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Description
We seek a motivated and skilled microbiology fellow to join our Culture Independent and Metagenomic Subtyping group (CIMS) in the Enteric Diseases Laboratory Branch (EDLB) in the Division of Food, Water-borne and Enteric Diseases (DFWED) within the National Center for Zoonotic Emerging Infectious Diseases (NCIZID) at the Centers for Disease Control and Prevention (CDC) in Atlanta, GA.
The fellow will work with a group of bioinformatics and laboratory scientists in CIMS to research and develop shotgun metagenomics approaches to characterize outbreaks and subtype foodborne pathogens, like Salmonella and Shiga toxin producing E coli, directly out of disease state stool samples. Among the key challenges to this approach is finding sufficient pathogen signal among a noisy background of host and commensal organism DNA to be able to recover subtyping data useful for public health surveillance and outbreak detection. Acute disease detection in the microbiome setting is a rapidly developing field as current metagenomic approaches do not provide the resolution to distinguish outbreaks.
Towards this end, the fellow will be involved in the evaluation and development of laboratory techniques to improve pathogen signal recovery through human signal removal, pathogen enrichment, and phasing for improved species binning. Additionally, stool sample transport continues to pose a practical challenge. The fellow will be involved in a project to evaluate a number of chemistries for stool sample transport without refrigeration designed to preserve nucleic acid content. Finally, the fellow will collaborate on a research project where we seek to use metagenomic shotgun sequencing on a large number of healthy and disease state stool samples to improve outbreak and antimicrobial resistance element characterization.
Activities
This position requires working with human pathogen isolates and human clinical specimens (primarily stool). Extensive training and oversight will be provided. In addition, this position will require vaccinations for working with primary samples where blood and bodily fluids are sometimes present. Biosafety and chemical safety training will also be provided.
Qualifications
How to apply
Apply through Zintellect site at top, or send CV and cover letter to Andrew Huang at [email protected]
Description
We seek a motivated and skilled microbiology fellow to join our Culture Independent and Metagenomic Subtyping group (CIMS) in the Enteric Diseases Laboratory Branch (EDLB) in the Division of Food, Water-borne and Enteric Diseases (DFWED) within the National Center for Zoonotic Emerging Infectious Diseases (NCIZID) at the Centers for Disease Control and Prevention (CDC) in Atlanta, GA.
The fellow will work with a group of bioinformatics and laboratory scientists in CIMS to research and develop shotgun metagenomics approaches to characterize outbreaks and subtype foodborne pathogens, like Salmonella and Shiga toxin producing E coli, directly out of disease state stool samples. Among the key challenges to this approach is finding sufficient pathogen signal among a noisy background of host and commensal organism DNA to be able to recover subtyping data useful for public health surveillance and outbreak detection. Acute disease detection in the microbiome setting is a rapidly developing field as current metagenomic approaches do not provide the resolution to distinguish outbreaks.
Towards this end, the fellow will be involved in the evaluation and development of laboratory techniques to improve pathogen signal recovery through human signal removal, pathogen enrichment, and phasing for improved species binning. Additionally, stool sample transport continues to pose a practical challenge. The fellow will be involved in a project to evaluate a number of chemistries for stool sample transport without refrigeration designed to preserve nucleic acid content. Finally, the fellow will collaborate on a research project where we seek to use metagenomic shotgun sequencing on a large number of healthy and disease state stool samples to improve outbreak and antimicrobial resistance element characterization.
Activities
- Extraction of DNA from stool and complex samples
- Testing and evaluation of stool preservatives under different storage conditions
- Preparation of Illumina next-generation sequencing libraries
- Evaluation and troubleshooting of human content removal, pathogen enrichment, and phasing chemistries
- Bioinformatic analysis of shotgun metagenomic data for quality and community bias evaluation
- Collaboration with stool banks, state public health laboratories, and other external partners involved in stool collection project
This position requires working with human pathogen isolates and human clinical specimens (primarily stool). Extensive training and oversight will be provided. In addition, this position will require vaccinations for working with primary samples where blood and bodily fluids are sometimes present. Biosafety and chemical safety training will also be provided.
Qualifications
- Masters or PhD degree in biological sciences, microbiology, bioinformatics, or related field (graduation within last three years)
- At least two years of relevant molecular biology laboratory experience (PCR experience required, DNA extraction and Next Generation sequencing experience a plus)
- UNIX command line bioinformatics experience a plus
- Microbiology or primary clinical stool sample experience a plus
- Good written and oral communication skills
- Good lab safety and aseptic technique
- Comfortable working in an interdisciplinary team environment
How to apply
Apply through Zintellect site at top, or send CV and cover letter to Andrew Huang at [email protected]