## 2 Diversity of Gut Prokaryotes and the Principles of Microbiota Transfer  
### Challenges in Defining the Structure of Gut Microbiota  
A significant obstacle in projecting potential outcomes of FMT or FVT is the overwhelming diversity of microorganisms, both between individual hosts and within them. A general overview of publications describing a typical human gut microbiota composition reveals that the most ubiquitous phyla, frequently found to constitute over 90% of all bacteria in the gut, are _Bacteroidota_ (also known as _Bacteroidetes_) and _Bacilotta_ (also recognised as _Firmicutes_) [5,6]. _Bacteroidota_, encompassing species such as _Bacteroides fragilis_ or _Prevotella ruminicola_, are well-known proteo- and sacchaolytic agents in the gut [7,8]. In the phylum _Bacilotta_, prevalent bacteria include different species within the genus _Clostridium_, among which there exist both symbiotic and potentially pathogenic strains. A crucial species of _Clostridium_ is _C. butyticum_, known for exerting immunoregulatory effects and tightening the gastrointestinal barrier through production of short-chained fatty acids (SCFAs) such as butyric acid and acetic acid [9]. While the beneficial effects of _C. butyticum_ presence in the gut has made it a promising component of probiotic preparations [10], it is important to note that some of its strains can actually be pathogenic. For example, certain strains of _C. butyticum_ can cause botulism--traditionally associated with _C. botulinum_--possibly because of horizontal, intraspecific transfer of botulin-coding genes [11,12]. On the other hand, while particular species related to _Clostridium_ such as _Clostridioides difficile_ are generally considered pathogenic because of the enzymes and toxins produced by proliferating cells during an infection [13], there are also nonpathogenic strains of these species that, because of their intraspecific competition with toxicien varieties, can be administered therapeutically to significantly reduce the reoccurrence rate of infections [14]. It is therefore vital to note that in many cases, differences between the role and functionality of specific strains within the same species can be significant, complicating the already cumbersome challenge of characterising the microbial composition of the gut using species-specific quantification methods. In fact, the very concept of a'species', central to modern classification of organisms into higher clades, had for decades been subjected to discussion and critique [15], and while it remains a crucial and essential part of modern taxonomy, its shortcomings are especially apparent when dealing with prokaryotes of different strains occupying various ecological niches [16]. Therefore, some researchers have proposed altering the approach to characterising gut microbial communities by focusing on their metabolomic profile, which is supposed to more accurately describe the actual functionality of the gut microorganism consortium and its potential effect on the host. In fact, in many cases significant similarities between metabolic profiles of phylogenetically distant species, as well as stark metabolic differences between closely related strains, were observed [17], which complements the aforementioned examples of _C. butyricum_ and _C. difficile_. While the pursuit of other forms of characterisation--including proteomics and metabolomics--might be a promising direction in gut science, the concept of a species was, is, and will probably remain the basic unit for describing gut microbiotas. Because of the difficulties with applying genus-based metrics to very complex microbiomes, such as bacterial consortia in the gut, higher-order clades or synthetic functionality-based groups can be used to describe them. Many studies have emphasised the utilisation of _Firmicutes/Bacteroidetes_ (_Bacilota/Bacteroidota_) ratio as a useful metric for assessing microbiome-host interactions frequently associated with the production of specific SCFAs by specific phyla [18; 19; 20].