Data from: Interspecific variation in gut microbiome diversity across the Etosha National Park herbivore community

Data (both phyloseq-R object from imported QIIME2 artifacts, and demultiplexed EMP-paired end sequences from Argonne National laboratory) and R code Raw sequencing reads from Argonne National Laboratory: - Undetermined_S0_L001_I1_001.fastq (barcodes)- Undetermined_S0_L001_R1_001.fastq (forward)- Undetermined_S0_L001_R2_001.fastq (reverse) HerbivoreMeta2.tsv – Metadata file with each row representing individual samples and columns representing sample ID (SampleID), host species (sample_Species), sex (Sex), geographic zone each sample was collected from in Etosha National Park (Zone), feeding strategy of host species (FeedStrat), gut morphology of host species (GutMorph), waterhole site sample was collected from (Waterhole), and host taxonomic family (Family) Herbivorerooted-tree-filtered.qza – QIIME2 artifact created after filtering sequences and creating rooted tree for phylogenetic diversity analyses Herbivoretable-clean-unassigned-Unk-Euk.qza – QIIME2 artifact created by filtering out mitochondria, chloroplasts, unassigned taxa, Bacteria-only assigned taxa, and Eukaryota-only assigned taxa from Argonne National Lab sequences Physeq_srs2.rds – Normalized phyloseq object Physeq2.rds – Phyloseq object created with HerbivoreMeta2.tsv, herbivorerooted-tree-filtered.qza, herbivoretable-clean-unassigned-Unk-Euk.qza, and taxonomySILVA.qza and used for downstream analysis in R Pseq.rel2.rds – Normalized phyloseq object with bacterial community composition taxonomySILVA.qza – QIIME2 artifact created from SILVA reference database to assign taxonomy to Argonne National Lab sequences Herbivore_points.csv – Latitude and longitude GPS points of each herbivore sample used for calculating geographic distance for Mantel tests QIIME2 steps.rtf – Step-by-step code used in miniconda3 for joining, quality-filtering, and demultiplexing EMP-paired end sequences from Argonne National Laboratory and creating QIIME2 artifacts for downstream analysis Phyloseq.R – Creates phyloseq object from imported QIIME2 artifacts Phyla_tests.R – Identifying core phyla in each herbivore species; ANOVA tests analyzing significant core phylum (Verrucomicrobiota) abundance by zone; generating Figs. 2, 3a, S1_Table Genera_tests.R – Identifying core genera in each herbivore species; ANOVA and t-tests analyzing significant core genera (Christensenellaceae_R-7 group, P-251-05, Monoglobus, RF39, and Alistipes) by sex, gut morphology, waterhole site, and zone; generating Figs. 3b, 3c, 3d, 4, 5, and S1_Table Alpha_tests.R – Analyzing significant alpha diversity metrics (richness and Bulla evenness) by sex and host species, generating Fig. 6 Beta_tests.R – PERMANOVA tests