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Bacterial peptide display libraries enable the rapid and efficient selection of peptides that have high affinity and selectivity toward their targets. Using a 15‐mer random library on the outer surface of  Escherichia coli (E.coli) , high‐affinity peptides were selected against a staphylococcal enterotoxin B (SEB) protein after four rounds of biopanning. On‐cell screening analysis of affinity and specificity were measured by flow cytometry and directly compared to the synthetic peptide, off‐cell, using peptide‐ELISA. DNA sequencing of the positive clones after four rounds of microfluidic magnetic sorting (MMS) revealed a common consensus sequence of (S/T)CH(Y/F)W for the SEB‐binding peptides R338, R418, and R445. The consensus sequence in these bacterial display peptides has similar amino acid characteristics with SEB peptide sequences isolated from phage display. The  K  d  measured by peptide‐ELISA off‐cell was 2.4 nM for R418 and 3.0 nM for R445. The bacterial peptide display methodology using the semiautomated MMS resulted in the discovery of selective peptides with affinity for a food safety and defense threat. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.  Journal of Molecular Recognition  published by John Wiley & Sons, Ltd.

Screening and characterization of anti‐SEB peptides using a bacterial display library and microfluidic magnetic sorting