Genome-resolved metagenomics and culturomics reveal a fiber- degrading gut microbiome in Dahuabai pigs with culture-validated cellulase activity

Background Local Chinese pig breeds such as Dahuabai (DHB) are noted for fiber tolerance. We compared the gut microbiota and fiber-degrading functions of DHB and Duroc pigs and built a genome-resolved resource to characterize cellulose/hemicellulose degradation. Results We first profiled fecal metagenomes from Dahuabai (DHB) pigs ( n  = 30) and Duroc pigs ( n  = 30). DHB harbored higher relative abundances of Methanobrevibacter (14.31% vs . 3.03%, Wilcoxon p =  0.032) and Lactobacillus (17.43% vs . 1.73%, p =  0.007); at the species level, Methanobrevibacter smithii and Lactobacillus amylovorus were dominant in DHB. Functionally, DHB microbiomes contained more CAZymes overall (147,829 vs. 63,825) and were enriched for cellulose-degrading (GH1, GH5, GH6, GH7, GH9, GH12, GH45) and hemicellulose-degrading (GH10, GH26, GH39, GH42, GH43, GH51) families ( p  < 0.05). Guided by these inter-breed differences, we constructed a genome-resolved resource focused on DHB by integrating Illumina and Oxford Nanopore Technologies (ONT) metagenomes with whole-genome sequencing (WGS) of cultured isolates. This dataset comprised 888 genomes (382 Illumina Metagenome-Assembled Genomes (MAGs), 489 ONT MAGs, and 17 isolate genomes), of which 449 met high-quality criteria. We then predicted cellulose-degrading capacity using the presence of endoglucanases, exoglucanases, and β-glucosidases as criteria. In total, 258 genomes showed potential for cellulose degradation, and 129 were classified as high potential. Finally, we evaluated cultured representatives in vitro . Primary Congo red screening identified 14 fiber-degrading isolates, and liquid assays detected carboxymethylcellulase (CMCase) activity in four strains: Bacillus velezensis D7-1 (136.82 U/mL), Bacillus subtilis D6-1 (24.88 U/mL), Bacillus safensis X6-1 (7.83 U/mL), and Bacillus_A cereus Y9-1 (2.76 U/mL), highlighting Bacillus spp. as cultured hosts with measurable cellulolytic activity. Conclusions In conclusion, there are differences in gut composition and function between DHB and Duroc. DHB have formed a special intestinal microbial community during long-term natural domestication, and tolerance to rough feeding is significantly higher than that of commercial pig breed. However, more extensive research is needed on the application potential of fiber-degrading bacteria in actual production.