Fig. 6.

Pathogen identification of hard-to-classify pathogens: FunSoCs assigned to genes by SeqScreen. Abbreviated gene names are listed in pink cells if at least one read from the gene had a UniProt e-value < 0.0001 was assigned a FunSoC and was from the expected genus (i.e., Escherichia or Shigella, Clostridium, Streptococcus, Lactobacillus). FunSoCs with at least one gene that met the criteria for detection in at least one isolate were included in the table. The removal of genes from genera that were not expected in these bacterial isolates allowed for removal of genes that were likely derived from likely contaminating organisms (e.g., PhiX Illumina sequencing control). An expanded table for cells denoted by (*) and complete gene names are listed within each cell in Table S3. (a and b) E. coli O157:H7 is shown to have presence of the shiga toxin (stxB) as seen in the cytotoxicity FunSoC, as well as an additional hit to the secreted effector protein (espF(U)), labeled with secreted effector and virulence regulator FunSoCs, compared to E. coli K12 MG1655. (c and d) C. botulinum showed four distinct FunSoCs (disable organ, cytotoxicity, degrade ecm and virulence regulator) and presence of the botA and orf-X2 genes compared to C. sporogenes. (e and f) S. pyogenes showed presence of the induce inflammation FunSoC in contrast to the near neighbor pathogen S. dysgalactiae with the counter immunoglobulin FunSoC. (g and h). S. salivarius and L. gasseri are well-known commensals that are generally considered harmless. Both show presence of antibiotic resistance genes, while S. salivarius also contains some genes associated with secretion. The commensals have hits to the least number of FunSoCs