Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents

Host–microbe interactions within the gastrointestinal tract (GIT) play a pivotal role in shaping host physiology, ecology, and life history. However, these interactions vary across gut regions due to changes in the physical environment or host immune system activity, thereby altering the microbial community. Each animal species may harbor their own unique microbial community due to host species-specific ecological traits such as dietary habits, micro-habitat preferences, and mating behavior as well as physiological traits. While the gut microbiota in wild animals has received much attention over the last decade, most studies comparing closely related species only utilized fecal or colon samples. In this study, we first compared the gut microbial community from the small intestine, cecum, colon, and rectum within three sympatric species of wild rodents (i.e. Apodemus speciosus, A. argenteus, and Myodes rufocanus). We then compared each gut region among host species to determine the effect of both gut region and host species on the gut microbiota. We found that the small intestine harbored a unique microbiome as compared to the lower GIT in all three host species, with the genus Lactobacillus in particular having higher abundance in the small intestine of all three host species. There were clear interspecific differences in the microbiome within all gut regions, although some similarity in alpha diversity and community structure within the small intestine was found. Finally, fecal samples may be appropriate for studying the lower GIT in these species, but not the small intestine.

DNA metabarcoding dietary analyses of the wood mouse Apodemus speciosus on Innoshima Island, Japan, and implications for primer choice

We used DNA metabarcoding to assess the seasonal diets of the large Japanese wood mouse, Apodemus speciosus (Muridae, Rodentia), in forest edges adjacent to citrus orchards on Innoshima Island, Japan. We used one chloroplast and three mitochondrial DNA barcoding markers to determine mouse diets. Among the various plant and invertebrate diets, A. speciosus typically consumed Chinese cork oak (Quercus variabilis) in early spring (likely acorns preserved during winter) and gypsy moths (Lymantria dispar, a forest pest) in late spring and summer. In addition, we found that A. speciosus also preyed on orchard pests, including the gutta stink bug and other potentially harmful invertebrates. The season during which A. speciosus preyed on stink bugs corresponded with the harvest of orchard products. This study revealed several of the ecological roles of A. speciosus within the boundary zone between forest and human ecosystems. Furthermore, based on the performance of various mitochondrial markers in dietary profiling of invertebrate food items, we recommend the multi-locus DNA metabarcoding method to comprehensively assess the diet of A. speciosus.

Dietary niche breadth influences the effects of urbanization on the gut microbiota of sympatric rodents

Cities are among the most extreme forms of anthropogenic ecosystem modification and urbanization processes exert profound effects on animal populations through multiple ecological pathways. Increased access to human associated food items may alter species’ foraging behavior and diet, in turn modifying the normal microbial community of the gastrointestinal tract, ultimately impacting their health. It is crucial we understand the role of dietary niche breadth and the resulting shift in the gut microbiota as urban animals navigate novel dietary resources. We combined stable isotope analysis of hair and microbiome analysis of four gut regions across the gastrointestinal tract to investigate the effects of urbanization on the diet and gut microbiota of two sympatric species of rodent with different dietary niches; the omnivorous large Japanese field mouse (Apodemus speciosus) and the relatively more herbivorous grey red-backed vole (Myodes rufocanus). Both species exhibited an expanded dietary niche width within the urban areas potentially attributable to novel anthropogenic foods and altered resource availability. We detected a dietary shift in which urban A. speciosus consumed more terrestrial animal protein and M. rufocanus more plant leaves and stems. Such changes in resource use may be associated with an altered gut microbial community structure. There was an increased abundance of the presumably probiotic Lactobacillus in the small intestine of urban A. speciosus and potentially pathogenic Helicobacter in the colon of M. rufocanus. Together, these results suggest that even taxonomically similar species may exhibit divergent responses to urbanization with consequences for the gut microbiota and broader ecological interactions.

