Additional file 11 of Metabolic modeling of microbial communities in the chicken ceca reveals a landscape of competition and co-operation

Supplementary Material 11. Supplementary Table 5. Detailed characteristics and classification of the 237 reconstructed MAGs. This table provides details on all metagenome-assembled genomes (MAGs) reconstructed from 33 chicken cecal samples. The table includes quality metrics (completeness, contamination, N50) for each MAG along with taxonomic classification, abundance data, and sample category (HB: High Bacteroides; NB: No Bacteroides). The"binID used for metabolic reconstruction"column indicates which specific MAG was used to create the metabolic model for each species. Our naming convention reflects the assembly strategy used: i. SpecieName_pooled: For most species present across multiple samples, reads were pooled from all samples where the species was detected, reassembled, and binned to generate a single high-quality MAG. ii. Ecoli_cluster1 through Ecoli_cluster5: Due to E. coli's high prevalence (23 samples) and strain heterogeneity, we clustered the original E. coli bins into 5 groups based on average nucleotide identity (ANI). For each cluster, reads were pooled from samples within that cluster to generate 5 distinct strain-specific MAGs. Each E. coli strain model was only included in community models for samples belonging to that specific cluster. iii. Sample_SpecieName: For species unique to a single sample, MAGs were derived directly from individual sample assemblies. iv. SpecieName_coassembly: Five species (Bacteroides fragilis, Anaerostipes butyraticus, Alistipes excrementavium, Limihabitans stercoravium, and Caccovivens sp944345705) yielded higher quality MAGs from co-assembly of all 33 samples rather than from pooled reads.