The gut microbiome plays a pivotal role in host nutritional uptake, behavior, and immune system function. Maintaining a properly functioning gut microbiome may help animals adapt to novel anthropogenic modified ecosystems, yet it can also be altered by these same environments. There is growing evidence that intestinal helminths can change the gut microbiome composition of the host and may help maintain gut homeostasis as well as increase the abundance of bacteria beneficial for the host. It is currently unknown if apparent helminth – gut microbiome interactions remain under novel stressors or if preserving the intestinal helminth community can help animals adapt to novel anthropogenic environments through maintaining a beneficial gut microbial community. Using joint species distribution modeling (JSDM) we determined co-occurrences between intestinal helminths and microbial taxa that remain across natural and urban habitats in four gut regions of two sympatric species of rodents (Apodemus speciosus and Myodes rufocanus). We found both positive and negative abundance related co-occurrences of helminths and microbial taxa in A. speciosus but only positive presence / absence co-occurrences in M. rufocanus. These co-occurrences were not restricted to the gut region where the helminth resides indicating indirect interactions. Notably, higher abundance of the probiotic bacterial group Lactobacillus was found in relation to higher abundance of the nematode Heligmosomoides kurilensis in A. speciosus. Our results demonstrate that while the type of co-occurrence relationship (i.e. abundance or presence / absence) differs among host, helminth, and bacteria taxa, some of these potential helminth gut microbiome interactions remain in the face of anthropogenic ecosystem modification.