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Background  Giardiasis is an important gastrointestinal parasitic disease in humans and other mammals caused by the protozoan  Giardia duodenalis . This species complex is represented by genetically distinct groups (assemblages A-H) with varying zoonotic potential and host preferences. Wild rodents can harbor potentially zoonotic assemblages A and B, and the rodent-specific assemblage G. Other  Giardia  spp. found in these animals are  Giardia muris  and  Giardia microti . For the latter, only limited information on genetic typing is available. It has been speculated that wild rodents might represent an important reservoir for parasites causing human giardiasis. The aim of this study was to investigate the occurrence and distribution of  Giardia  spp. and assemblage types in wild rodents from different study sites in Germany.    Results  Screening of 577 wild rodents of the genera  Apodemus ,  Microtus  and  Myodes , sampled at eleven study sites in Germany, revealed a high overall  Giardia  prevalence.  Giardia  species determination at the  SSU  rDNA gene locus revealed that  Apodemus  mice, depending on species, were predominantly infected with one of two distinct  G. muris  sequence types.  Giardia microti  was the predominant parasite species found in voles of the genera  Microtus  and  Myodes . Only a few animals were positive for potentially zoonotic  G. duodenalis . Subtyping at the beta-giardin ( bg ) and glutamine dehydrogenase ( gdh ) genes strongly supported the existence of different phylogenetic subgroups of  G. microti  that are preferentially harbored by distinct host species.    Conclusions  The present study highlights the preference of  G. muris  for  Apodemus , and  G. microti  for  Microtus  and  Myodes  hosts and argues for a very low prevalence of zoonotic  G. duodenalis  assemblages in wild rodents in Germany. It also provides evidence that  G. muris  and  G. microti  subdivide into several phylogenetically distinguishable subgroups, each of which appears to be preferentially harbored by species of a particular rodent host genus. Finally, the study expands the database of sequences relevant for sequence typing of  G. muris  and  G. microti  isolates which will greatly help future analyses of these parasites’ population structure.    Electronic supplementary material  The online version of this article (10.1186/s13071-018-2802-z) contains supplementary material, which is available to authorized users.

Occurrence and distribution of Giardia species in wild rodents in Germany