Rodent-Borne Orthohantaviruses in Vietnam, Madagascar and Japan

Hantaviruses are harbored by multiple small mammal species in Asia, Europe, Africa, and the Americas. To ascertain the geographic distribution and virus-host relationships of rodent-borne hantaviruses in Japan, Vietnam, Myanmar, and Madagascar, RNAlater™-preserved lung tissues of 981 rodents representing 40 species, collected in 2011–2017, were analyzed for hantavirus RNA by RT-PCR. Our data showed Hantaan orthohantavirus Da Bie Shan strain in the Chinese white-bellied rat (Niviventer confucianus) in Vietnam, Thailand; orthohantavirus Anjo strain in the black rat (Rattus rattus) in Madagascar; and Puumala orthohantavirus Hokkaido strain in the grey-sided vole (Myodes rufocanus) in Japan. The Hokkaido strain of Puumala virus was also detected in the large Japanese field mouse (Apodemus speciosus) and small Japanese field mouse (Apodemus argenteus), with evidence of host-switching as determined by co-phylogeny mapping.

Natural selection in the origin: how does selection act on snails’ shell colour in the source of a diversified population?

The mechanisms of adaptive radiation with phenotypic diversification and further adaptive speciation have been becoming clearer through a number of studies. Natural selection is one of the primary factors that contribute to these mechanisms. It has been demonstrated that divergent natural selection acts on a certain trait in adaptive radiation. However, it is not often known how natural selection acts on the source of a diversified population, although it has been detected in phylogenetic studies. Our study demonstrates how selection acts on a trait in a source population of diversified population using the Japanese land snail Euhadra peliomphala simodae. This snail’s shell colour has diversified due to disruptive selection after migration from the mainland to islands. We used trail-camera traps to identify the cause of natural selection on both the mainland and an island. We then conducted a mark-recapture experiment on the mainland to detect natural selection and compare the shape and strength of it to previous study in an island. In total, we captured and marked around 1,700 snails, and some of them were preyed on by an unknown predator. The trail-camera traps showed that the predator is the large Japanese field mouse Apodemus speciosus, but this predation did not correlate with shell colour. A Bayesian approach showed that the stabilising selection from factors other than predation acted on shell colour. Our results suggest that natural selection was changed by migration, which could explain the ultimate cause of phenotypic diversification in adaptive radiation that was not due to predation.

Histological analysis of implantation embryos in large Japanese field mouse (Apodemus speciosus) and estimation of developmental stage

The large Japanese field mice (Apodemus speciosus) are small rodent specie endemic to Japan. The genetic characteristics of A. speciosus is different chromosome numbers within one species. Furthermore, A. speciosus is used for research in radiation and genetics. In this present study, a pregnant A. speciosus was obtained, and histochemical analysis of the implanted embryos was performed and compared with developmental stages of the mouse. Although there were some differences, the structures of the implanted embryos including the primitive streak and placenta of A. speciosus were similar to that of the mouse. Our study will be important report in the construction of a developmental atlas of A. speciosus.

Genetic characteristics of Apodemus speciosus at Akiyoshidai Quasi-National Park in Yamaguchi Prefecture

The large Japanese field mouse (Apodemus speciosus) is a small rodent endemic to Japan. The mice have a genetic characteristic in which the number of chromosomes differs between those from western Japan and those from eastern Japan. A. spesiosus, found throughout Japan, is used as a model animal for geogenetics and monitoring of radiation effects of wildlife. In this present study, to elucidate the genetic characteristics of the mice Akiyoshidai Quasi-National Park in Yamaguchi Prefecture, we investigated mitochondrial DNA and chromosome numbers. As a result, A. speciosus from Yamaguchi Prefecture were classified into the Honshu-Shikoku-Kyushu group and had a western Japan-type chromosome set of 2n=46; however, some Yamaguchi Prefecture mice formed a genetic cluster in Yamaguchi Prefecture, suggesting that continuous monitoring is needed to reveal the dynamics of genetic diversity.

Radiocesium contamination in wild mouse in Fukushima, Japan

<div><span>The large Japanese field mouse (<em>Apodemus speciosus</em>) which endemic wild mice living in Japanese forest, was monitored after the Fukushima nuclear power plant released a large amount of radioactive materials due to accident. We will introduce current status of radiocesium contamination, estimated radiation dose, and effect in the field mouse. According to calculation of radiation dose using Monte Carlo electron-photon transport code EGS5, it was clarified that dose rate level of the field mouse fall under derived consideration reference level determined by ICRP. Analysis of the oxidative stress in male mice testis revealed the damage in testicular cells of mice collected in 2012, when monitoring began.</span></div>