Page 29 - Read Online

Horwell et al. Microbiome Res Rep 2025;4:1 https://dx.doi.org/10.20517/mrr.2024.32 Page 7 of 20

metagenomic studies of fresh milk and milk stored at 4 °C show no significant difference, there is a
significant reduction in viable bacterial species - for instance, Lactobacillus and Streptococcus spp., possibly
explaining the differences in the microbiome of these two cohorts of children (i.e., fresh human breast milk
[101]
vs. refrigerated human breast milk) .

Human breast milk has a complex mixture of essential macronutrients that help a newborn’s normal
development, as well as acting as a prebiotic. It also contains immunogenic compounds, such as SIgA (and,
to a lesser extent, IgM and IgG), which provide a degree of passive immunity for the newborn to specific
pathogens [102,103] . As with the mode of delivery, the difference between the microbiomes of children who are
formula- vs. breast milk-fed has been proposed as a causative factor for several associated pathologies.
Voluminous epidemiological studies and the cumulative power of their meta-analyses have shown clear
associations between breastfeeding and beneficial health outcomes. The comprehensive list includes a
[104]
reduced risk of: asthma [104]* , eczema , respiratory infections [105]* , IBD [106]* , infectious diarrhoeal

[113]
[112]
diseases [105,107]* , leukaemia [108]* , diabetes melitus [109,110] , obesity [111]* , acute otitis media , dental caries , and
general intelligence . Several of these papers have gone further to demonstrate a protective dose response
[114]
to the aforementioned ( ) pathologies, giving credence to a mechanistic link. The precise time when the
*
benefits from EBF start to taper off is not clear, with conflicting evidence between four and six months as
the cut-off times. A Cochrane review found that the balance of evidence supports EBF for six months,
which is reflected in the international guidance [115-117] .
After breastfeeding (the transitional and stable phases)
At approximately 12 months, coinciding when the majority of infants have completed weaning, the
microbiome changes sharply. The cessation of EBF and the introduction of solid food results in a shift
towards species that are predominantly fermenters of plant-based polysaccharides and fibres, converting
them into SCFAs, such as butyrate . SCFAs are known to be essential for colonocyte metabolic health, as
[17]
[118]
well as having anti-inflammatory and anti-carcinogenic properties . This is characterised by an increase in
Bacteroides, Clostridium, Enterobacteria, Enterococci, and Streptococcus [17,119] . Infants with a high-fibre diet
[120]
display a considerable increase in Bacteroidetes . In the distal colon, these phyla further contribute to the
host through the biosynthesis of vitamins and essential amino acids . It has been suggested that a
[119]
westernised diet during this period reduces the populations of Bacteroidetes and Prevotella, which may lead
to dysbiosis and partly explain the increased risk of IBD . Interestingly, this shift in the microbiome is
[119]
[17]
most apparent when breastfeeding stops, rather than when food is introduced . This effect is less evident
in formula-fed infants as their diet already included complex nutritional compounds that had resulted in a
more diverse microbiome earlier in life . After 12-24 months, this highly plastic phase starts to stabilise
[121]
and resembles the microbiome of adults. It is during this period that other environmental stimuli start to
have an impact on the microbiome.

ENVIRONMENTAL FACTORS
The home environment
[122]
Studies have shown that modern humans spend just under 90% of their time indoors . It, therefore,
logically follows that the home environment would have a significant environmental influence on the
microbiome of children. The microbiome of modern homes, compared to pre-industrial home
environments that were intertwined with soil, plant and animal microbial life, is low in both diversity and
abundance. This is exacerbated by the scarcity of nutrients, modern surface materials, and chemicals used to
keep homes clean. These selective pressures result in a relative increase in environmental exposure to
Basidiomycota, Deinococcus, Enhydrobacter, Micrococcus, Paracoccus, Staphylococcus, and Streptococcus [123,124] .
It has been suggested that indoor plants go some way in increasing microbial diversity and provide
a protected environment for microbial life, allowing stabilisation of the home