Internal

Internal Team Organization

Sponsor: Sandrine M. Miller Montgomery

Executive Director of the Center for Microbiome Innovation at UCSD

sandrinemiller@eng.ucsd.edu

Sponsor's Fiscal Contact Person: Jeff Woods

Email: jewoods@eng.ucsd.edu

Original Project Description

Background:

Recent quality control experiments have demonstrated that the widely available and

inexpensive fecal occult blood test (FOBT) cards are an effective tool for collecting and stabilizing stool for downstream microbiome analyses such as 16S rRNA amplicon sequencing, whole shotgun metgenomics, and mass-spectrometry based metabolomics. However, compared to widespread sampling methods based on swabs or semi-homogenized liquid samples FOBT cards can only be processed in a low-throughput manner that is subject to high risk of cross contamination from the tools used to cut or extract the material from the collection device into a 96-well plate for high-throughput

downstream analyses. With the swab-based devices we can currently extract >100K samples per year with a team of four trained technicians while the same group is unable to process more than 10K samples per year using the current manual process. Automated solutions on the market, such as the

Hamilton easyPunch Starlet are not compatible with microbiome analyses due to the high risk for cross

contamination and the laborious dismantling and intervention required to sterilize the device between

each punch. A new tool and method is needed to enable researchers to enable the widespread adoption

of this system, affordable, and effective microbiome sampling devices.

Summary of MAE156 Project Objective:

The project objective is to design, build, test, and document a semi-automated or effort-multiplying

system that makes the processing of 100K samples per year feasible with a team of 4 researchers. The

final test will take in the Knight Lab when users utilize the tool on a subset of samples for a quality

control microbiome experiment, comparing the results of samples processed with the designed system

with those of the standard swab-based method.

Note: No testing on pathogenic samples is expected as part of this project. Any testing with

biological samples will be performed by employees trained on the appropriate biosafety

procedures.

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