Background: The impact of maternal obesity on offspring health remains a major and pressing issue. We investigated its impact on the development of the infant gut microbiome during the first six months of life, examining the taxonomic composition, metabolic pathways, and antibiotic resistance genes. Methods: Twenty-four mother–infant pairs were divided into maternally obese (OB, BMI > 36) and normal weight (BM) groups. Shotgun metagenomic sequencing was performed on stool samples collected at birth and at 1, 3, and 6 months. A total of 12 maternal samples and 23 infant samples (n = 35) in the obese group and 12 maternal samples and 30 infant samples (n = 42) in the control group were sequenced. The analysis included taxonomic profiling (MetaPhlAn 4), metabolic pathway analysis (HUMAnN 3), and antibiotic resistance gene screening (CARD/ABRicate). Results: The OB group showed reduced alpha diversity in the first month (p ≤ 0.01) and an increased Firmicutes/Bacteroidetes ratio, peaking at 3 months (p ≤ 0.001). The metabolic profiling revealed enhanced carbohydrate breakdown (p ≤ 0.001) in the BM group and lipid biosynthesis (p ≤ 0.0001) in the OB group pathways. Strong correlations emerged between Lactobacillales and fatty acid biosynthesis (r = 0.7, p ≤ 0.0001) and between Firmicutes and lincosamide (r = 0.8, p ≤ 0.0001). Conclusions: The infants of obese mothers had significantly altered development of the infant gut microbiome, affecting both composition and metabolic potential. These changes may have long-term health consequences and suggest potential therapeutic targets for intervention.

Background/Objectives: The gut and liver are functionally coupled along the gut–liver axis, yet most studies treat the intestine as a single compartment and sample feces alone. We tested whether a plant-derived beetroot–tarragon microgreen beverage engages this axis in a segment-selective, colon-anchored manner in a rat model of paracetamol-induced liver injury with the intestinal dysbiosis characteristic of this model. Methods: In a rat model of paracetamol-induced liver injury with the intestinal dysbiosis characteristic of this model, three paracetamol-exposed groups—a paracetamol-only model (APAP) and two treatment arms receiving either the beetroot–tarragon microgreen beverage (APAP+MG) or a licorice-root decoction (APAP+LIC)—were compared against an intact control serving as a reference. The gut–liver axis was interrogated end-to-end by combining liver histology, serum ¹H-NMR metabolomics and vitamin profiling, and 16S rRNA gene sequencing across five intestinal sites (duodenum, jejunum, ileum, colon, and faeces). Group differences were resolved with consensus differential-abundance testing, and colonic microbiota were linked to circulating metabolites through paired microbiome–metabolome integration. Results: Paracetamol produced a reproducible sub-massive injury. Microgreens were associated with less histological injury, less weight loss, and a serum metabolome closest to the intact state among the treated arms, although no individual metabolite contrast survived FDR correction. Community separation localised to the colon as a genuine centroid shift (Aitchison PERMANOVA R² = 0.22; PERMDISP non-significant), whereas small-intestinal separation partly reflected dispersion. The microgreen arm showed higher abundance of SCFA-associated Lachnospiraceae and lower Escherichia–Shigella, with a broader colonic response than licorice (27 vs. 4 differentially abundant genera). The microbiome–metabolome association was directional but exploratory; no genus–metabolite pair survived FDR correction. Conclusions: The beverage was associated with attenuation of paracetamol-induced hepatic injury (assessed histologically only; serum ALT/AST were not measured) through a colon-localised, SCFA-oriented remodelling with a directional but non-significant shift of the serum metabolome toward the intact profile, extending the microbiome-modulating benefits of microgreens to an acute drug-injury setting and supporting their further development as functional beverages, subject to a dedicated safety evaluation. As a pilot study with modest sample sizes and non-time-matched group endpoints, these findings require confirmation in adequately powered, time-matched cohorts.