## 2 Diversity of Gut Prokaryotes and the Principles of Microbiota Transfer
### Enterotypes of Human and Animal Guts  
The concept of enterotypes seems to be one of the more intriguing ideas in gut microbial characterization in recent years. They were described in 2011 as discrete gut microbiota profiles characterised by increased abundances of specific genera (such as _Prevotella_, _Bacteroides_, and _Ruminococcus_), which in turn positively or negatively affected other bacterial taxa [23; 24]. While the establishment of well-defined microbial clusters shared between individuals would indubitably be of incredible importance for microbiologists and dieticians alike, some later reports have challenged its central premise and postulated that the profiles are of more gradual nature and are not distinctive enough to be used to accurately describe gut microbiotas [25; 26]. Yet the concept seems to have gained significant popularity in the scientific community, and in recent years many papers have been published that present this idea in favourable light [27; 28]. The prevalence of _Bacteroides_--dubbed Enterotype 1--has been linked to the characteristics of a typical Western-style diet, rich in lipids and protein, which is theorized to negatively affect _Prevotella_ growth through several mechanisms, including the stimulation of bile production and lower bicarbonate levels in the gut [29; 30]. Conversely, Enterotype 2--associated with _Prevotella_ dominance--is most commonly found in communities and individuals following diets that are heavily reliant on plant consumption [31]. Yet there are many obstacles to characterising enterotypes in a simple and concise way--as an example, one paper described _Prevotella_ strains linked to high-fat, high-protein diets, as well as _Bacteroides_ strains flourishing in the gut of vegetarians and vegans [32]. Several models for enterotype classification have been proposed; the original paper from 2011 postulated the distinctiveness of a _Ruminococcus_-associated enterotype [24], and a subsequent publication by many of the original authors tried to reformulate the division between _Bacteroides_- and _Prevotella_-dominated enterotypes by taking additional factors into account [33]. Some authors also propose the existence of other enterotypes, such as an _Escherichia_-dominated enterotype often identified in Asian countries [34]. However, it is crucial to note that enterotype-oriented research initiatives often utilise significantly different methodologies [27], while the common denominator of essentially all these studies is the usage of faeces as the source of research material [29; 34; 35; 36]. Conversely, enterotype-oriented studies that focus on the mucosal microbiota of humans are virtually nonexistent, mostly because of issues with material collection. As the mucosal microbiota of the gut is quite different from the faecal one [37], it would certainly be an interesting avenue for future research. While the results of research oriented towards exploring human enterotypes remain ambiguous, animal enterotypes seem to be even less well-explored. However, even the scarce results that are currently available show some interesting similarities between species while also providing initial insight into enterotypic characterisations of certain animals. According to an early study, wild house mice tend to exhibit two well-defined enterotypes--one dominated by _Bacteroides_, and one dominated by _Robinsoniella_ and other _Lachospiraceae_[38]. The authors, taking into consideration the close phylogenetic relationship between _Lachospiraceae_ and _Ruminococcus_, drew parallels between proposed murine and human enterotypes, noticing the absence of a _Prevotella_-derived enterotype in mice. Unfortunately, the availability of enterotype-oriented analyses of murine gut microbiota is quite low, despite the importance of the mouse as a model organism.