analyzing beta diversity metrics (weighted and unweighted UniFrac) by each of the six intrinsic and extrinsic variables; Mantel tests; generating Fig. 7 FDR_phyla.csv – Raw p-values from significance tests of Verrucomicrobiota abundance by zone for FDR adjustment FDR_genera.csv – Raw p-values from significance tests of core genera abundance by sex, zone, waterhole site, and gut morphology for FDR adjustment FDR_alpha.csv – Raw p-values from significance tests of richness and evenness by host species, gut morphology, and sex for FDR adjustment本数据集包含两类数据：一是从导入的QIIME2产出物（QIIME2 artifacts）生成的phyloseq-R对象（phyloseq-R object），二是来自阿贡国家实验室（Argonne National Laboratory）的解复用EMP双端测序序列（EMP-paired end sequences），同时配套相关R代码。 阿贡国家实验室的原始测序读段如下： - Undetermined_S0_L001_I1_001.fastq：标签序列（barcode）文件 - Undetermined_S0_L001_R1_001.fastq：正向测序读段文件 - Undetermined_S0_L001_R2_001.fastq：反向测序读段文件 HerbivoreMeta2.tsv：元数据文件，每行对应一个独立样本，列分别为样本ID（"SampleID"）、宿主物种（"sample_Species"）、性别（"Sex"）、样本采集地所在的埃托沙国家公园地理区域（"Zone"）、宿主物种取食策略（"FeedStrat"）、宿主物种肠道形态（"GutMorph"）、样本采集的水源点（"Waterhole"）以及宿主分类学科水平分类单元（"Family"）。 Herbivorerooted-tree-filtered.qza：经序列过滤并构建用于系统发育多样性分析的有根树后生成的QIIME2产出物（QIIME2 artifacts）。 Herbivoretable-clean-unassigned-Unk-Euk.qza：从阿贡国家实验室的测序序列中过滤出线粒体、叶绿体、未分类类群、仅注释为细菌的类群以及仅注释为真核生物的类群后生成的QIIME2产出物（QIIME2 artifacts）。 Physeq_srs2.rds：标准化后的phyloseq-R对象（phyloseq-R object）。 Physeq2.rds：结合HerbivoreMeta2.tsv、Herbivorerooted-tree-filtered.qza、Herbivoretable-clean-unassigned-Unk-Euk.qza以及taxonomySILVA.qza构建得到的phyloseq-R对象（phyloseq-R object），用于下游R语言分析。 Pseq.rel2.rds：包含细菌群落组成的标准化phyloseq-R对象（phyloseq-R object）。 taxonomySILVA.qza：基于SILVA参考数据库构建的QIIME2产出物（QIIME2 artifacts），用于对阿贡国家实验室的测序序列进行分类学注释。 Herbivore_points.csv：用于计算曼特尔检验（"Mantel test"）所需地理距离的每个草食动物样本的GPS经纬度坐标文件。 QIIME2 steps.rtf：在miniconda3环境中运行的分步代码，用于拼接、质量过滤和解复用阿贡国家实验室的EMP双端测序序列，并生成用于下游分析的QIIME2产出物（QIIME2 artifacts）。 Phyloseq.R：用于从导入的QIIME2产出物（QIIME2 artifacts）中构建phyloseq-R对象（phyloseq-R object）的R脚本。 Phyla_tests.R：用于鉴定每个草食动物物种的核心菌门；通过方差分析（ANOVA，Analysis of Variance）检验按地理区域划分的核心菌门疣微菌门（"Verrucomicrobiota"）的丰度差异；用于生成图2、图3a以及补充表S1_Table。 Genera_tests.R：用于鉴定每个草食动物物种的核心菌属；通过方差分析（ANOVA，Analysis of Variance）和t检验分析按性别、肠道形态、水源点以及地理区域划分的核心菌属（"Christensenellaceae_R-7 group"、"P-251-05"、"Monoglobus"、"RF39"以及"Alistipes"）的丰度差异；用于生成图3b、3c、3d、4、5以及补充表S1_Table。 Alpha_tests.R：用于分析按性别和宿主物种划分的显著α多样性指标（群落丰富度和Bulla均匀度）；用于生成图6。 Beta_tests.R：通过置换多元方差分析（PERMANOVA，Permutational Multivariate Analysis of Variance）检验按6个内在和外在变量划分的β多样性指标（加权和未加权UniFrac距离）；包含曼特尔检验（"Mantel test"）；用于生成图7。 FDR_phyla.csv：用于错误发现率（FDR，False Discovery Rate）校正的、按地理区域划分的疣微菌门（"Verrucomicrobiota"）丰度显著性检验的原始p值文件。 FDR_genera.csv：用于错误发现率（FDR，False Discovery Rate）校正的、按性别、地理区域、水源点以及肠道形态划分的核心菌属丰度显著性检验的原始p值文件。 FDR_alpha.csv：用于错误发现率（FDR，False Discovery Rate）校正的、按宿主物种、肠道形态以及性别划分的群落丰富度和均匀度显著性检验的原始p值文件。