A diagnostic method, comprising: detecting the presence or absence in a biological sample of: one or more markers of cytolethal distending toxin; or CDT; wherein the biological sample has been obtained from a subject selected from the group consisting of: a subject in need of a diagnosis regarding irritable bowel syndrome, a subject in need of a diagnosis regarding a subset of IBS, a subject in need of a determination of a likelihood of having or developing IBS, a subject in need of a determination of a likelihood of having or developing a subset of IBS,a subject who desires a prognosis of a response to antibiotic treatment for IBS, a subject who desires a prognosis of a response to antibiotic treatment to reduce the likelihood of having IBS and combinations thereof, a subject in need of a determination regarding small intestinal bacterial overgrowth (SIBO), a subject in need of a determination of a susceptibility to having SIBO, a subject in need of a diagnosis regarding non-ulcer dyspepsia; and correlating the presence of: one or more markers of CDT; or CDT; with a likely presence of IBS, a likely presence of a subset of IBS, a likelihood of having or developing IBS, a likelihood of having or developing a subset of IBS, a higher likelihood of having a beneficial result from antibiotic treatment for IBS,a higher likelihood of having a beneficial result from antibiotic treatment to reduce the likelihood of having IBS,a likely presence of SIBO, a higher susceptibility to having SIBO, and/or a likely presence of NUD; or correlating an absence of: one or more markers of CDT; or CDT; with a likely absence of IBS, a likely absence of the subset of IBS, a lower likelihood of having or developing IBS, a lower likelihood of having or developing the subset of IBS, a lower likelihood of having a beneficial result from antibiotic treatment for IBS, a lower likelihood of having a beneficial result from antibiotic treatment to reduce the likelihood of having IBS, a likely absence of SIBO, a lower susceptibility to having SIBO, and /or a likely absence of NUD; wherein the one or more markers of CDT is/are selected from the group consisting of: one or more CdtA, CdtB, CdtC subunits of CDT; one or more antibodies to CDT, CdtA, CdtB, CdtC or a fragment thereof; and/or one or more nucleic acids that encode CDT, CdtA, CdtB, CdtC or a fragment thereof. detecting the presence or absence in a biological sample of: one or more markers of cytolethal distending toxin; or CDT; one or more markers of cytolethal distending toxin; or CDT; wherein the biological sample has been obtained from a subject selected from the group consisting of: a subject in need of a diagnosis regarding irritable bowel syndrome, a subject in need of a diagnosis regarding a subset of IBS, a subject in need of a determination of a likelihood of having or developing IBS, a subject in need of a determination of a likelihood of having or developing a subset of IBS,a subject who desires a prognosis of a response to antibiotic treatment for IBS, a subject who desires a prognosis of a response to antibiotic treatment to reduce the likelihood of having IBS and combinations thereof, a subject in need of a determination regarding small intestinal bacterial overgrowth (SIBO), a subject in need of a determination of a susceptibility to having SIBO, a subject in need of a diagnosis regarding non-ulcer dyspepsia; and correlating the presence of: one or more markers of CDT; or CDT; one or more markers of CDT; or CDT; with a likely presence of IBS, a likely presence of a subset of IBS, a likelihood of having or developing IBS, a likelihood of having or developing a subset of IBS, a higher likelihood of having a beneficial result from antibiotic treatment for IBS,a higher likelihood of having a beneficial result from antibiotic treatment to reduce the likelihood of having IBS,a likely presence of SIBO, a higher susceptibility to having SIBO, and/or a likely presence of NUD; or correlating an absence of: one or more markers of CDT; or CDT; one or more markers of CDT; or CDT; with a likely absence of IBS, a likely absence of the subset of IBS, a lower likelihood of having or developing IBS, a lower likelihood of having or developing the subset of IBS, a lower likelihood of having a beneficial result from antibiotic treatment for IBS, a lower likelihood of having a beneficial result from antibiotic treatment to reduce the likelihood of having IBS, a likely absence of SIBO, a lower susceptibility to having SIBO, and /or a likely absence of NUD; one or more CdtA, CdtB, CdtC subunits of CDT; one or more antibodies to CDT, CdtA, CdtB, CdtC or a fragment thereof; and/or one or more nucleic acids that encode CDT, CdtA, CdtB, CdtC or a fragment thereof.