Spatial Organization of Bacterial Communities and Predicted Functional Profiles Along the Digestive Tract of Weaned Altay Lambs

This study examined the spatial organization of bacterial communities and predicted functional profiles along the digestive tract of weaned Altay lambs. We analyzed 144 samples from 12 consecutive digestive tract sites in 12 Altay lambs using 16S rRNA gene sequencing. Functional profiles were predicted with PICRUSt2. The six male and six female lambs were weaned at 45 days and sampled at 75 days of age under a management system combining daytime grazing with evening supplementation. Analyses accounted for repeated sampling within lambs. Digestive tract site explained 23.6% of bacterial compositional variation (PERMANOVA, R2 = 0.236, p < 0.001). Anatomically constrained clustering with whole-lamb bootstrap resampling consistently identified transitions at the esophagus–rumen, duodenum–jejunum, and cecum–colon boundaries. Sharing of amplicon sequence variants (ASVs) and abundance retention distinguished the patterns at these transitions. At duodenum–jejunum, shared ASVs represented a mean of 3.07% of the ASV union but contributed 47.39% of downstream relative abundance, although potential low-biomass effects could not be excluded. Colon–rectum had the highest mean downstream retention despite a small but significant compositional difference. Paired comparisons detected differences in 122, 84, and 89 predicted functional features at esophagus–rumen, duodenum–jejunum, and cecum–colon, respectively (q < 0.05). These findings show that ASV membership and the abundance contributed by shared ASVs describe different aspects of spatial community organization. The results provide a reference for anatomically matched sampling and identify local taxonomic and predicted functional differences for further investigation in weaned lambs.