Additional file 2 of Environmental drivers of the resistome across the Baltic Sea

Additional file 2 (Supplementary-Tables.xls): Supplementary Table S1 Metadata: Sample information and environmental factors from Broman et al. (2022). Metagenomics sequence codes, site descriptors, i.e. region, station, haversine distance (km), coordinates, and physicochemical factors, i.e., water depth (m), salinity, temperature, dissolved O2 (mg/L), concentrations of total carbon (TC) and total nitrogen (TN) (µmol/g), and their ratio—C/N, and isotopic signatures, i.e., stable 13C and 15N isotope compositions (‰). Supplementary Table S2 Metagenomics data processing information: Sequence codes, raw read counts, quality-filtered and adapter trimmed, contaminant filtered, error corrected read counts, and contig assembly stat values. Supplementary Table S3 Relative abundance table of the microbial community based on mOTUs profiler. Supplementary Table S4 Comparison of methods for antimicrobial resistance gene (ARG) profiling. Supplementary Table S5 Antimicrobial resistance gene (ARG) data: Reads per kilobase million (RPKM) absolute counts. Supplementary Table S6 Mobile resistance gene (MRG) data: RPKM absolute counts. Supplementary Table S7 Mobile genetic elements (MGE) data: RPKM absolute counts. Supplementary Table S8 Virulence factor gene (VFG) data: RPKM absolute counts. Supplementary Table S9 Differential abundance test by Random Forests for ARG subtypes per region. Supplementary Table S10 Antimicrobial resistance genes (ARG) alpha diversity estimates per sample. Supplementary Table S11 Statistical results of Levene’s test for homogeneity of variance of the alpha diversity estimates. Supplementary Table S12 Statistical results of the permutation test for homogeneity of multivariate dispersions and permutation test for adonis under a reduced model for the microbial composition, ARG, MRG, MGE, and VFG data. Supplementary Table S13 Differential abundance test by Random Forests for the species per region. Supplementary Table S14 Summary statistics of the partial least squares path model (PLS-PM) in R of the latent variables—microbial communities, MGEs, VFGs, ARGs, and MRGs. Supplementary Table S15 Statistical results of the Procrustes analysis in R of ARG composition based on Bray-Curtis distance against the microbial communities, MRGs, MGEs, and VFGs. Supplementary Table S16 Statistical results of the Mantel test in R of ARG composition based on Bray-Curtis distance against the microbial communities, MRGs, MGEs, and VFGs. Supplementary Table S17 Statistical results of the General additive models (GAMs) in R of the alpha diversity and environmental factors. Supplementary Table S18 Statistical results of the permutation test for dbRDA analyses in R of the ARG composition and environmental factors. Supplementary Table S19 Spearman’s rank correlation between ARG alpha diversity metrics and environmental factors.

附加文件2（Supplementary-Tables.xls）：补充表S1元数据：取自Broman等人（2022年）的样本信息与环境因子，包含宏基因组学序列编码、位点描述符（即区域、采样站位、哈弗辛距离（km）、坐标），以及理化因子：水深（m）、盐度、温度、溶解氧（mg/L）、总碳（TC）和总氮（TN）浓度（µmol/g）、二者比值C/N，还有同位素特征，即稳定¹³C与¹⁵N同位素组成（‰）。
补充表S2：宏基因组学数据处理信息，包含序列编码、原始读长计数、经质量过滤与接头修剪、污染物去除、错误校正后的读长计数，以及重叠群组装统计值。
补充表S3：基于mOTUs profiler的微生物群落相对丰度表。
补充表S4：抗菌耐药基因（antimicrobial resistance gene, ARG）分型方法对比。
补充表S5：抗菌耐药基因（ARG）数据：每千碱基百万读长（Reads per kilobase million, RPKM）绝对计数。
补充表S6：移动耐药基因（mobile resistance gene, MRG）数据：RPKM绝对计数。
补充表S7：移动遗传元件（mobile genetic elements, MGE）数据：RPKM绝对计数。
补充表S8：毒力因子基因（virulence factor gene, VFG）数据：RPKM绝对计数。
补充表S9：针对各区域ARG亚型的随机森林差异丰度检验结果。
补充表S10：各样本的ARGα多样性估计值。
补充表S11：α多样性估计值方差齐性的莱文检验统计结果。
补充表S12：针对微生物群落、ARG、MRG、MGE及VFG数据，多元离散度齐性置换检验及简化模型下adonis置换检验的统计结果。
补充表S13：针对各区域物种的随机森林差异丰度检验结果。
补充表S14：R语言中偏最小二乘路径模型（partial least squares path model, PLS-PM）的潜变量——微生物群落、MGE、VFG、ARG及MRG的统计汇总结果。
补充表S15：R语言中基于Bray-Curtis距离的ARG组成与微生物群落、MRG、MGE及VFG的普洛克鲁斯忒斯分析（Procrustes analysis）统计结果。
补充表S16：R语言中基于Bray-Curtis距离的ARG组成与微生物群落、MRG、MGE及VFG的曼特尔检验统计结果。
补充表S17：R语言中α多样性与环境因子的广义加性模型（General additive models, GAMs）统计结果。
补充表S18：R语言中ARG组成与环境因子的距离约束冗余分析（distance-based redundancy analysis, dbRDA）置换检验统计结果。
补充表S19：ARGα多样性指标与环境因子的斯皮尔曼秩相关分析结果。