Assistant Research Scientist

Job Title Assistant Research Scientist Agency Texas A&M Agrilife Research Department Animal Science Proposed Minimum Salary Commensurate Job Location College Station, Texas Job Type Staff Job Description About Texas A&M AgriLife Texas A&M AgriLife is comprised of the following Texas A&M University System members:

• Texas A&M AgriLife Extension Service
• Texas A&M AgriLife Research
• College of Agriculture and Life Sciences at Texas A&M University
• Texas A&M Forest Service
• Texas A&M Veterinary Medical Diagnostic Laboratory As the nation’s largest most comprehensive agriculture program, Texas A&M AgriLife brings together a college and four state agencies focused on agriculture and life sciences within The Texas A&M University System. With over 5,000 employees and a presence in every county across the state, Texas A&M AgriLife is uniquely positioned to improve lives, environments and the Texas economy through education, research, extension and service. Click here to learn more about joining AgriLife! Position Information Job Summary: This Assistant Research Scientist position supports the Dass Microbial Ecology Laboratory’s Food Safety and Defense and Farm-to-Plate Antimicrobial Resistance research pillars. The incumbent will lead the meta-omics and biofilm-ecology, which characterizes multi-species biofilm communities recovered from beef- and pork-processing environments and determines how these communities influence pathogen persistence, sanitizer tolerance, and antimicrobial resistance. The work integrates shotgun metagenomics, metatranscriptomics, genome-scale metabolic modeling, and culture-based synthetic-community experiments, and is conducted in long-standing collaboration with the

Usda-ars U.s.

Meat Animal Research Center (USMARC). The incumbent will develop analysis pipelines and biofilm model systems for this workstream, coordinate with federal collaborators, mentor graduate students, and contribute to publications, technical reports, and grant proposals. Responsibilities: Research

• Conducts independent research on the collective dynamics of microbial interactions in multi-species biofilms of built (food-processing) environments, with defined ownership of the laboratory’s meta-omics and biofilm-ecology.
• Designs and executes shotgun metagenomic and metatranscriptomic studies of floor-drain and processing-surface biofilms from beef- and pork-processing plants; generates genome-resolved profiles of community composition, active functional pathways, antimicrobial resistance genes, secondary-metabolite potential, and phage–host interactions.
• Constructs and applies genome-scale metabolic models (KBase, ModelSEED, flux balance analysis, SMETANA) to predict metabolite exchange and cross-feeding among biofilm community members.
• Designs, builds, and tests synthetic microbial communities under meat-processing-relevant conditions, including stainless-steel coupon assays, psychrotrophic growth studies, BioFlux microfluidic biofilm assays, and sanitizer challenge and recovery experiments to evaluate pathogen integration (e.g., E. coli O157:H7, Salmonella enterica) and community-mediated protection.
• Performs nucleic-acid extraction (DNA, total RNA, metatranscriptomic RNA), library preparation coordination, qRT-PCR validation, and fluorescence microscopy imaging and quantitative analysis for biofilm experiments.
• Develops, documents, and maintains reproducible Linux/R/Bash workflows on high-performance computing resources for read quality control, assembly, binning, gene prediction, annotation, differential expression, and statistical analysis; produces publication-quality visualizations.
• Curates and manages laboratory sequencing datasets, metadata, and analysis code in accordance with the laboratory data-management policy so that results remain reproducible and accessible to the research team.
• Analyzes research data, summarizes results, and prepares manuscripts as lead or contributing author for peer-reviewed journals; contributes to research articles and publications from collaborating projects.
• Assists with grant acquisition by drafting preliminary-data sections, methods, figures, and budget justifications for federal, foundation, and industry proposals.
• Coordinates collaborative projects with USDA-ARS scientists and other external partners, including sample logistics, data sharing, and joint analyses.
• Assists with the preparation, organization, and cleaning of the laboratory worksite; maintains biosafety, chemical-safety, and aseptic-technique standards. Mentoring
• Assists and trains graduate students, postdoctoral researchers, and undergraduate student researchers in metagenomic and metatranscriptomic data analysis, metabolic modeling, and biofilm and molecular-biology techniques related to the project.
• Reviews student analyses and drafts, provides technical guidance, and helps students troubleshoot computational and wet-laboratory workflows. Presentations and Reporting
• Prepares presentation materials on research topics for laboratory meetings, industry stakeholders (e.g., Beef Industry Food Safety Council), and scientific conferences (e.g., IAFP, ASM Microbe, CRWAD), and presents to small and/or large groups.
• Actively participates in the preparation of required technical progress reports to research sponsors, including USDA-ARS cooperative agreements, NIST, and other federal and industry funders.
• Other duties as assigned. Required Qualifications:
• Ph.D. in Animal Science, Microbiology, Biotechnology, Environmental Engineering, Bioinformatics, or a closely related field.
• A minimum of three years of research experience (may include doctoral research) in microbial ecology, food-safety microbiology, or a related discipline.
• Demonstrated experience analyzing shotgun metagenomic and transcriptomic datasets from raw reads through annotation and statistical interpretation.
• Record of peer-reviewed publications as first or co-first author.
• Knowledge of microbial ecology, biofilm biology, antimicrobial resistance, and food-safety microbiology as applied to red-meat processing.
• Proficiency in R and Bash on Linux/HPC systems (including SLURM), and with metagenomic and transcriptomic tools such as MEGAHIT, metaSPAdes, metaWRAP, metaBAT2, GTDB-Tk, Prokka, eggNOG-mapper, Kraken2, MetaPhlAn, Salmon, DESeq2/edgeR, antiSMASH, VirSorter2, and DefenseFinder.
• Proficiency in metabolic modeling platforms (KBase, ModelSEED, SMETANA) and network visualization (Cytoscape).
• Skill in wet-laboratory techniques including aseptic technique, bacterial isolation and enumeration, mono-/dual-/multi-species biofilm models, nucleic-acid extraction and quality assessment, PCR and qRT-PCR, and fluorescence microscopy with ImageJ-based quantification.
• Ability to plan and execute independent research projects, manage multiple concurrent analyses, and meet publication and reporting deadlines.
• Strong scientific writing and oral communication skills for peer-reviewed publications, sponsor reports, and presentations to academic and industry audiences.
• Ability to work collaboratively with faculty, federal scientists, students, and industry partners. Preferred Qualifications:
• Doctoral research focused on multi-species biofilms in food-processing or other built environments.
• Experience with genome-resolved metagenomics, metatranscriptomics, and genome-scale metabolic modeling of microbial communities.
• Experience designing and testing synthetic microbial communities and conducting sanitizer challenge assays with foodborne pathogens.
• Experience with microfluidic (e.g., BioFlux) biofilm cultivation and fluorescence-microscopy-based biofilm quantification.
• Established working relationships with USDA-ARS or other federal research partners.
• Teaching or mentoring experience in a laboratory or instructional setting. Other Requirements
• Ability to work in a BSL-2 laboratory environm