Abstract
The domestication of the laboratory mouse has influenced the composition of its native gut microbiome, which is now known to differ from that of its wild ancestor. However, limited exploration of the rodent gut microbiome beyond the model species Mus musculus has made it difficult to interpret microbiome variation in a broader phylogenetic context. Here, we analyse 120 de novo and 469 public metagenomically-sequenced faecal and caecal samples from 16 rodent hosts representing wild, laboratory and captive lifestyles. Distinct gut bacterial communities were observed between rodent host genera, with broadly distributed species originating from the as-yet-uncultured bacterial genera UBA9475 and UBA2821 in the families Oscillospiraceae and Lachnospiraceae, respectively. In laboratory mice, Helicobacteraceae were generally depleted relative to wild mice and specific Muribaculaceae populations were enriched in different laboratory facilities, suggesting facility-specific outgrowths of this historically dominant rodent gut family. Several bacterial families of clinical interest, including Akkermansiaceae, Streptococcaceae and Enterobacteriaceae, were inferred to have gained over half of their representative species in mice within the laboratory environment, being undetected in most wild rodents and suggesting an association between laboratory domestication and pathobiont emergence.
Highlights
The process of animal domestication involves significant changes to the environment, diet and genetics of the organism
CAG-508 Acutalibacteraceae Ruminococcaceae Oscillospiraceae Lachnospiraceae parks) and laboratory sources: Rattus norvegicus, Microtus ochrogaster, Neotoma albigula, Neotoma stephensi (Stephen’s woodrat, wild samples [62]), Neotoma lepida, Castor canadensis, Erethizon dorsatum, Cavia porcellus and Hydrochoerus hydrochaeris (Fig. 1a). To these hosts we added samples from wild rodent populations obtained in Lithuania; Apodemus agrarius, Apodemus flavicollis
Presence/absence-based comparison of laboratory and wild rodents To complement our assessment of enrichment between laboratory and wild rodents we identified potential gain and loss of species events associated with laboratory usage based on the pattern of presence/absence across closely related rodent hosts
Summary
The process of animal domestication involves significant changes to the environment, diet and genetics of the organism. Reconstitution via implantation of laboratory mouse embryos into wild mice produced offspring displaying immune responses more closely resembling that of adult humans [7]. Rewilding via introduction of laboratory mice to a controlled outdoor environment resulted in improved maturation and activation of the immune system associated with colonisation by fungi [10]. These data demonstrate that the observed differences between the gut microbiomes of laboratory and wild mice are phenotypically relevant, prompting discussion of the inclusion of ‘dirty’ mice within the model system [11]
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