Top-down mining of a lactobacilli-enriched gut niche in Tunchang pigs identifies a host-derived Limosilactobacillus reuteri strain with anti-colitis activity

The conventional ‘isolate-and-screen’ strategy for probiotic discovery often lacks ecological context, resulting in strains with uncertain safety profiles and unpredictable functional performance. Indigenous pig breeds, particularly those thriving under low-input husbandry conditions, represent underexplored ‘living libraries’ that offer host- and environment-shaped gut niches. Tunchang (TC) pigs, an indigenous breed from Hainan Province in southeastern China, provide a useful model for top-down, ecology-guided mining of host-derived probiotics from native gut niches. By combining cross-sectional age-gradient metagenomics with cross-breed comparisons, we defined a TC-pig gut niche with a lower overall burden of annotated VF/ARG features than that of Duroc × Landrace × Yorkshire (DLY) pigs. Notably, Limosilactobacillus reuteri was consistently detected within a lactobacilli-enriched core microbiota across developmental-stage groups and showed limited associations with annotated VF/ARG features at the community level. This niche was associated with higher relative levels of several host–microbe co-metabolites, including indoleacrylic acid and N-decanoylglycine. Guided by this framework, we isolated a TC pig-derived L. reuteri strain (TC-Lr) and a co-isolated Lactobacillus johnsonii strain (TC-Lj). Targeted profiling of cell-free culture supernatants revealed a distinct tryptophan-associated metabolic profile of these two isolates, with TC-Lr showing higher concentrations of indole-3-lactic acid and tryptophol than TC-Lj. In a mouse model of dextran sulphate sodium (DSS)-induced colitis, TC-Lr, but not TC-Lj, alleviated weight loss and disease activity, attenuated colon shortening and reduced inflammation-associated haematological alterations. TC-Lr also partially restored DSS-disrupted colonic metabolism, increasing adenosine while reducing creatinine and histamine levels. These findings support an ecology-guided, top-down framework for prioritising host-derived probiotics from indigenous livestock breeds. They further suggest that the TC pig gut, characterised by a lactobacilli-enriched community and a lower annotated VF/ARG burden at the community level, may serve as an ecological source for prioritising host-derived probiotic candidates. Video Abstract