Novel microbial cell measurements drive advances in U.S. biotechnology (e.g. biofuels) and biomanufacturing (e.g. sterility of cell and gene therapy products) and support cutting-edge microbial research (e.g. microbiome dynamics). Many of these technologies are related to cell counting (“enumeration”) since cell count is often essential for interpretation of more complex measurements. Cell counting can seem like an easy measurement, but developing a method that performs well across all types of microbial samples is very challenging. The difficulty increases considerably when quantifying microbial mixtures, which are increasingly relevant for many microbial applications and could unlock new biotechnology capabilities. Well-characterized, “ground-truth” materials are critically needed to evaluate the performance of new counting and characterization technologies for microbial cells and mixtures. NIST is currently developing highly defined, single strain microbial cell materials and measuring them using a suite of cell enumeration and characterization methods (1). This research opportunity will build upon these efforts to launch the next step of establishing and measuring defined microbial communities.

Natural microbiomes often contain 10 or more distinct species or strains, and currently only molecular methods (e.g. polymerase chain reaction, sequencing) are able to differentially enumerate microbes in such a mixture. However, measurement bias in these methods is a well-known problem (2). This research opportunity focuses on creating highly defined mixtures of microbial cells, developing suitable methods to quantify the mixtures, and applying the characterized mixtures to high priority applications to demonstrate increased confidence in output data. Proposals for this opportunity are strongly encouraged to focus on developing new tools and methods to differentially enumerate microbes in mixtures (e.g., flow cytometry, microscopy, sequencing, MALDI-TOF, etc.) Results from this work are anticipated to support stakeholders in a wide range of microbial-related industries and research sectors. Our research group is interdisciplinary, drawing from diverse previous research experiences including wet-lab and computational work. Interested candidates are invited to reach out to discuss potential proposals. 

(1) https://www.biorxiv.org/content/10.1101/2025.02.18.638308v1.full

(2) https://www.nature.com/articles/s41598-024-57981-4

key words

Microbiology; Cell Count; Enumeration; Microbial Communities; Flow Cytometry; Microbiome; Reference Materials; Bioinformatics; Engineering Biology;

Citizenship:  Open to U.S. citizens

Level:  Open to Postdoctoral applicants