Extended Data Fig. 2: BASEHIT optimization with AIEC identifies conditions that yield selectivity and specificity and are broadly specific across diverse known host-microbe interactions.
From: A host–microbiota interactome reveals extensive transkingdom connectivity
a, Enrichment of CD55 and CEACAM1 by AIEC using different bead:cell ratios. Enrichment is defined as the fold change in frequency of reads for the indicated protein in the post-selection library relative to the pre-selection library. Enrichment of both CD55 and CEACAM1 decreases with increasing cell:bead ratio. b, Enrichment of CD55 and CEACAM1 by AIEC labelled with variable concentrations of sulfo-NHS-biotin reagent. Increasing or decreasing concentrations of biotin decrease enrichment of CD55 and CEACAM1. c, Enrichment of CD55 and CEACAM1 by various E. coli strains with or without expression of Dr-family adhesins as indicated. CD55 and CEACAM1 are specifically enriched by the Dr-adhesin containing AIEC strain. d, Exoproteome-wide host exoprotein binding pattern of AIEC determined by BASEHIT. CD55 and CEACAM1 are enriched substantially more than any other protein. Data in a, b represent the mean ± s.d., from n = 3 independent samples. e, Diverse bacterial strains with previously described interactions with human exoproteins were screened by BASEHIT and assessed for enrichment. Interactions that were successfully detected by BASEHIT are shown as filled circles, while interactions that BASEHIT failed to detect are shown as empty circles. The overall rate of detection of previously reported interactions (54%) is shown in the pie chart on the right.
