides difficile, during
infancy are positively correlated with a greater risk of asthma development by the age of four or older [94,95] .

Metabolic disorders
The composition and function of the GM have been related to metabolic disorders, such as obesity and
obesity-related diseases. Adequate gut barrier function appears to be pivotal for metabolic health , but
[96]
various factors that disrupt this barrier and microbial eubiosis during early life play a critical role in
overweight, obesity development, and childhood adiposity later in life. The GM, by increasing energy
expenditure, may regulate obesity behavior and peripheral metabolism through the so-called obesogenic
[97]
microbiota . Several studies have indicated that various factors that impact the establishment of the GM
during infancy could contribute to the risk of obesity later in life, such as feed, maternal obesity, mode of
delivery, intestinal permeability, pathogenic infections, and antibiotic exposure [98-100] . Microbiota-related
obesity studies in humans have indicated that early microbial profiles may serve as predictors for
overweight in children . In this sense, it has been reported that overweight in seven-year-old children is
[101]
associated with increased abundance of members of the phylum Bacillota and decreased abundance of the
genus Bifidobacterium , while Bacteroides fragilis levels at 1 month of age were significantly correlated
[102]
with an increased body mass index in children .
[103]