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Table 2. Quality assessment using the adapted NOS of all included articles
Selection Selection Selection Selection Comparability Outcome Outcome Outcome
Author, year Total
1 2 3 4 1 1 2 3
* * * * ** * * *
Arboleya et al., B A A A A B A A 9
2020 [31]
[36] * * * ** * * *
Cong et al., 2017 E A A A A B A A 8
Ford et al., 2019 [33] A * A * A * A * A ** B * A * A * 9
[19] * * * * * * * *
Gregory et al., 2016 B A A A B B A A 8
* * * * ** * * *
Khumbare et al., A A A A A B A A 9
2022 [34]
[37] * * * * ** * * *
Morais et al., 2021 A A A A A B A A 9
Parra-Llorca et al., B * A * A * A * A ** B * no FU n.a. 7
[35]
2018
Piñeiro-Ramos et al., B * A * A * A * A ** B * no FU n.a. 7
[32]
2021
Scoring by means of letters and stars are further explained in Supplementary File 2. Maximum score is 9 stars. A study can be awarded a
maximum of one star for each numbered item within the selection and outcome categories. A maximum of two stars can be given for
comparability. NOS: Newcastle-Ottawa Scale; FU: follow-up; n.a.: not applicable.

Taxonomy
The primary taxonomy differences between groups from birth till PMA 36 weeks are summarized in Table 3
and graphically depicted in Figure 3. Below are recurring differences mentioned across multiple studies,
categorized by phylum, to illustrate commonalities in this heterogeneous section. The MOM group serves as
a reference group in text, tables, and figures. No consistent differences at the taxonomic level were apparent
between subgroup A and subgroup B. Therefore, no distinction between the subgroups was made in the
text. [32]

Firmicutes
Seven studies reported differences in the Firmicutes phylum at different taxonomic levels [19,32-37] .

Ford et al., Morais et al., and Parra-Llorca et al. reported a higher abundance of Firmicutes at the phylum
level [33,35,37] in DHM-fed infants. Within the class Bacilli, two studies reported differences at the order
level [19,36] , two studies reported differences at the family level [32,35] , and four studies reported differences at the
genus level [33-35,37] . There are conflicting results at the order level, with Cong et al. stating a lower abundance
of Lactobacillales and Bacillales at all three time points , whereas Gregory et al. stated the abundance of the
[36]
two orders to be higher in DHM-fed infants . Within the reported outcomes in the class Bacilli, there are
[19]
commonalities in the reported differences within the Staphylococcaceae family. Piñeiro-Ramos et al.
reported higher abundances of the Staphylococcaceae family , and in the same direction, Parra-Llorca et
al., Morais et al., and Ford et al. showed an increased abundance of the Staphylococcus genus [33,35,37] .

Four studies stated differences at different taxonomic levels within the class Clostridia. Parra-Llorca et al.
reported a higher abundance of the Clostridiaceae family in DHM-fed infants. Khumbare et al. and Parra-
[35]
Llorca et al. stated a higher abundance of the genus Clostridium, whereas only Morais et al. stated a lower
abundance in the DHM cohorts [34-37] .

Actinobacteria
Seven studies reported consistent differences in the Actinobacteria phylum at different taxonomic