## 2 Endophytes-Current State of the Art
### Endophytes as a Feeding Niche for Animals

Table 2: Specified animal microbiota potentially of endophytic origin. Selected microorganisms based on the literature and own studies combined with sharing of common taxa between endophytic microorganisms and the gut microbiota. tract of mice and modulate the gut microbiome after oral administration of the juice for 28 days [135]. One of the microorganisms may also be _Lactobacillus plantarum_, which is present in plants, intestinal tracts of animals and fermented food. These plant microbes may have specific features like the ability to degrade plant fibers, production of specific metabolites and enzymes having health-beneficial activities [127]. Another microorganism that can be proposed is _Clostridium_ sp., which is an endophyte also present in the animal gut; it has cellulose degradation capabilities due to having cellulosomes [128]. [PERSON] et al. [136] have determined that the core microbiome of _Capeolus caproclus_ is composed of the following genera, such as _Fretibacterium_, _Latilactobacillus_, _Syntrophococcus_, _Streptococcus_, _Lentilactobacillus_, _Ralstonia_, _Tyzzerella_, _Catenisphaera_, _Enterococcus_ and _Leuconostoc_. What is more, it highlighted the key microorganisms responsible for converting naturally available nutrients of different botanical origins [136]. [PERSON] et al. [137] studied the bacterial microbiota composition in animals experiencing semi-captive and captive management conditions, compared with free-living red deer. The bacterial microbiota of winter-gated and all-year-gated were mainly composed of Firmicutes (60.1-67.1%), followed by Bacteroidetes (24.6-31.2%). The authors reported that the free-living individuals also had a bacterial microbiome firmly founded on Firmicutes (61.4%) and Bacteroidetes (18.5%) but additionally harbored a substantial contribution from Proteobacteria (15.3%) [137]. What is more, they indicated that free-living individuals had a substantially higher representation of the Pseudomonasaceae family (10.8%), which may suggest an endophytic origin of these microorganisms [136]. Other microorganisms identified in the microbiome of _Cervus elaphus_ are the bacterial families such as Lachnospiraceae, Rikenelleaceae, Flavobacteriaceae and Eggertheliaceae, which were also significantly more abundant in free-living individuals. We would also like to point out that among the above-mentioned components of microbiomes, there are microbes that are also potentially endophytic microorganisms and potentially probiotics for plants, especially strains belonging to the Flavobacteriaceae. Positive correlations were reported between Firmicutes and the intake of plant fiber and carbohydrate. They were key microbes that helped red deer deal with wild plant resources [138]. These authors suggested that the combinations of Firmicutes were represented by Eubacteriales and Clostridia. This study indicates that high abundance of Firmicutes is an important guarantee for red deer to adapt to the wild feeding environment. We emphasize that microorganisms belonging to Clostridia can also occur as endophytic partners of plants. New data from our labs [139] indicated that invertebrate animals are also involved in the processing/persistance of endophytes. Our results suggested that trophic activity of the earthworm increases the reservoir of plant endophytes. It should be emphasized that the activity of the _Aporrectodea caliginos_ earthworm in the soil led to the emergence of 11.66% of all bacteria [139]. It is worth emphasizing that human health is not isolated but connected to the health of animals, plants and environments. As a summary, Figure 3 shows how various soil microbes are also in plant's leaves, human guts, and the guts of other animals. Soil microbes have also been proven to perform beneficial roles for animals [140]. The soil environment can be a source of animal microbiomes. Similarly, the current paper presents that endophytic microorganisms can be a source of animal microbiomes as another component of the ecosystem.