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.tsv
Processed 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.tsv
OD600 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.tsv
Summary 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.tsv
Endpoint 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.