Fig. 4: Bifidobacterium species drive resistance to antimicrobial resistance and pathogen colonization.

a, Counts of detected AMR and virulence genes in driver species genomes, with median values enclosed in brackets. Wilcoxon test (two-sided) with FDR correction; number of genomes (isolates in brackets): BB N = 297 (30), EF N = 561 (54) and BL N = 391 (49). b, Carriage of high-risk AMR genes associated with ESBL in the day-7 NGM community state samples based on raw metagenomic assemblies (BB N = 207, EF N = 498, BL N = 444). The x axis shows the most clinically prevalent ESBL genes belonging to CTX-M, OXA, SHV and TEM families. c, Proportion of species genomes, indicated by a colour gradient, predicted to utilize HMOs or their primary downstream products, lactose and fucose. The actual proportions are labelled for genotypes that are not completely present. The predictions are based on the presence of both the gene and its encoded transporters required for utilization of each substrate. 2′-fucosyllactose (2′-FL) liberates lactose and fucose which are also present in breast milk. Utilizations of LNnT, LNT and LNB will all liberate lactose. d, NGM driver species BB confers pathogen colonization resistance in vivo. The boxplot depicts the relative abundance of BB compared to the opportunistic pathogen species EF or K. oxytoca (KO). The x axis represents three experimental groups co-colonized as follows: (1) BB type strain DSM 20213 (2′-FL⁺) with EF; (2) BB natural variant D19 (2′-FL⁻, isolated from a BBS neonate) with EF; and (3) BB type strain (2′-FL⁺) with KO (D63). The BB genotype (2′-FL^+/−) indicates whether the strain encodes the α-l-fucosidase (GH95) enzyme encoding for 2′-FL metabolism. In each co-colonization group, one group of mice also received a 2′-FL supplement (50 mg ml⁻¹ per day) in their daily drinking water. The y axis for BB co-colonization with KO is shown on a log scale. Each experimental condition included 3–5 mice per cage and 3 technical replicate cages. Statistical differences between treatment groups were determined using a t-test with Welch’s correction (two-sided). Boxplot centre line indicates the median, box limits indicate upper and lower quartiles, and whiskers indicate 1.5× the interquartile range.