Journal: bioRxiv

Article Title: Metabolic blueprints of monocultures enable prediction and design of synthetic microbial consortia

doi: 10.64898/2026.01.11.698878

Figure Lengend Snippet: A ) The 15 microorganisms used in this study were isolated from the soil surrounding a switchgrass plant, Brachypodium distachyon . The isolates or communities were grown in a defined medium (NLDM) for cultivation and exometabolite profiling of soil bacteria (Supplementary Table 2). B ) Isolates were grown in batch for 3 days, where growth yields were read using a spectrophotometer every 20 min, and metabolites in the spent media were sampled intermittently when cells were roughly grown at 25%, 50%, 75% and 100% of the final growth yields (Supplementary Fig. 1). C ) Schematic of consumer resource modeling and model prediction of sub-community assembly. Organisms consume resources to produce biomass, meanwhile leaking metabolic byproducts into the shared environment, which can then be utilized by other co-cultured organisms for growth (see Methods). Key parameters in the consumer resource models including Ciα, Di, βα, gi were derived from the experimental data collected from monoculture. D ) For model performance validation, communities containing 2, 15, or 14 (leave-1-out) strains were grown and passaged, and the final composition was determined by 16S sequencing. E ) Consumer resource models fitted from monoculture were used to predict synthetic community abundances and design sub-communities with high entropy.

Article Snippet: The 16S ribosomal RNA gene amplicon libraries were prepared for sequencing on the Illumina MiSeq platform at Quintara Bio, Boston, MA.

Techniques: Isolation, Bacteria, Spectrophotometry, Cell Culture, Derivative Assay, Biomarker Discovery, Sequencing

Journal: bioRxiv

Article Title: Metabolic blueprints of monocultures enable prediction and design of synthetic microbial consortia

doi: 10.64898/2026.01.11.698878

Figure Lengend Snippet: A) Co-culture experimental and simulated outcomes using experimentally-informed consumer resource models. Each strain is represented by a unique color. The un-patterned bars show relative abundance of strains in experimental co-cultures, and the patterned bars show the predicted co-culture abundances from the CRM. B) Average strain abundance in co-culture predicted by the model compared to average measured strain abundance from 16s data, summarizing information from A. Standard error bars are shown. Strain colors are consistent with A. C) The predictive power (Pearson’s coefficient) of using growth rates or using consumer resource models with or without cross-feeding enabled in recapitulating community composition in co-cultures. Strain colors are consistent with A. D) Interaction networks for Mucilaginibacter, with Variovorax and Paenibacillus , showing significant cross-feeding of amino acids that benefits Mucilaginibacter . Production arrows are red and consumption arrows are blue, with widths relating to the rate of consumption or production determined from exometabolomic profiling. Comprehensive interaction networks of other strains can be explored interactively in the supplementary materials. Strain node colors are consistent with A, and metabolite node colors are consistent with metabolite classes in .

Article Snippet: The 16S ribosomal RNA gene amplicon libraries were prepared for sequencing on the Illumina MiSeq platform at Quintara Bio, Boston, MA.

Techniques: Co-Culture Assay

Journal: bioRxiv

Article Title: Metabolic blueprints of monocultures enable prediction and design of synthetic microbial consortia

doi: 10.64898/2026.01.11.698878

Figure Lengend Snippet: A,B) Experimental dynamics of community composition in a synthetic ecosystem consisting of all 15 strains cultured for 10 days in 5 passages in NLDM media. 2 experiments were performed, each with 4 biological replicates. 16S relative abundances are shown as stacked bars. C) Whole community (15-member) simulated abundances across 5 48-hr periods with passages in between. Fitted CRM parameters are used, and relative abundances of strains in the final community are shown as stacked bars. D) Whole community (15-member) simulated abundances across 5 48-hr periods with passages in between. Cross-feeding was turned off by setting leakage parameters for every strain = 0 (See Methods). Relative abundances of strains in the final community are shown as stacked bars. E) The correlation (Spearman’s coefficient) between the abundance ratio of 15 inoculated strains at each passage between 16S measurements and CRM simulations with cross-feeding (orange line) or CRM simulations without cross-feeding (green line). Strain abundances from simulations were compared to both instances of whole community experiments (dashed and solid lines). F) The simulated and experimentally observed strain abundances in the community across leave-out experiments of all other 14 members, one at a time. The star for each represents that strains abundance in the complete 15-member community. In green are the simulated predicted abundances, and in orange is the experimentally measured abundance.

Article Snippet: The 16S ribosomal RNA gene amplicon libraries were prepared for sequencing on the Illumina MiSeq platform at Quintara Bio, Boston, MA.

Techniques: Cell Culture

Journal: bioRxiv

Article Title: Metabolic blueprints of monocultures enable prediction and design of synthetic microbial consortia

doi: 10.64898/2026.01.11.698878

Figure Lengend Snippet: A) Distribution of the Shannon entropy of 455 3-strain synthetic sub-communities assembled in silico . The red vertical lines specify the communities chosen for the experiments shown in . Red lines at the right end of the distribution correspond to communities in the high predicted Shannon entropy group, while red lines towards the lower end of the distribution correspond to those in the low predicted Shannon entropy group. B) The taxonomic composition of selected groups of 3-strain subcommunities (Supplementary Table 4) at the end of a 10-day growth experiment. There are 10 sub-communities containing 3 strains in the initial inoculum predicted to have a low Shannon entropy (<0.7) on the left compared with 10 sub-communities predicted to have a high Shannon entropy (>1). C) Distribution of the Shannon entropy of selected 3-strain sub-communities from the 16S measurements (“Experimental”) and from simulation (“Simulated”) at the end of the final passage (Day 10). The statistical significance of the 16S measurements (p<0.01) and the simulation (p<0.0001) from two groups are noted.

Article Snippet: The 16S ribosomal RNA gene amplicon libraries were prepared for sequencing on the Illumina MiSeq platform at Quintara Bio, Boston, MA.

Techniques: In Silico