| Pathogen | Small bowel | Colon |
| Bacteria | Salmonella* Escherichia coli¶ Clostridium perfringens Staphylococcus aureus Aeromonas hydrophila Bacillus cereus Vibrio cholerae | Campylobacter* Shigella Clostridioides difficile Yersinia Vibrio parahaemolyticus Enteroinvasive E. coli Plesiomonas shigelloides Klebsiella oxytoca (rare) |
| Virus | Rotavirus Norovirus Astrovirus | Cytomegalovirus* Adenovirus Herpes simplex virus |
| Protozoa | Cryptosporidium* Microsporidium* Cystoisospora Cyclospora Giardia lamblia | Entamoeba histolytica |
