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Early life is a critical window for the establishment of the infant gut microbiome and the shaping of its metabolic functions, and gestational age and feeding mode are considered key determinants of this process. [Objective] To compare the fecal gut microbiome and metabolome between preterm and full-term infants under breastfeeding and non-breastfeeding conditions, thus exploring the effects of feeding mode and gestational age on early-life gut microbial ecology and metabolic features. [Methods] Infants were assigned into four groups: breastfeeding preterm infants (BPI), non-breastfeeding preterm infants (NBPI), breastfeeding full-term infants (BTI), and non-breastfeeding full-term infants (NBTI), with 10 infants per group. The 16S rRNA gene sequencing and untargeted metabolomics analysis were performed. Alpha/beta diversity analyses, differential abundance testing, and linear discriminant analysis effect size (LEfSe) were performed to identify key microbial taxa. Partial least squares-discriminant analysis (PLS-DA), volcano plots, and KEGG pathway enrichment were employed to determine differential metabolites and functional pathways, followed by microbiome-metabolite association network analysis. [Results] The 16S rRNA gene sequencing showed that the gut microbiome in the BTI group was dominated by Actinomycetota, Bifidobacterium (45.98%), and Bifidobacterium breve, forming a typical “breastfeeding-type” structure. The BPI group showed enrichment of Pseudomonadota and Streptococcus, with attenuated dominance of Bifidobacterium. Among non-breastfed infants, the NBTI group was dominated by Enterococcus (59.20%), whereas the NBPI group showed a fluctuating gut microbiome. Untargeted metabolomics further revealed functional differences consistent with these compositional patterns. KEGG enrichment indicated that differential metabolites were mainly involved in amino acid metabolism, lipid metabolism, bile acid-related pathways, and carbohydrate digestion and absorption. At the level of key metabolites, the BPI group showed significant enrichment of metabolites related to antioxidant and immune support, such as glutathione and vitamin D sulfate conjugates; the BTI group enriched long-chain polyunsaturated fatty acids and indole-derived metabolites; and non-breastfeeding groups generally exhibited accumulation of fermentable carbohydrates and specific bile acid derivatives. Correlation analysis confirmed a strong positive association between Bifidobacterium and indole-related metabolite outputs in breastfeeding groups, whereas microbiome–metabolite networks were looser in non-breastfeeding groups. [Conclusion] Both gestational age and feeding mode are related to differences in the early gut microbiome structure and related metabolic characteristics of infants, with the association between feeding mode and metabolic profile differences being more prominent. Gestational age may affect the establishment pattern of dominant microbial taxa in the context of breastfeeding. As a pioneering exploratory study, this study preliminarily reveals the specificity of gut microbiome structure and functional metabolism in different populations of infants, providing a basis for subsequent prospective cohort validation, mechanism research, and early nutritional intervention optimization.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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