Our research goals focus on the systematic bioprospecting of soil microbiomes to identify, characterize, and isolate novel antimicrobial compounds capable of neutralizing multidrug-resistant pathogens.

Success in this research project relies on a structured progression, where each phase serves as a critical foundation that must be finalized before the next can begin.

Phase I: Ecological Sampling and Biosafety Screening

The research begins with the collection of soil samples from diverse ecological regions across Texas, leveraging the state's vast geographical variance to maximize microbial diversity. To ensure researcher safety and environmental integrity, all primary processing occurs under Biosafety Level 2 (BSL-2) conditions. Within certified biosafety cabinets, samples undergo a rigorous screening process to detect and exclude known soil-associated pathogens before advancing to the discovery pipeline.

Phase II: Isolate Characterization and Library Development

Once cleared, microorganisms are revived and cultured to establish a robust research library. The ACDC follows a strict standardized protocol for each specimen:

  • Phenotypic Documentation: Researchers record colony morphology, pigmentation, texture, and growth rates.
  • Standardized Nomenclature: Each unique isolate is assigned a specific identifier, beginning with APS1 (Antimicrobial Producing Specimen 1).
  • Biobanking: To ensure reproducibility, the center generates both active working stocks and long-term archived stocks for every isolate.

Phase III: The ESKAPE Pathogen Challenge

A primary goal of the ACDC is to identify specimens that secrete compounds inhibitory to the ESKAPE pathogens (highly virulent, antibiotic-resistant bacteria). This is achieved through a multi-tiered testing strategy:

  • Direct Interaction (Kirby-Bauer Test): Using a standardized turbidity of 0.5 McFarland, live specimens are tested against ESKAPE organisms. The resulting Zone of Inhibition (ZOI) is measured to quantify the specimen's baseline antimicrobial efficacy.
  • Cell-Free Supernatant Analysis: To determine if the inhibitory effect is caused by secreted metabolites, researchers expose pathogens to the specimen’s cell-free supernatant. This confirms that the antimicrobial activity is independent of the living donor cell.

Phase IV: Metabolite Extraction and Molecular Identification

The final stage of the ACDC research plan transitions from microbiology to biochemistry and genomics. For isolates demonstrating significant inhibitory zones, the team optimizes growth conditions to maximize secondary metabolite production. These metabolites are then extracted and re-tested to confirm their potency in a concentrated form.

Simultaneously, the center performs Molecular Identification on the most promising candidates. This involves:

  • Genomic Isolation: Extracting the DNA of the specimen.
  • Sequence Analysis: Utilizing high-throughput sequencing to compare the specimen's DNA against global bacterial gene banks.

Through this comprehensive approach, the ACDC aims to bridge the gap between environmental microbiology and clinical application, providing the foundational data necessary for the next generation of life-saving antimicrobial therapies.