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Chen et al. Microbiome Res Rep 2025;4:8 https://dx.doi.org/10.20517/mrr.2024.44 Page 11 of 18

et al., 2018, feeding differences based on observed OTUs (P = (Family level) ↑ Clostridiaceae ↓ Bifidobacteriaceae
[35]
Spain achieved 0.001) (both P < 0.05)
(Genus Level) ↓ Bifidobacterium, unclassified
Enterobacteriaceae (both P < 0.05)
DESeq2: ↑ Staphylococcus, Clostridium, Serratia, Coprococcus,

Aggregatibacter, Lactobacillus, ↓ Bacteroides, Acinetobacter,
Haemophilus (all P < 0.05)
* ** ***
This includes a formula feeding group; model adjusted for: gestational age, mode of delivery, z-scores growth parameters at birth, infant’s antibiotic therapy received within 8 days prior to fecal collection; total
number of samples, unknown number for subgroups. DoL: Day of life; WoL: week of life; OTU: operational taxonomic unit; DHM: donor human milk; MOM: mother’s own milk; PMA: postmenstrual age; PCoA:
principal coordinates analysis; UNIFRAC: unique fraction metric; PERMANOVA: permutational multivariate analysis of variance; RT-PCR: reverse transcription polymerase chain reaction; RDA: redundancy analysis.

levels [19,31,33-37] . Ford et al., Morais et al., and Parra-Llorca et al. stated lower abundances of Actinobacteria at the phylum level in the DHM groups [33,35,37] . Cong et
al. stated Actinomycetales at the order level have lower abundances . There are quite some commonalities in the Bifidobacteriales order in that Cong et al.
[36]
stated lower abundance of the Bifidobacteriales order, while Ford et al., Morais et al., and Parra-Llorca et al. stated lower abundance of the Bifidobacterium
genus and Khumbare et al. stated lower prevalence of the Bifidobacterium genus in the samples from mostly DHM-fed infants [33-35,37] . Arboleya et al. focused
solely on the Bifidobacterial population at the species level . Although in both feeding groups, B. breve and B. longum ssp. longum were the species with the
[31]
highest abundances during the study period, there were some differences in the abundances of other species. Notably, B. animalis ssp lactis, B. bifidum, and B.
dentium were higher in the DHM group in terms of relative abundance. Only Gregory et al. stated no differences in the succession of Bifidobacteriales .
[19]
Proteobacteria
[33]
Ford et al. reported an increasing relative abundance of Proteobacteria in all study subjects over time . Five studies reported differences in the Proteobacteria
phylum at different taxonomic levels, with conflicting results [32,34-37] . Morais et al. stated lower abundances of the Proteobacteria phylum . In the
[37]
Enterobacterales order, Cong et al. stated higher abundances of Enterobacterales . Khumbare et al. and Parra-Llorca et al. stated lower abundances of an
[36]
unclassified genus of the Enterobacteriaceae family [34,35] . In addition, Morais et al. stated a lower abundance of the E. coli species and Serratia genus, whereas
Parra-Llorca et al. stated a higher abundance of Serratia [35,37] .

In the Pasteurellales order, a similar pattern of inconsistency is visible. Cong et al. stated a lower abundance of the Pasteurellales order . Piñeiro-Ramos et al.
[36]
stated a higher abundance of the Pasteurellaceae family . At the genus level, Parra-Llorca et al. stated higher abundances of the Aggregatibacter genus and
[32]
lower abundances of the Haemophilus genus .
[35]
Bacteroidetes
Three studies reported consistent differences in the Bacteroidetes phylum at different taxonomic levels [33,35,37] . At the phylum level, Morais et al. stated a lower
relative abundance of Bacteroidetes . At the genus level, both Ford et al. and Parra-Llorca et al. stated a lower abundance of Bacteroides [33,35] .
[37]