Data and analysis tables for "Community state shifts driven by total carbon availability over resource complexity in a synthetic microbial community"

Description This dataset contains downstream data tables used to reproduce analyses for the manuscript “Community state shifts driven by total carbon availability over resource complexity in a synthetic microbial community”. The study tested how total carbon availability and resource complexity shape the composition, biomass, diversity, and state transitions of a serially transferred 16-species synthetic bacterial community grown across 96 resource environments. The dataset includes processed 16S rRNA amplicon-derived community composition tables, optical density measurements across the resource grid, monoculture growth trait summaries for dominant species, and pH/OD measurements for individual strains. Raw 16S rRNA amplicon sequencing reads are available from the European Nucleotide Archive under accession PRJEB108454. File descriptions community_composition.tsvProcessed endpoint community composition table from the 16-day serial passage experiment. Contains 9,984 rows for 768 community samples × 13 detected strains. Columns include sample ID, strain ID, R2A-derived carbon percentage, total carbon concentration, replicate, OD600, raw relative abundance, and copy-number-corrected relative abundance. resource_grid_od.tsvOD600 measurements for communities across the resource grid. Contains 5,118 observations with replicate number, total carbon concentration, R2A-derived carbon percentage, and OD600. monoculture_growth_summary.tsvSummary growth traits for monocultures of the three dominant species: HAMBI_1287, HAMBI_1972, and HAMBI_1977. Contains 288 rows across 16 glucose concentrations and six replicates per species. Columns include lag time, maximum growth rate, AUC, maximum OD increase per minute, mean OD, and yield. strain_ph_od.tsvEndpoint pH and OD600 measurements for individual strains grown in high-glucose M9 medium. Contains replicate-level measurements for 14 strains. Data dictionary sample_id: Unique sample identifier.strain_id: HAMBI strain identifier.r2a_percent: Percentage of total carbon derived from R2A medium.carbon_g_per_l: Total carbon concentration, g C L⁻¹.replicate: Biological replicate number.od600: Optical density at 600 nm.rel_abundance_raw: Raw relative abundance from 16S rRNA read mapping.rel_abundance_corrected: Relative abundance corrected for 16S rRNA gene copy number.species_label: Short label for monoculture strain.media_label: Internal glucose medium label.glucose_g_per_l: Glucose concentration, g L⁻¹.lagtime_h: Estimated lag phase duration in hours.rho_max: Estimated maximum growth rate parameter.auc: Area under the growth curve.maxrate_od_per_min: Maximum OD600 increase per minute.mean_od: Mean OD600 across the growth curve.yield_od: Yield-associated OD600 estimate.ph_end: Endpoint pH after incubation.数据集说明 本数据集包含用于复现论文《合成微生物群落中资源复杂度下总碳可利用性驱动的群落状态转变》分析流程的下游数据表。本研究探究了总碳可利用性与资源复杂度如何调控在96种资源环境中连续传代培养的16物种合成细菌群落的组成、生物量、多样性及状态转变过程。本数据集涵盖经处理的16S rRNA扩增子（16S rRNA amplicon）衍生的群落组成表、资源网格的光密度测量数据、优势物种单培养生长性状汇总表，以及单菌株的pH/光密度测量数据。 原始16S rRNA扩增子测序读数可于欧洲核苷酸档案馆（European Nucleotide Archive）以登录号PRJEB108454获取。 文件说明 community_composition.tsv：16天连续传代实验的经处理终点群落组成表。包含768个群落样本与13个检测菌株对应的9984行数据。列字段包括样本ID、菌株ID、R2A培养基衍生碳百分比、总碳浓度、生物学重复、OD600、原始相对丰度，以及经16S rRNA基因拷贝数校正后的相对丰度。 resource_grid_od.tsv：资源网格中群落的OD600测量数据。包含5118条观测记录，字段涵盖重复编号、总碳浓度、R2A衍生碳百分比及OD600。 monoculture_growth_summary.tsv：三种优势菌株HAMBI_1287、HAMBI_1972及HAMBI_1977的单培养生长性状汇总表。包含288行数据，对应16个葡萄糖浓度梯度及每个物种的6次生物学重复。列字段包括延滞期时长、最大生长速率、生长曲线下面积、每分钟最大OD增幅、平均OD及产量。 strain_ph_od.tsv：高葡萄糖M9培养基中培养的单菌株的终点pH及OD600测量数据。包含14个菌株的重复水平测量值。 数据字典 sample_id：唯一样本标识符。 strain_id：HAMBI菌株标识符。 r2a_percent：源自R2A培养基的碳占比。 carbon_g_per_l：总碳浓度，单位为g C L⁻¹。 replicate：生物学重复编号。 od600：600 nm波长下的光密度。 rel_abundance_raw：基于16S rRNA读段比对得到的原始相对丰度。 rel_abundance_corrected：经16S rRNA基因拷贝数校正后的相对丰度。 species_label：单培养菌株的简短标签。 media_label：内部葡萄糖培养基标签。 glucose_g_per_l：葡萄糖浓度，单位为g L⁻¹。 lagtime_h：估算的延滞期时长，单位为小时。 rho_max：估算的最大生长速率参数。 auc：生长曲线下面积。 maxrate_od_per_min：每分钟最大OD600增幅。 mean_od：生长周期内的平均OD600。 yield_od：与产量相关的OD600估算值。 ph_end：培养结束后的终点pH值。