The animal facility of the IMG is a part of the Czech Centre for Phenogenomics and the work there was supported in part by following grants: LM2015040, LM2018126, OP RDI CZ.1.05/2.1.00/19.0395, OP RDI BIOCEV CZ.1.05/1.1.00/02.0109 provided by the Czech Ministry of Education, Youth and Sports and the European Regional Development Fund. AM performed most of the experiments. VN, LS, MP, AD, RS, TM, AN, KK, PS, OS performed experiments. AM, VN, and OS analyzed data and finalized figures. JKu and JM analyzed the transcriptomic data. JN analyzed the TCR profiling data. DC and JKr analyzed the S16 sequencing data. RS and PS provided feral mice. TH and HK provided germ-free mice. MK, HK, JKr, PS, and OS supervised the work. OS conceived the study.

Major evolutionary transitions were always accompanied by genetic remodelling of phenotypic traits. For example, the vertebrate transition from water to land was accompanied by rapid evolution of olfactory receptors and by the expansion of genes encoding lipocalins, which – due to their transporting functions – represent an important interface between the external and internal organic world of an individual and also within an individual. Similarly, some lipocalin genes were lost along other genes when this transition went in the opposite direction leading, for example, to cetaceans. In terrestrial vertebrates, lipocalins are involved in the transport of lipophilic substances, chemical signalling, odour reception, antimicrobial defence and background odour clearance during ventilation. Many ancestral lipocalins have clear physiological functions across the vertebrate taxa while many other have – due to pleiotropic effects of their genes – multiple or complementary functions within the body homeostasis and development. The aim of this review is to deconstruct the physiological functions of lipocalins in light of current OMICs techniques. We concentrated on major findings in the house mouse in comparison to other model taxa (e.g., voles, humans, and birds) in which all or most coding genes within their genomes were repeatedly sequenced and their annotations are sufficiently informative.

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Animal-associated microbiota is expected to impose crucial effects on the host's fitness-related performance, including reproduction. Most research to date has focused on interactions between the host with its gut microbiota; however, there remain considerable gaps in knowledge regarding microbial consortia in other organs, including interspecific divergence, temporal stability, variation drivers, and their effects on the host. To fill these gaps, we examined oral and vaginal microbiota composition in four free-living mouse species of the genus Apodemus, each varying in the degree of female promiscuity. To assess temporal stability and microbiota resistance to environmental change, we exposed one of the species, Apodemus uralensis, to standardized captive conditions and analyzed longitudinal changes in its microbiota structure. Our results revealed the existence of a "core" oral microbiota that was not only shared among all four species but also persisted almost unchanged in captivity. On the other hand, vaginal microbiota appears to be more plastic in captive conditions and less species-specific in comparison with oral microbiota. This study is amongst the first to describe oral microbiota dynamics. Furthermore, the vaginal microbiota results are especially surprising in light of the well-known role of stable vaginal microbiota as a defense against pathogens. The results indicate the existence of diverse mechanisms that shape each microbiota. On the other hand, our data provides somewhat ambiguous support for the systematic effect of phylogeny and social system on both oral and vaginal microbiota structures. Symbiotic microbiota have adapted to the diverse conditions found within animal bodies and have a profound effect on many aspects of an individual's life, including its health 1 and fitness 2,3. Species-specific microbiota alter the body's odor 4 , protect its host against pathogens 5,6 , and influence mating preferences 7 or behavior in general 8. However, most research to date has focused on gut microbiota 7,9,10 ; thus, most body parts remain unexplored in non-human hosts. For example, skin microbiota 6 or vaginal microbiota 11 also contribute to the host's health and fitness and it has been shown that tissue-specific differences exist in the expression of antimicrobial proteins, which presumably regulate the abundance and diversity of microbiota along the eyes-nose-oral cavity-gut axis 12-14. As such, the detection of particular factors that shape microbial composition in particular tissues is challenging. Variation in microbiota between geographically distinct, but ecologically comparable, populations of the same species suggests that local environmental pools are important sources for host-associated microbiota 15. Especially the diet seems to be crucial for the gut microbiota composition. The standardized diet in captivity not only alters the microbiota but also hinders the microbiota recovery after releasing back into the natural environment 16. At the same time, however, environmental microbiota dif...

Antigen-inexperienced memory-like T (AIMT) cells are functionally unique T cells representing one of the two largest subsets of murine CD8+ T cells. However, differences between laboratory inbred strains, insufficient data from germ-free mice, a complete lack of data from feral mice, and unclear relationship between AIMT cells formation during aging represent major barriers for better understanding of their biology. We performed a thorough characterization of AIMT cells from mice of different genetic background, age, and hygienic status by flow cytometry and multi-omics approaches including analyses of gene expression, TCR repertoire, and microbial colonization. Our data showed that AIMT cells are steadily present in mice independently of their genetic background and hygienic status. Despite differences in their gene expression profiles, young and aged AIMT cells originate from identical clones. We identified that CD122 discriminates two major subsets of AIMT cells in a strain-independent manner. Whereas thymic CD122LOW AIMT cells (innate memory) prevail only in young animals with high thymic IL-4 production, peripheral CD122HIGH AIMT cells (virtual memory) dominate in aged mice. Co-housing with feral mice changed the bacterial colonization of laboratory strains, but had only minimal effects on the CD8+ T-cell compartment including AIMT cells.